From 131788e37a7519a7fc35efa9b6fbd9d1ff919def Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 21 Sep 2023 17:36:54 +0200 Subject: [PATCH 01/25] restore nf-test tests for sra workflow --- .../sra_custom_ena_metadata_fields.nf.test | 33 + ...ra_custom_ena_metadata_fields.nf.test.snap | 573 +++++++ .../sra/tests/sra_default_parameters.nf.test | 30 + .../tests/sra_default_parameters.nf.test.snap | 1353 +++++++++++++++++ .../tests/sra_force_sratools_download.nf.test | 31 + .../sra_force_sratools_download.nf.test.snap | 1351 ++++++++++++++++ .../sra_nf_core_pipeline_atacseq.nf.test | 31 + .../sra_nf_core_pipeline_atacseq.nf.test.snap | 1353 +++++++++++++++++ .../tests/sra_nf_core_pipeline_rnaseq.nf.test | 31 + .../sra_nf_core_pipeline_rnaseq.nf.test.snap | 1353 +++++++++++++++++ .../sra_nf_core_pipeline_taxprofiler.nf.test | 31 + ..._nf_core_pipeline_taxprofiler.nf.test.snap | 1353 +++++++++++++++++ .../sra_nf_core_pipeline_viralrecon.nf.test | 31 + ...a_nf_core_pipeline_viralrecon.nf.test.snap | 1353 +++++++++++++++++ .../sra/tests/sra_skip_fastq_download.nf.test | 31 + .../sra_skip_fastq_download.nf.test.snap | 37 + 16 files changed, 8975 insertions(+) create mode 100644 workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test create mode 100644 workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap create mode 100644 workflows/sra/tests/sra_default_parameters.nf.test create mode 100644 workflows/sra/tests/sra_default_parameters.nf.test.snap create mode 100644 workflows/sra/tests/sra_force_sratools_download.nf.test create mode 100644 workflows/sra/tests/sra_force_sratools_download.nf.test.snap create mode 100644 workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test create mode 100644 workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap create mode 100644 workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test create mode 100644 workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap create mode 100644 workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test create mode 100644 workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap create mode 100644 workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test create mode 100644 workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap create mode 100644 workflows/sra/tests/sra_skip_fastq_download.nf.test create mode 100644 workflows/sra/tests/sra_skip_fastq_download.nf.test.snap diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test new file mode 100644 index 00000000..45280ab0 --- /dev/null +++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test @@ -0,0 +1,33 @@ +nextflow_workflow { + + name "Test workflow: sra/main.nf" + script "workflows/sra/main.nf" + workflow "SRA" + tag "workflows" + tag "workflows_sra" + tag "sra_custom_ena_metadata_fields" + + test("Parameters: --nf_core_pipeline rnaseq --ena_metadata_fields ... --sample_mapping_fields ...") { + + when { + workflow { + """ + input[0] = Channel.from('DRR026872','DRR028935','ERR1109373','ERR1160846','GSE214215','GSM4907283','SRR12848126','SRR13191702','SRR14593545','SRR14709033','SRR9984183') + """ + } + params { + outdir = "results" + nf_core_pipeline = "rnaseq" + ena_metadata_fields = "run_accession,experiment_accession,library_layout,fastq_ftp,fastq_md5" + sample_mapping_fields = "run_accession,library_layout" + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot(workflow.out).match() } + ) + } + } +} diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap new file mode 100644 index 00000000..a2537a95 --- /dev/null +++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap @@ -0,0 +1,573 @@ +{ + "Parameters: --nf_core_pipeline rnaseq --ena_metadata_fields ... --sample_mapping_fields ...": { + "content": [ + { + "0": [ 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assert workflow.success }, + { assert snapshot(workflow.out).match() } + ) + } + } +} diff --git a/workflows/sra/tests/sra_default_parameters.nf.test.snap b/workflows/sra/tests/sra_default_parameters.nf.test.snap new file mode 100644 index 00000000..b8dc88ca --- /dev/null +++ b/workflows/sra/tests/sra_default_parameters.nf.test.snap @@ -0,0 +1,1353 @@ +{ + "Parameters: default": { + "content": [ + { + "0": [ + [ + { + "id": "DRX024467_DRR026872", + "run_accession": "DRR026872", + "experiment_accession": "DRX024467", + "sample_accession": "SAMD00023098", + "secondary_sample_accession": "DRS033740", + "study_accession": "PRJDB4356", + "secondary_study_accession": "DRP003256", + "submission_accession": "DRA002758", + "run_alias": "DRR026872", + "experiment_alias": "DRX024467", + "sample_alias": "SAMD00023098", + "study_alias": "DRP003256", + "library_layout": "SINGLE", + "library_selection": "Restriction Digest", + "library_source": "GENOMIC", + "library_strategy": "OTHER", + 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assertAll( + { assert workflow.success }, + { assert snapshot(workflow.out).match() } + ) + } + } +} diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test.snap b/workflows/sra/tests/sra_force_sratools_download.nf.test.snap new file mode 100644 index 00000000..4e1b8aaf --- /dev/null +++ b/workflows/sra/tests/sra_force_sratools_download.nf.test.snap @@ -0,0 +1,1351 @@ +{ + "Parameters: --force_sratools_download": { + "content": [ + { + "0": [ + [ + { + "id": "DRX024467_DRR026872", + "run_accession": "DRR026872", + "experiment_accession": "DRX024467", + "sample_accession": "SAMD00023098", + "secondary_sample_accession": "DRS033740", + "study_accession": "PRJDB4356", + "secondary_study_accession": "DRP003256", + "submission_accession": "DRA002758", + "run_alias": "DRR026872", + "experiment_alias": "DRX024467", + "sample_alias": "SAMD00023098", + "study_alias": "DRP003256", + "library_layout": "SINGLE", + "library_selection": "Restriction Digest", + "library_source": 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snapshot(workflow.out).match() } + ) + } + } +} diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap new file mode 100644 index 00000000..f6528e52 --- /dev/null +++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap @@ -0,0 +1,1353 @@ +{ + "Parameters: --nf_core_pipeline atacseq": { + "content": [ + { + "0": [ + [ + { + "id": "DRX024467_DRR026872", + "run_accession": "DRR026872", + "experiment_accession": "DRX024467", + "sample_accession": "SAMD00023098", + "secondary_sample_accession": "DRS033740", + "study_accession": "PRJDB4356", + "secondary_study_accession": "DRP003256", + "submission_accession": "DRA002758", + "run_alias": "DRR026872", + "experiment_alias": "DRX024467", + "sample_alias": "SAMD00023098", + "study_alias": "DRP003256", + "library_layout": "SINGLE", + "library_selection": "Restriction Digest", + "library_source": "GENOMIC", + "library_strategy": "OTHER", + 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assertAll( + { assert workflow.success }, + { assert snapshot(workflow.out).match() } + ) + } + } +} diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap new file mode 100644 index 00000000..124877ae --- /dev/null +++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap @@ -0,0 +1,1353 @@ +{ + "Parameters: --nf_core_pipeline rnaseq": { + "content": [ + { + "0": [ + [ + { + "id": "DRX024467_DRR026872", + "run_accession": "DRR026872", + "experiment_accession": "DRX024467", + "sample_accession": "SAMD00023098", + "secondary_sample_accession": "DRS033740", + "study_accession": "PRJDB4356", + "secondary_study_accession": "DRP003256", + "submission_accession": "DRA002758", + "run_alias": "DRR026872", + "experiment_alias": "DRX024467", + "sample_alias": "SAMD00023098", + "study_alias": "DRP003256", + "library_layout": "SINGLE", + "library_selection": "Restriction Digest", + "library_source": 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"taxprofiler" + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot(workflow.out).match() } + ) + } + } +} diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap new file mode 100644 index 00000000..b63ad4b7 --- /dev/null +++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap @@ -0,0 +1,1353 @@ +{ + "Parameters: --nf_core_pipeline taxprofiler": { + "content": [ + { + "0": [ + [ + { + "id": "DRX024467_DRR026872", + "run_accession": "DRR026872", + "experiment_accession": "DRX024467", + "sample_accession": "SAMD00023098", + "secondary_sample_accession": "DRS033740", + "study_accession": "PRJDB4356", + "secondary_study_accession": "DRP003256", + "submission_accession": "DRA002758", + "run_alias": "DRR026872", + "experiment_alias": "DRX024467", + "sample_alias": "SAMD00023098", + "study_alias": "DRP003256", + "library_layout": "SINGLE", + 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} + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot(workflow.out).match() } + ) + } + } +} diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap new file mode 100644 index 00000000..1387f422 --- /dev/null +++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap @@ -0,0 +1,1353 @@ +{ + "Parameters: --nf_core_pipeline viralrecon": { + "content": [ + { + "0": [ + [ + { + "id": "DRX024467_DRR026872", + "run_accession": "DRR026872", + "experiment_accession": "DRX024467", + "sample_accession": "SAMD00023098", + "secondary_sample_accession": "DRS033740", + "study_accession": "PRJDB4356", + "secondary_study_accession": "DRP003256", + "submission_accession": "DRA002758", + "run_alias": "DRR026872", + "experiment_alias": "DRX024467", + "sample_alias": "SAMD00023098", + "study_alias": "DRP003256", + "library_layout": "SINGLE", + "library_selection": "Restriction 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"SRX9504942_SRR13055520", + "run_accession": "SRR13055520", + "experiment_accession": "SRX9504942", + "sample_accession": "SAMN16793052", + "secondary_sample_accession": "SRS7713669", + "study_accession": "PRJNA678298", + "secondary_study_accession": "SRP292504", + "submission_accession": "SRA1158402", + "run_alias": "GSM4907283_r4", + "experiment_alias": "GSM4907283", + "sample_alias": "GSM4907283", + "study_alias": "GSE159787", + "library_layout": "PAIRED", + "library_selection": "other", + "library_source": "TRANSCRIPTOMIC", + "library_strategy": "OTHER", + "library_name": "", + "instrument_model": "NextSeq 550", + "instrument_platform": "ILLUMINA", + "base_count": "2214488", + "read_count": "29138", + "tax_id": "9606", + "scientific_name": "Homo sapiens", + "sample_title": "A20-35 A11A20-35 A11_ROI009PanCK+", + "experiment_title": "NextSeq 550 sequencing: GSM4907283: A20-35 A11A20-35 A11_ROI009PanCK+ Homo sapiens OTHER", + "study_title": "Temporal and Spatial Heterogeneity of Host Response to SARS-CoV-2 Pulmonary Infection [gene expression]", + "sample_description": "A20-35 A11A20-35 A11_ROI009PanCK+", + "fastq_md5": "795d460abff6009c7f5ff7c14b773fbe;c3f34379356b28d6dac7212abc1a0a04", + "fastq_bytes": "709867;716862", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_2.fastq.gz", + "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_2.fastq.gz", + "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_2.fastq.gz", + "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_1.fastq.gz", + "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/020/SRR13055520/SRR13055520_2.fastq.gz", + "md5_1": "795d460abff6009c7f5ff7c14b773fbe", + "md5_2": "c3f34379356b28d6dac7212abc1a0a04", + "single_end": false + }, + [ + "SRX9504942_SRR13055520_1.fastq.gz:md5,795d460abff6009c7f5ff7c14b773fbe", + "SRX9504942_SRR13055520_2.fastq.gz:md5,c3f34379356b28d6dac7212abc1a0a04" + ] + ], + [ + { + "id": "SRX9626017_SRR13191702", + "run_accession": "SRR13191702", + "experiment_accession": "SRX9626017", + "sample_accession": "SAMN16980141", + "secondary_sample_accession": "SRS7827211", + "study_accession": "PRJNA682076", + "secondary_study_accession": "SRP295653", + "submission_accession": "SRA1166126", + "run_alias": "S.170804.00784_662_L001_R1_001.fastq.gz", + "experiment_alias": "S.170804.00784", + "sample_alias": "S.170804.00784_662", + "study_alias": "PRJNA682076", + "library_layout": "PAIRED", + "library_selection": "PCR", + "library_source": "METAGENOMIC", + "library_strategy": "AMPLICON", + "library_name": "S.170804.00784", + "instrument_model": "Illumina HiSeq 2500", + "instrument_platform": "ILLUMINA", + "base_count": "45682", + "read_count": "91", + "tax_id": "408170", + "scientific_name": "human gut metagenome", + "sample_title": "Metagenome or environmental sample from human gut metagenome", + "experiment_title": "Illumina HiSeq 2500 sequencing: Stool Microbiome Features to Discriminate Clostridium Difficile Colonization and Infection", + "study_title": "Stool Microbiome Features to Discriminate Clostridium Difficile Colonization and Infection", + "sample_description": "Metagenome or environmental sample from human gut metagenome", + "fastq_md5": "89c5be920021a035084d8aeb74f32df7;56271be38a80db78ef3bdfc5d9909b98", + "fastq_bytes": "15420;16324", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz", + "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz", + "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz", + "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz", + "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz", + "md5_1": "89c5be920021a035084d8aeb74f32df7", + "md5_2": "56271be38a80db78ef3bdfc5d9909b98", + "single_end": false + }, + [ + "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7", + "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98" + ] + ] + ], + "mappings": [ + "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565" + ], + "samplesheet": [ + "samplesheet.csv:md5,4aec9029e063bae998b3fa3dc3481556" + ], + "versions": [ + "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", + "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8", + "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", + "versions.yml:md5,e977678bd13a54fc9c31addf135be15e", + "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd" + ] + } + ], + "timestamp": "2023-09-11T18:34:25.049818" + } +} \ No newline at end of file diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test b/workflows/sra/tests/sra_skip_fastq_download.nf.test new file mode 100644 index 00000000..67abee3b --- /dev/null +++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test @@ -0,0 +1,31 @@ +nextflow_workflow { + + name "Test workflow: sra/main.nf" + script "workflows/sra/main.nf" + workflow "SRA" + tag "workflows" + tag "workflows_sra" + tag "sra_skip_fastq_download" + + test("Parameters: --skip_fastq_download") { + + when { + workflow { + """ + input[0] = Channel.from('DRR026872','DRR028935','ERR1109373','ERR1160846','GSE214215','GSM4907283','SRR12848126','SRR13191702','SRR14593545','SRR14709033','SRR9984183') + """ + } + params { + outdir = "results" + skip_fastq_download = true + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot(workflow.out).match() } + ) + } + } +} diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap b/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap new file mode 100644 index 00000000..3b04b917 --- /dev/null +++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap @@ -0,0 +1,37 @@ +{ + "Parameters: --skip_fastq_download": { + "content": [ + { + "0": [ + + ], + "1": [ + "samplesheet.csv:md5,7cf3503b651fe016bc1e5fb3c2e996d5" + ], + "2": [ + "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565" + ], + "3": [ + "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", + "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", + "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd" + ], + "fastq": [ + + ], + "mappings": [ + "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565" + ], + "samplesheet": [ + "samplesheet.csv:md5,7cf3503b651fe016bc1e5fb3c2e996d5" + ], + "versions": [ + "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", + "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", + "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd" + ] + } + ], + "timestamp": "2023-09-11T18:56:34.175665" + } +} \ No newline at end of file From 23b75bc70aa22c2d1dd66ce0d1ff3c0ed1a4ff6c Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 21 Sep 2023 19:21:10 +0200 Subject: [PATCH 02/25] restore module tests --- .../tests/main.nf.test | 31 ++++ .../tests/main.nf.test.snap | 52 +++++++ .../local/sra_fastq_ftp/tests/main.nf.test | 34 +++++ .../sra_fastq_ftp/tests/main.nf.test.snap | 140 ++++++++++++++++++ .../sra_ids_to_runinfo/tests/main.nf.test | 32 ++++ .../tests/main.nf.test.snap | 21 +++ .../sra_merge_samplesheet/tests/main.nf.test | 32 ++++ .../tests/main.nf.test.snap | 27 ++++ .../sra_runinfo_to_ftp/tests/main.nf.test | 31 ++++ .../tests/main.nf.test.snap | 21 +++ .../sra_to_samplesheet/tests/main.nf.test | 34 +++++ .../tests/main.nf.test.snap | 113 ++++++++++++++ 12 files changed, 568 insertions(+) create mode 100644 modules/local/multiqc_mappings_config/tests/main.nf.test create mode 100644 modules/local/multiqc_mappings_config/tests/main.nf.test.snap create mode 100644 modules/local/sra_fastq_ftp/tests/main.nf.test create mode 100644 modules/local/sra_fastq_ftp/tests/main.nf.test.snap create mode 100644 modules/local/sra_ids_to_runinfo/tests/main.nf.test create mode 100644 modules/local/sra_ids_to_runinfo/tests/main.nf.test.snap create mode 100644 modules/local/sra_merge_samplesheet/tests/main.nf.test create mode 100644 modules/local/sra_merge_samplesheet/tests/main.nf.test.snap create mode 100644 modules/local/sra_runinfo_to_ftp/tests/main.nf.test create mode 100644 modules/local/sra_runinfo_to_ftp/tests/main.nf.test.snap create mode 100644 modules/local/sra_to_samplesheet/tests/main.nf.test create mode 100644 modules/local/sra_to_samplesheet/tests/main.nf.test.snap diff --git a/modules/local/multiqc_mappings_config/tests/main.nf.test b/modules/local/multiqc_mappings_config/tests/main.nf.test new file mode 100644 index 00000000..3bf79537 --- /dev/null +++ b/modules/local/multiqc_mappings_config/tests/main.nf.test @@ -0,0 +1,31 @@ +nextflow_process { + + name "Test process: MULTIQC_MAPPINGS_CONFIG" + script "modules/local/multiqc_mappings_config/main.nf" + process "MULTIQC_MAPPINGS_CONFIG" + tag "modules" + tag "modules_local" + tag "multiqc_mappings_config" + + test("Should run without failures") { + + when { + params { + outdir = "$outputDir" + } + + process { + """ + input[0] = file(params.test_data['modules_local']['multiqc_mappings_config'], checkIfExists: true) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } +} diff --git a/modules/local/multiqc_mappings_config/tests/main.nf.test.snap b/modules/local/multiqc_mappings_config/tests/main.nf.test.snap new file mode 100644 index 00000000..9cf7fb38 --- /dev/null +++ b/modules/local/multiqc_mappings_config/tests/main.nf.test.snap @@ -0,0 +1,52 @@ +{ + "SRX9626017_SRR13191702": { + "content": [ + { + "0": [ + [ + "multiqc_config.yml:md5,7f3cb10fff83ba9eb3e8fa6862d1290a", + "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73" + ] + ], + "1": [ + "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73" + ], + "versions": [ + "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73" + ], + "yml": [ + [ + "multiqc_config.yml:md5,7f3cb10fff83ba9eb3e8fa6862d1290a", + "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73" + ] + ] + } + ], + "timestamp": "2023-08-17T12:02:35+0000" + }, + "Should run without failures": { + "content": [ + { + "0": [ + [ + "multiqc_config.yml:md5,7f3cb10fff83ba9eb3e8fa6862d1290a", + "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73" + ] + ], + "1": [ + "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73" + ], + "versions": [ + "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73" + ], + "yml": [ + [ + "multiqc_config.yml:md5,7f3cb10fff83ba9eb3e8fa6862d1290a", + "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73" + ] + ] + } + ], + "timestamp": "2023-08-17T12:02:35+0000" + } +} \ No newline at end of file diff --git a/modules/local/sra_fastq_ftp/tests/main.nf.test b/modules/local/sra_fastq_ftp/tests/main.nf.test new file mode 100644 index 00000000..7892d156 --- /dev/null +++ b/modules/local/sra_fastq_ftp/tests/main.nf.test @@ -0,0 +1,34 @@ +nextflow_process { + + name "Test process: SRA_FASTQ_FTP" + script "modules/local/sra_fastq_ftp/main.nf" + process "SRA_FASTQ_FTP" + tag "modules" + tag "modules_local" + tag "sra_fastq_ftp" + + test("Should run without failures") { + + when { + params { + outdir = "$outputDir" + } + + process { + """ + input[0] = [ + [ id:'SRX9626017_SRR13191702', single_end:false, md5_1: '89c5be920021a035084d8aeb74f32df7', md5_2: '56271be38a80db78ef3bdfc5d9909b98' ], // meta map + params.test_data['modules_local']['sra_fastq_ftp'] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } +} diff --git a/modules/local/sra_fastq_ftp/tests/main.nf.test.snap b/modules/local/sra_fastq_ftp/tests/main.nf.test.snap new file mode 100644 index 00000000..c0d5ffdc --- /dev/null +++ b/modules/local/sra_fastq_ftp/tests/main.nf.test.snap @@ -0,0 +1,140 @@ +{ + "SRX9626017_SRR13191702": { + "content": [ + { + "0": [ + [ + { + "id": "SRX9626017_SRR13191702", + "single_end": false, + "md5_1": "89c5be920021a035084d8aeb74f32df7", + "md5_2": "56271be38a80db78ef3bdfc5d9909b98" + }, + [ + "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7", + "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98" + ] + ] + ], + "1": [ + [ + { + "id": "SRX9626017_SRR13191702", + "single_end": false, + "md5_1": "89c5be920021a035084d8aeb74f32df7", + "md5_2": "56271be38a80db78ef3bdfc5d9909b98" + }, + [ + "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997", + "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945" + ] + ] + ], + "2": [ + "versions.yml:md5,6b9d69dea1c1305f74a65197ee871f1b" + ], + "fastq": [ + [ + { + "id": "SRX9626017_SRR13191702", + "single_end": false, + "md5_1": "89c5be920021a035084d8aeb74f32df7", + "md5_2": "56271be38a80db78ef3bdfc5d9909b98" + }, + [ + "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7", + "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98" + ] + ] + ], + "md5": [ + [ + { + "id": "SRX9626017_SRR13191702", + "single_end": false, + "md5_1": "89c5be920021a035084d8aeb74f32df7", + "md5_2": "56271be38a80db78ef3bdfc5d9909b98" + }, + [ + "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997", + "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945" + ] + ] + ], + "versions": [ + "versions.yml:md5,6b9d69dea1c1305f74a65197ee871f1b" + ] + } + ], + "timestamp": "2023-08-06T23:31:57+0000" + }, + "Should run without failures": { + "content": [ + { + "0": [ + [ + { + "id": "SRX9626017_SRR13191702", + "single_end": false, + "md5_1": "89c5be920021a035084d8aeb74f32df7", + "md5_2": "56271be38a80db78ef3bdfc5d9909b98" + }, + [ + "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7", + "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98" + ] + ] + ], + "1": [ + [ + { + "id": "SRX9626017_SRR13191702", + "single_end": false, + "md5_1": "89c5be920021a035084d8aeb74f32df7", + "md5_2": "56271be38a80db78ef3bdfc5d9909b98" + }, + [ + "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997", + "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945" + ] + ] + ], + "2": [ + "versions.yml:md5,6b9d69dea1c1305f74a65197ee871f1b" + ], + "fastq": [ + [ + { + "id": "SRX9626017_SRR13191702", + "single_end": false, + "md5_1": "89c5be920021a035084d8aeb74f32df7", + "md5_2": "56271be38a80db78ef3bdfc5d9909b98" + }, + [ + "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7", + "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98" + ] + ] + ], + "md5": [ + [ + { + "id": "SRX9626017_SRR13191702", + "single_end": false, + "md5_1": "89c5be920021a035084d8aeb74f32df7", + "md5_2": "56271be38a80db78ef3bdfc5d9909b98" + }, + [ + "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997", + "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945" + ] + ] + ], + "versions": [ + "versions.yml:md5,6b9d69dea1c1305f74a65197ee871f1b" + ] + } + ], + "timestamp": "2023-08-06T23:31:57+0000" + } +} \ No newline at end of file diff --git a/modules/local/sra_ids_to_runinfo/tests/main.nf.test b/modules/local/sra_ids_to_runinfo/tests/main.nf.test new file mode 100644 index 00000000..f8a44086 --- /dev/null +++ b/modules/local/sra_ids_to_runinfo/tests/main.nf.test @@ -0,0 +1,32 @@ +nextflow_process { + + name "Test process: SRA_IDS_TO_RUNINFO" + script "modules/local/sra_ids_to_runinfo/main.nf" + process "SRA_IDS_TO_RUNINFO" + tag "modules" + tag "modules_local" + tag "sra_ids_to_runinfo" + + test("Should run without failures") { + + when { + params { + outdir = "$outputDir" + } + + process { + """ + input[0] = 'SRR13191702' + input[1] = '' + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } +} diff --git a/modules/local/sra_ids_to_runinfo/tests/main.nf.test.snap b/modules/local/sra_ids_to_runinfo/tests/main.nf.test.snap new file mode 100644 index 00000000..dbca931f --- /dev/null +++ b/modules/local/sra_ids_to_runinfo/tests/main.nf.test.snap @@ -0,0 +1,21 @@ +{ + "Should run without failures": { + "content": [ + { + "0": [ + "SRR13191702.runinfo.tsv:md5,3a1be35781ca6e8a28d8fd4d2f3bbe85" + ], + "1": [ + "versions.yml:md5,1c14442e9b494b586eafe41e77300fae" + ], + "tsv": [ + "SRR13191702.runinfo.tsv:md5,3a1be35781ca6e8a28d8fd4d2f3bbe85" + ], + "versions": [ + "versions.yml:md5,1c14442e9b494b586eafe41e77300fae" + ] + } + ], + "timestamp": "2023-08-06T23:30:51+0000" + } +} \ No newline at end of file diff --git a/modules/local/sra_merge_samplesheet/tests/main.nf.test b/modules/local/sra_merge_samplesheet/tests/main.nf.test new file mode 100644 index 00000000..e37039bd --- /dev/null +++ b/modules/local/sra_merge_samplesheet/tests/main.nf.test @@ -0,0 +1,32 @@ +nextflow_process { + + name "Test process: SRA_MERGE_SAMPLESHEET" + script "modules/local/sra_merge_samplesheet/main.nf" + process "SRA_MERGE_SAMPLESHEET" + tag "modules" + tag "modules_local" + tag "sra_merge_samplesheet" + + test("Should run without failures") { + + when { + params { + outdir = "$outputDir" + } + + process { + """ + input[0] = params.test_data['modules_local']['sra_merge_samplesheet_samplesheets'].collect { file(it, checkIfExists: true) } + input[1] = params.test_data['modules_local']['sra_merge_samplesheet_mappings'].collect { file(it, checkIfExists: true) } + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } +} diff --git a/modules/local/sra_merge_samplesheet/tests/main.nf.test.snap b/modules/local/sra_merge_samplesheet/tests/main.nf.test.snap new file mode 100644 index 00000000..c5f06aac --- /dev/null +++ b/modules/local/sra_merge_samplesheet/tests/main.nf.test.snap @@ -0,0 +1,27 @@ +{ + "Should run without failures": { + "content": [ + { + "0": [ + "samplesheet.csv:md5,ef756557b0735becd2574c2a3f5840b2" + ], + "1": [ + "id_mappings.csv:md5,07262807636ce4b50102308eabdcf253" + ], + "2": [ + "versions.yml:md5,410006679d5e496d8c55e58e78ca6b34" + ], + "mappings": [ + "id_mappings.csv:md5,07262807636ce4b50102308eabdcf253" + ], + "samplesheet": [ + "samplesheet.csv:md5,ef756557b0735becd2574c2a3f5840b2" + ], + "versions": [ + "versions.yml:md5,410006679d5e496d8c55e58e78ca6b34" + ] + } + ], + "timestamp": "2023-07-06T13:16:36+0000" + } +} \ No newline at end of file diff --git a/modules/local/sra_runinfo_to_ftp/tests/main.nf.test b/modules/local/sra_runinfo_to_ftp/tests/main.nf.test new file mode 100644 index 00000000..1558ff39 --- /dev/null +++ b/modules/local/sra_runinfo_to_ftp/tests/main.nf.test @@ -0,0 +1,31 @@ +nextflow_process { + + name "Test process: SRA_RUNINFO_TO_FTP" + script "modules/local/sra_runinfo_to_ftp/main.nf" + process "SRA_RUNINFO_TO_FTP" + tag "modules" + tag "modules_local" + tag "sra_runinfo_to_ftp" + + test("Should run without failures") { + + when { + params { + outdir = "$outputDir" + } + + process { + """ + input[0] = file(params.test_data['modules_local']['sra_runinfo_to_ftp'], checkIfExists: true) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } +} diff --git a/modules/local/sra_runinfo_to_ftp/tests/main.nf.test.snap b/modules/local/sra_runinfo_to_ftp/tests/main.nf.test.snap new file mode 100644 index 00000000..71a25f99 --- /dev/null +++ b/modules/local/sra_runinfo_to_ftp/tests/main.nf.test.snap @@ -0,0 +1,21 @@ +{ + "Should run without failures": { + "content": [ + { + "0": [ + "SRR13191702.runinfo_ftp.tsv:md5,94378c448c044b3e20e5c54e442ab62e" + ], + "1": [ + "versions.yml:md5,e95f8185f665127a73622a19d321bcca" + ], + "tsv": [ + "SRR13191702.runinfo_ftp.tsv:md5,94378c448c044b3e20e5c54e442ab62e" + ], + "versions": [ + "versions.yml:md5,e95f8185f665127a73622a19d321bcca" + ] + } + ], + "timestamp": "2023-08-06T23:13:20+0000" + } +} \ No newline at end of file diff --git a/modules/local/sra_to_samplesheet/tests/main.nf.test b/modules/local/sra_to_samplesheet/tests/main.nf.test new file mode 100644 index 00000000..b2ec5b11 --- /dev/null +++ b/modules/local/sra_to_samplesheet/tests/main.nf.test @@ -0,0 +1,34 @@ +nextflow_process { + + name "Test process: SRA_TO_SAMPLESHEET" + script "modules/local/sra_to_samplesheet/main.nf" + process "SRA_TO_SAMPLESHEET" + tag "modules" + tag "modules_local" + tag "sra_to_samplesheet" + + test("Should run without failures") { + + when { + params { + outdir = "$outputDir" + } + + process { + """ + input[0] = [id:'ERX1188904_ERR1109373', run_accession:'ERR1109373', experiment_accession:'ERX1188904', sample_accession:'SAMEA3643867', experiment_alias:'ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7', run_alias:'ena-RUN-CAM-03-11-2015-17:01:52:847-7', sample_alias:'sample_56', study_alias:'ena-STUDY-CAM-02-11-2015-17:42:24:189-13', library_layout:'PAIRED', experiment_title:'Illumina HiSeq 2500 paired end sequencing', sample_title:'RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome', sample_description:'RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome', fastq_md5:'8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9', fastq_ftp:'ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz', fastq_1:'./results/fastq/ERX1188904_ERR1109373_1.fastq.gz', fastq_2:'./results/fastq/ERX1188904_ERR1109373_2.fastq.gz', md5_1:'9fd57225d6c07a31843276d6df9b15c0', md5_2:'5a62e8f785687dce890cfb4fe3e607f9', single_end:false] + input[1] = 'rnaseq' + input[2] = 'auto' + input[3] = 'experiment_accession,run_accession,sample_accession,experiment_alias,run_alias,sample_alias,experiment_title,sample_title,sample_description' + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } +} diff --git a/modules/local/sra_to_samplesheet/tests/main.nf.test.snap b/modules/local/sra_to_samplesheet/tests/main.nf.test.snap new file mode 100644 index 00000000..e60c646a --- /dev/null +++ b/modules/local/sra_to_samplesheet/tests/main.nf.test.snap @@ -0,0 +1,113 @@ +{ + "Should run without failures": { + "content": [ + { + "0": [ + [ + { + "id": "ERX1188904_ERR1109373", + "run_accession": "ERR1109373", + "experiment_accession": "ERX1188904", + "sample_accession": "SAMEA3643867", + "experiment_alias": "ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7", + "run_alias": "ena-RUN-CAM-03-11-2015-17:01:52:847-7", + "sample_alias": "sample_56", + "study_alias": "ena-STUDY-CAM-02-11-2015-17:42:24:189-13", + "library_layout": "PAIRED", + "experiment_title": "Illumina HiSeq 2500 paired end sequencing", + "sample_title": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", + "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", + "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", + "fastq_1": "./results/fastq/ERX1188904_ERR1109373_1.fastq.gz", + "fastq_2": "./results/fastq/ERX1188904_ERR1109373_2.fastq.gz", + "md5_1": "9fd57225d6c07a31843276d6df9b15c0", + "md5_2": "5a62e8f785687dce890cfb4fe3e607f9", + "single_end": false + }, + "ERX1188904_ERR1109373.samplesheet.csv:md5,e7898191d57258e049ee7129d36f5c08" + ] + ], + "1": [ + [ + { + "id": "ERX1188904_ERR1109373", + "run_accession": "ERR1109373", + "experiment_accession": "ERX1188904", + "sample_accession": "SAMEA3643867", + "experiment_alias": "ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7", + "run_alias": "ena-RUN-CAM-03-11-2015-17:01:52:847-7", + "sample_alias": "sample_56", + "study_alias": "ena-STUDY-CAM-02-11-2015-17:42:24:189-13", + "library_layout": "PAIRED", + "experiment_title": "Illumina HiSeq 2500 paired end sequencing", + "sample_title": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", + "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", + "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", + "fastq_1": "./results/fastq/ERX1188904_ERR1109373_1.fastq.gz", + "fastq_2": "./results/fastq/ERX1188904_ERR1109373_2.fastq.gz", + "md5_1": "9fd57225d6c07a31843276d6df9b15c0", + "md5_2": "5a62e8f785687dce890cfb4fe3e607f9", + "single_end": false + }, + "ERX1188904_ERR1109373.mappings.csv:md5,d09ddb4f0709675e5dfe1eadf12c608f" + ] + ], + "mappings": [ + [ + { + "id": "ERX1188904_ERR1109373", + "run_accession": "ERR1109373", + "experiment_accession": "ERX1188904", + "sample_accession": "SAMEA3643867", + "experiment_alias": "ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7", + "run_alias": "ena-RUN-CAM-03-11-2015-17:01:52:847-7", + "sample_alias": "sample_56", + "study_alias": "ena-STUDY-CAM-02-11-2015-17:42:24:189-13", + "library_layout": "PAIRED", + "experiment_title": "Illumina HiSeq 2500 paired end sequencing", + "sample_title": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", + "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", + "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", + "fastq_1": "./results/fastq/ERX1188904_ERR1109373_1.fastq.gz", + "fastq_2": "./results/fastq/ERX1188904_ERR1109373_2.fastq.gz", + "md5_1": "9fd57225d6c07a31843276d6df9b15c0", + "md5_2": "5a62e8f785687dce890cfb4fe3e607f9", + "single_end": false + }, + "ERX1188904_ERR1109373.mappings.csv:md5,d09ddb4f0709675e5dfe1eadf12c608f" + ] + ], + "samplesheet": [ + [ + { + "id": "ERX1188904_ERR1109373", + "run_accession": "ERR1109373", + "experiment_accession": "ERX1188904", + "sample_accession": "SAMEA3643867", + "experiment_alias": "ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7", + "run_alias": "ena-RUN-CAM-03-11-2015-17:01:52:847-7", + "sample_alias": "sample_56", + "study_alias": "ena-STUDY-CAM-02-11-2015-17:42:24:189-13", + "library_layout": "PAIRED", + "experiment_title": "Illumina HiSeq 2500 paired end sequencing", + "sample_title": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", + "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", + "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9", + "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", + "fastq_1": "./results/fastq/ERX1188904_ERR1109373_1.fastq.gz", + "fastq_2": "./results/fastq/ERX1188904_ERR1109373_2.fastq.gz", + "md5_1": "9fd57225d6c07a31843276d6df9b15c0", + "md5_2": "5a62e8f785687dce890cfb4fe3e607f9", + "single_end": false + }, + "ERX1188904_ERR1109373.samplesheet.csv:md5,e7898191d57258e049ee7129d36f5c08" + ] + ] + } + ], + "timestamp": "2023-08-23T09:38:15+0000" + } +} \ No newline at end of file From c95793e1e82b144ffb16ba8703e8072e80929aa5 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 21 Sep 2023 19:22:53 +0200 Subject: [PATCH 03/25] restore CI --- .github/workflows/ci.yml | 89 +++++++++++++++++++++++++++------------- 1 file changed, 61 insertions(+), 28 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 566ef509..7b7070e7 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -1,28 +1,67 @@ +# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors name: nf-core CI # This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors on: pull_request: release: types: [published] + merge_group: + types: + - checks_requested + branches: + - master + - dev + - refactor env: NXF_ANSI_LOG: false + NFTEST_VER: "0.8.0-rc1" concurrency: group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" cancel-in-progress: true jobs: + changes: + name: Check for changes + runs-on: ubuntu-latest + outputs: + # Expose matched filters as job 'tags' output variable + tags: ${{ steps.filter.outputs.changes }} + steps: + - uses: actions/checkout@v3 + - uses: dorny/paths-filter@v2 + id: filter + with: + filters: ".github/tags.yml" + + define_nxf_versions: + name: Choose nextflow versions to test against depending on target branch + runs-on: ubuntu-latest + outputs: + matrix: ${{ steps.nxf_versions.outputs.matrix }} + steps: + - id: nxf_versions + run: | + if [[ "${{ github.event_name }}" == "pull_request" && "${{ github.base_ref }}" == "dev" && "${{ matrix.NXF_VER }}" != "latest-everything" ]]; then + echo matrix='["latest-everything"]' | tee -a $GITHUB_OUTPUT + else + echo matrix='["latest-everything", "22.10.1"]' | tee -a $GITHUB_OUTPUT + fi + test: - name: Run pipeline with test data - # Only run on push if this is the nf-core dev branch (merged PRs) - if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/fetchngs') }}" + name: ${{ matrix.tags }} ${{ matrix.profile }} NF ${{ matrix.NXF_VER }} + needs: [changes, define_nxf_versions] + if: needs.changes.outputs.tags != '[]' runs-on: ubuntu-latest strategy: + fail-fast: false matrix: - NXF_VER: - - "23.04.0" - - "latest-everything" + NXF_VER: ${{ fromJson(needs.define_nxf_versions.outputs.matrix) }} + tags: ["${{ fromJson(needs.changes.outputs.tags) }}"] + profile: + - "docker" + steps: - name: Check out pipeline code uses: actions/checkout@v3 @@ -32,29 +71,23 @@ jobs: with: version: "${{ matrix.NXF_VER }}" - - name: Run pipeline with test data + - name: Install nf-test run: | - nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results + wget -qO- https://code.askimed.com/install/nf-test | bash -s $NFTEST_VER + sudo mv nf-test /usr/local/bin/ - parameters: - name: Test workflow parameters - if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/fetchngs') }} - runs-on: ubuntu-latest - strategy: - matrix: - parameters: - - "--nf_core_pipeline rnaseq" - - "--ena_metadata_fields run_accession,experiment_accession,library_layout,fastq_ftp,fastq_md5 --sample_mapping_fields run_accession,library_layout" - - "--skip_fastq_download" - - "--force_sratools_download" - steps: - - name: Check out pipeline code - uses: actions/checkout@v2 - - - name: Install Nextflow + - name: Run nf-test run: | - wget -qO- get.nextflow.io | bash - sudo mv nextflow /usr/local/bin/ - - name: Run pipeline with various parameters + nf-test test --tag ${{ matrix.tags }} --profile "test,${{ matrix.profile }}" --junitxml=test.xml + + - name: Output log on failure + if: failure() run: | - nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results ${{ matrix.parameters }} + sudo apt install bat > /dev/null + batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/meta/nextflow.log + + - name: Publish Test Report + uses: mikepenz/action-junit-report@v3 + if: always() # always run even if the previous step fails + with: + report_paths: test.xml From 7e935bbbd1705853fd5f8858d9ca50dea4f466fa Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 21 Sep 2023 19:26:37 +0200 Subject: [PATCH 04/25] forgot some files --- .gitattributes | 1 + .gitignore | 3 +++ nf-test.config | 16 ++++++++++++++++ 3 files changed, 20 insertions(+) create mode 100644 nf-test.config diff --git a/.gitattributes b/.gitattributes index 7a2dabc2..c1c17000 100644 --- a/.gitattributes +++ b/.gitattributes @@ -1,4 +1,5 @@ *.config linguist-language=nextflow *.nf.test linguist-language=nextflow +tests/**/*nf.test.snap linguist-generated modules/nf-core/** linguist-generated subworkflows/nf-core/** linguist-generated diff --git a/.gitignore b/.gitignore index 5124c9ac..b1b5890a 100644 --- a/.gitignore +++ b/.gitignore @@ -6,3 +6,6 @@ results/ testing/ testing* *.pyc +.nf-test/ +nf-test +.nf-test.log diff --git a/nf-test.config b/nf-test.config new file mode 100644 index 00000000..0799cb40 --- /dev/null +++ b/nf-test.config @@ -0,0 +1,16 @@ +config { + // location for all nf-tests + testsDir "." + + // nf-test directory including temporary files for each test + workDir ".nf-test" + + // location of library folder that is added automatically to the classpath + libDir "lib/" + + // location of an optional nextflow.config file specific for executing tests + configFile "nextflow.config" + + // run all test with the defined docker profile from the main nextflow.config + profile "" +} From e43e5f178e3812d000db3739f5f2c55a981e0e15 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 22 Sep 2023 09:39:50 +0200 Subject: [PATCH 05/25] fix NXF_VER --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 7b7070e7..59011a37 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -46,7 +46,7 @@ jobs: if [[ "${{ github.event_name }}" == "pull_request" && "${{ github.base_ref }}" == "dev" && "${{ matrix.NXF_VER }}" != "latest-everything" ]]; then echo matrix='["latest-everything"]' | tee -a $GITHUB_OUTPUT else - echo matrix='["latest-everything", "22.10.1"]' | tee -a $GITHUB_OUTPUT + echo matrix='["latest-everything", "23.04.0"]' | tee -a $GITHUB_OUTPUT fi test: From 185e930ca70cc3af853865b24af9f2ce893a1685 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 22 Sep 2023 09:45:59 +0200 Subject: [PATCH 06/25] fix linting --- .nf-core.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.nf-core.yml b/.nf-core.yml index 9975ac5b..d617b3a3 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -6,3 +6,4 @@ lint: files_unchanged: - assets/sendmail_template.txt - lib/NfcoreTemplate.groovy + - .gitattributes From b11c1d8da1e0d68e5b80641690b3d0e5590990c1 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 22 Sep 2023 10:21:03 +0200 Subject: [PATCH 07/25] restore file --- .github/tags.yml | 71 ++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 71 insertions(+) create mode 100644 .github/tags.yml diff --git a/.github/tags.yml b/.github/tags.yml new file mode 100644 index 00000000..a5914ccf --- /dev/null +++ b/.github/tags.yml @@ -0,0 +1,71 @@ +# local modules +multiqc_mappings_config: + - modules/local/multiqc_mappings_config/* +sra_fastq_ftp: + - modules/local/sra_fastq_ftp/* +sra_ids_to_runinfo: + - modules/local/sra_ids_to_runinfo/* +sra_merge_samplesheet: + - modules/local/sra_merge_samplesheet/* +sra_runinfo_to_ftp: + - modules/local/sra_runinfo_to_ftp/* +sra_to_samplesheet: + - modules/local/sra_to_samplesheet/* + +# workflow: sra +sra_custom_ena_metadata_fields: + - modules/local/sra_ids_to_runinfo/* + - modules/local/sra_runinfo_to_ftp/* + - modules/local/sra_fastq_ftp/* + - modules/local/sra_to_samplesheet/* + - modules/local/sra_merge_samplesheet/* + - workflows/sra/* +sra_default_parameters: + - modules/local/sra_ids_to_runinfo/* + - modules/local/sra_runinfo_to_ftp/* + - modules/local/sra_fastq_ftp/* + - modules/local/sra_to_samplesheet/* + - modules/local/sra_merge_samplesheet/* + - workflows/sra/* +sra_force_sratools_download: + - modules/local/sra_ids_to_runinfo/* + - modules/local/sra_runinfo_to_ftp/* + - modules/local/sra_fastq_ftp/* + - modules/local/sra_to_samplesheet/* + - modules/local/sra_merge_samplesheet/* + - workflows/sra/* +sra_nf_core_pipeline_atacseq: + - modules/local/sra_ids_to_runinfo/* + - modules/local/sra_runinfo_to_ftp/* + - modules/local/sra_fastq_ftp/* + - modules/local/sra_to_samplesheet/* + - modules/local/sra_merge_samplesheet/* + - workflows/sra/* +sra_nf_core_pipeline_rnaseq: + - modules/local/sra_ids_to_runinfo/* + - modules/local/sra_runinfo_to_ftp/* + - modules/local/sra_fastq_ftp/* + - modules/local/sra_to_samplesheet/* + - modules/local/sra_merge_samplesheet/* + - workflows/sra/* +sra_nf_core_pipeline_taxprofiler: + - modules/local/sra_ids_to_runinfo/* + - modules/local/sra_runinfo_to_ftp/* + - modules/local/sra_fastq_ftp/* + - modules/local/sra_to_samplesheet/* + - modules/local/sra_merge_samplesheet/* + - workflows/sra/* +sra_nf_core_pipeline_viralrecon: + - modules/local/sra_ids_to_runinfo/* + - modules/local/sra_runinfo_to_ftp/* + - modules/local/sra_fastq_ftp/* + - modules/local/sra_to_samplesheet/* + - modules/local/sra_merge_samplesheet/* + - workflows/sra/* +sra_skip_fastq_download: + - modules/local/sra_ids_to_runinfo/* + - modules/local/sra_runinfo_to_ftp/* + - modules/local/sra_fastq_ftp/* + - modules/local/sra_to_samplesheet/* + - modules/local/sra_merge_samplesheet/* + - workflows/sra/* From b0dd0a3c27a88371fa9ef5cdf6c42d334c845bb1 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 22 Sep 2023 10:23:07 +0200 Subject: [PATCH 08/25] do some tests --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 59011a37..5642602b 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -1,6 +1,5 @@ # This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors name: nf-core CI -# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors on: pull_request: release: @@ -12,6 +11,7 @@ on: - master - dev - refactor + - nf-test env: NXF_ANSI_LOG: false From aad776b1166eeea52eeba789c9558233f4e7a4f7 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 22 Sep 2023 10:35:23 +0200 Subject: [PATCH 09/25] 2 * --- .github/tags.yml | 108 +++++++++++++++++++++++------------------------ 1 file changed, 54 insertions(+), 54 deletions(-) diff --git a/.github/tags.yml b/.github/tags.yml index a5914ccf..03569f78 100644 --- a/.github/tags.yml +++ b/.github/tags.yml @@ -1,71 +1,71 @@ # local modules multiqc_mappings_config: - - modules/local/multiqc_mappings_config/* + - modules/local/multiqc_mappings_config/** sra_fastq_ftp: - - modules/local/sra_fastq_ftp/* + - modules/local/sra_fastq_ftp/** sra_ids_to_runinfo: - - modules/local/sra_ids_to_runinfo/* + - modules/local/sra_ids_to_runinfo/** sra_merge_samplesheet: - - modules/local/sra_merge_samplesheet/* + - modules/local/sra_merge_samplesheet/** sra_runinfo_to_ftp: - - modules/local/sra_runinfo_to_ftp/* + - modules/local/sra_runinfo_to_ftp/** sra_to_samplesheet: - - modules/local/sra_to_samplesheet/* + - modules/local/sra_to_samplesheet/** # workflow: sra sra_custom_ena_metadata_fields: - - modules/local/sra_ids_to_runinfo/* - - modules/local/sra_runinfo_to_ftp/* - - modules/local/sra_fastq_ftp/* - - modules/local/sra_to_samplesheet/* - - modules/local/sra_merge_samplesheet/* - - workflows/sra/* + - modules/local/sra_ids_to_runinfo/** + - modules/local/sra_runinfo_to_ftp/** + - modules/local/sra_fastq_ftp/** + - modules/local/sra_to_samplesheet/** + - modules/local/sra_merge_samplesheet/** + - workflows/sra/** sra_default_parameters: - - modules/local/sra_ids_to_runinfo/* - - modules/local/sra_runinfo_to_ftp/* - - modules/local/sra_fastq_ftp/* - - modules/local/sra_to_samplesheet/* - - modules/local/sra_merge_samplesheet/* - - workflows/sra/* + - modules/local/sra_ids_to_runinfo/** + - modules/local/sra_runinfo_to_ftp/** + - modules/local/sra_fastq_ftp/** + - modules/local/sra_to_samplesheet/** + - modules/local/sra_merge_samplesheet/** + - workflows/sra/** sra_force_sratools_download: - - modules/local/sra_ids_to_runinfo/* - - modules/local/sra_runinfo_to_ftp/* - - modules/local/sra_fastq_ftp/* - - modules/local/sra_to_samplesheet/* - - modules/local/sra_merge_samplesheet/* - - workflows/sra/* + - modules/local/sra_ids_to_runinfo/** + - modules/local/sra_runinfo_to_ftp/** + - modules/local/sra_fastq_ftp/** + - modules/local/sra_to_samplesheet/** + - modules/local/sra_merge_samplesheet/** + - workflows/sra/** sra_nf_core_pipeline_atacseq: - - modules/local/sra_ids_to_runinfo/* - - modules/local/sra_runinfo_to_ftp/* - - modules/local/sra_fastq_ftp/* - - modules/local/sra_to_samplesheet/* - - modules/local/sra_merge_samplesheet/* - - workflows/sra/* + - modules/local/sra_ids_to_runinfo/** + - modules/local/sra_runinfo_to_ftp/** + - modules/local/sra_fastq_ftp/** + - modules/local/sra_to_samplesheet/** + - modules/local/sra_merge_samplesheet/** + - workflows/sra/** sra_nf_core_pipeline_rnaseq: - - modules/local/sra_ids_to_runinfo/* - - modules/local/sra_runinfo_to_ftp/* - - modules/local/sra_fastq_ftp/* - - modules/local/sra_to_samplesheet/* - - modules/local/sra_merge_samplesheet/* - - workflows/sra/* + - modules/local/sra_ids_to_runinfo/** + - modules/local/sra_runinfo_to_ftp/** + - modules/local/sra_fastq_ftp/** + - modules/local/sra_to_samplesheet/** + - modules/local/sra_merge_samplesheet/** + - workflows/sra/** sra_nf_core_pipeline_taxprofiler: - - modules/local/sra_ids_to_runinfo/* - - modules/local/sra_runinfo_to_ftp/* - - modules/local/sra_fastq_ftp/* - - modules/local/sra_to_samplesheet/* - - modules/local/sra_merge_samplesheet/* - - workflows/sra/* + - modules/local/sra_ids_to_runinfo/** + - modules/local/sra_runinfo_to_ftp/** + - modules/local/sra_fastq_ftp/** + - modules/local/sra_to_samplesheet/** + - modules/local/sra_merge_samplesheet/** + - workflows/sra/** sra_nf_core_pipeline_viralrecon: - - modules/local/sra_ids_to_runinfo/* - - modules/local/sra_runinfo_to_ftp/* - - modules/local/sra_fastq_ftp/* - - modules/local/sra_to_samplesheet/* - - modules/local/sra_merge_samplesheet/* - - workflows/sra/* + - modules/local/sra_ids_to_runinfo/** + - modules/local/sra_runinfo_to_ftp/** + - modules/local/sra_fastq_ftp/** + - modules/local/sra_to_samplesheet/** + - modules/local/sra_merge_samplesheet/** + - workflows/sra/** sra_skip_fastq_download: - - modules/local/sra_ids_to_runinfo/* - - modules/local/sra_runinfo_to_ftp/* - - modules/local/sra_fastq_ftp/* - - modules/local/sra_to_samplesheet/* - - modules/local/sra_merge_samplesheet/* - - workflows/sra/* + - modules/local/sra_ids_to_runinfo/** + - modules/local/sra_runinfo_to_ftp/** + - modules/local/sra_fastq_ftp/** + - modules/local/sra_to_samplesheet/** + - modules/local/sra_merge_samplesheet/** + - workflows/sra/** From 89d39e98727f7f0c8beb868b243f726a27a8bbd5 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 22 Sep 2023 10:49:40 +0200 Subject: [PATCH 10/25] forgot this file --- conf/test_data.config | 36 ++++++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 conf/test_data.config diff --git a/conf/test_data.config b/conf/test_data.config new file mode 100644 index 00000000..42d3d818 --- /dev/null +++ b/conf/test_data.config @@ -0,0 +1,36 @@ +params { + // Base directory for test data + test_data_base = "https://raw.githubusercontent.com/nf-core/test-datasets/fetchngs" + + merge_samplesheet_ids = [ "DRX024467_DRR026872", "SRX11047067_SRR14709033", "SRX9504942_SRR13055517", "DRX026011_DRR028935", "SRX17709227_SRR21711856", "SRX9504942_SRR13055518", "ERX1188904_ERR1109373", "SRX17709228_SRR21711855", "SRX9504942_SRR13055519", "ERX1234253_ERR1160846", "SRX6725035_SRR9984183", "SRX9504942_SRR13055520", "SRX10940790_SRR14593545", "SRX9315476_SRR12848126", "SRX9626017_SRR13191702" ] + + def merge_samplesheet_url = "${params.test_data_base}/modules/local/sra_merge_samplesheet/samplesheets/" + def merge_mappings_url = "${params.test_data_base}/modules/local/sra_merge_samplesheet/mappings/" + def merge_samplesheet_urls = [] + def merge_mappings_urls = [] + + merge_samplesheet_ids.each { id -> + merge_samplesheet_urls += "${merge_samplesheet_url}${id}.samplesheet.csv" + merge_mappings_urls += "${merge_mappings_url}/${id}.mappings.csv" + } + + fastq_ftp_ids = ["SRR13191702"] + def fastq_ftp_url = "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/" + def fastq_ftp_urls = [] + + fastq_ftp_ids.each { id -> + fastq_ftp_urls += "${fastq_ftp_url}${id}_1.fastq.gz" + fastq_ftp_urls += "${fastq_ftp_url}${id}_2.fastq.gz" + } + + test_data { + 'modules_local' { + multiqc_mappings_config = "${params.test_data_base}/modules/local/multiqc_mappings_config/SRX9626017_SRR13191702.mappings.csv" + sra_merge_samplesheet_samplesheets = merge_samplesheet_urls + sra_merge_samplesheet_mappings = merge_mappings_urls + sra_to_samplesheet = "${params.test_data_base}/modules/local/sra_to_samplesheet/SRX9626017_SRR13191702.mappings.csv" + sra_fastq_ftp = fastq_ftp_urls + sra_runinfo_to_ftp = "${params.test_data_base}/modules/local/sra_runinfo_to_ftp/SRR13191702.runinfo.tsv" + } + } +} From d456c208def2bf4e046b520ab9a72e91c27c0b2e Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 22 Sep 2023 11:00:43 +0200 Subject: [PATCH 11/25] fix path to file to include and update snapshots --- .../tests/main.nf.test.snap | 27 +------ .../sra_fastq_ftp/tests/main.nf.test.snap | 71 +------------------ .../tests/main.nf.test.snap | 2 +- .../tests/main.nf.test.snap | 2 +- .../tests/main.nf.test.snap | 2 +- .../tests/main.nf.test.snap | 2 +- nextflow.config | 5 +- 7 files changed, 10 insertions(+), 101 deletions(-) diff --git a/modules/local/multiqc_mappings_config/tests/main.nf.test.snap b/modules/local/multiqc_mappings_config/tests/main.nf.test.snap index 9cf7fb38..1a4d16c4 100644 --- a/modules/local/multiqc_mappings_config/tests/main.nf.test.snap +++ b/modules/local/multiqc_mappings_config/tests/main.nf.test.snap @@ -1,29 +1,4 @@ { - "SRX9626017_SRR13191702": { - "content": [ - { - "0": [ - [ - "multiqc_config.yml:md5,7f3cb10fff83ba9eb3e8fa6862d1290a", - "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73" - ] - ], - "1": [ - "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73" - ], - "versions": [ - "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73" - ], - "yml": [ - [ - "multiqc_config.yml:md5,7f3cb10fff83ba9eb3e8fa6862d1290a", - "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73" - ] - ] - } - ], - "timestamp": "2023-08-17T12:02:35+0000" - }, "Should run without failures": { "content": [ { @@ -47,6 +22,6 @@ ] } ], - "timestamp": "2023-08-17T12:02:35+0000" + "timestamp": "2023-09-22T10:58:18.132284" } } \ No newline at end of file diff --git a/modules/local/sra_fastq_ftp/tests/main.nf.test.snap b/modules/local/sra_fastq_ftp/tests/main.nf.test.snap index c0d5ffdc..fb815455 100644 --- a/modules/local/sra_fastq_ftp/tests/main.nf.test.snap +++ b/modules/local/sra_fastq_ftp/tests/main.nf.test.snap @@ -1,73 +1,4 @@ { - "SRX9626017_SRR13191702": { - "content": [ - { - "0": [ - [ - { - "id": "SRX9626017_SRR13191702", - "single_end": false, - "md5_1": "89c5be920021a035084d8aeb74f32df7", - "md5_2": "56271be38a80db78ef3bdfc5d9909b98" - }, - [ - "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7", - "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98" - ] - ] - ], - "1": [ - [ - { - "id": "SRX9626017_SRR13191702", - "single_end": false, - "md5_1": "89c5be920021a035084d8aeb74f32df7", - "md5_2": "56271be38a80db78ef3bdfc5d9909b98" - }, - [ - "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997", - "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945" - ] - ] - ], - "2": [ - "versions.yml:md5,6b9d69dea1c1305f74a65197ee871f1b" - ], - "fastq": [ - [ - { - "id": "SRX9626017_SRR13191702", - "single_end": false, - "md5_1": "89c5be920021a035084d8aeb74f32df7", - "md5_2": "56271be38a80db78ef3bdfc5d9909b98" - }, - [ - "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7", - "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98" - ] - ] - ], - "md5": [ - [ - { - "id": "SRX9626017_SRR13191702", - "single_end": false, - "md5_1": "89c5be920021a035084d8aeb74f32df7", - "md5_2": "56271be38a80db78ef3bdfc5d9909b98" - }, - [ - "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997", - "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945" - ] - ] - ], - "versions": [ - "versions.yml:md5,6b9d69dea1c1305f74a65197ee871f1b" - ] - } - ], - "timestamp": "2023-08-06T23:31:57+0000" - }, "Should run without failures": { "content": [ { @@ -135,6 +66,6 @@ ] } ], - "timestamp": "2023-08-06T23:31:57+0000" + "timestamp": "2023-09-22T10:58:46.998421" } } \ No newline at end of file diff --git a/modules/local/sra_ids_to_runinfo/tests/main.nf.test.snap b/modules/local/sra_ids_to_runinfo/tests/main.nf.test.snap index dbca931f..241efe2a 100644 --- a/modules/local/sra_ids_to_runinfo/tests/main.nf.test.snap +++ b/modules/local/sra_ids_to_runinfo/tests/main.nf.test.snap @@ -16,6 +16,6 @@ ] } ], - "timestamp": "2023-08-06T23:30:51+0000" + "timestamp": "2023-09-22T10:58:56.721948" } } \ No newline at end of file diff --git a/modules/local/sra_merge_samplesheet/tests/main.nf.test.snap b/modules/local/sra_merge_samplesheet/tests/main.nf.test.snap index c5f06aac..203395ae 100644 --- a/modules/local/sra_merge_samplesheet/tests/main.nf.test.snap +++ b/modules/local/sra_merge_samplesheet/tests/main.nf.test.snap @@ -22,6 +22,6 @@ ] } ], - "timestamp": "2023-07-06T13:16:36+0000" + "timestamp": "2023-09-22T10:59:14.022116" } } \ No newline at end of file diff --git a/modules/local/sra_runinfo_to_ftp/tests/main.nf.test.snap b/modules/local/sra_runinfo_to_ftp/tests/main.nf.test.snap index 71a25f99..cd246303 100644 --- a/modules/local/sra_runinfo_to_ftp/tests/main.nf.test.snap +++ b/modules/local/sra_runinfo_to_ftp/tests/main.nf.test.snap @@ -16,6 +16,6 @@ ] } ], - "timestamp": "2023-08-06T23:13:20+0000" + "timestamp": "2023-09-22T10:58:36.16611" } } \ No newline at end of file diff --git a/modules/local/sra_to_samplesheet/tests/main.nf.test.snap b/modules/local/sra_to_samplesheet/tests/main.nf.test.snap index e60c646a..8cc8686a 100644 --- a/modules/local/sra_to_samplesheet/tests/main.nf.test.snap +++ b/modules/local/sra_to_samplesheet/tests/main.nf.test.snap @@ -108,6 +108,6 @@ ] } ], - "timestamp": "2023-08-23T09:38:15+0000" + "timestamp": "2023-09-22T10:58:27.169349" } } \ No newline at end of file diff --git a/nextflow.config b/nextflow.config index 01da14f6..28fb66a0 100644 --- a/nextflow.config +++ b/nextflow.config @@ -162,7 +162,10 @@ profiles { executor.cpus = 16 executor.memory = 60.GB } - test { includeConfig 'conf/test.config' } + test { + includeConfig 'conf/test.config' + includeConfig 'conf/test_data.config' + } test_synapse { includeConfig 'conf/test_synapse.config' } test_full { includeConfig 'conf/test_full.config' } } From cdaf06fa7150f2f994d9214d132f3e83b9e141b5 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 22 Sep 2023 11:30:43 +0200 Subject: [PATCH 12/25] use initialise subworkflows --- main.nf | 22 +------- modules.json | 5 ++ subworkflows/nf-core/initialise/main.nf | 68 ++++++++++++++++++++++++ subworkflows/nf-core/initialise/meta.yml | 33 ++++++++++++ 4 files changed, 108 insertions(+), 20 deletions(-) create mode 100644 subworkflows/nf-core/initialise/main.nf create mode 100644 subworkflows/nf-core/initialise/meta.yml diff --git a/main.nf b/main.nf index 355898d0..a5011951 100644 --- a/main.nf +++ b/main.nf @@ -17,26 +17,6 @@ nextflow.enable.dsl = 2 ======================================================================================== */ -include { paramsHelp; paramsSummaryLog; validateParameters } from 'plugin/nf-validation' - -def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs) -def citation = '\n' + WorkflowMain.citation(workflow) + '\n' - -// Print parameter summary log to screen -log.info logo + paramsSummaryLog(workflow) + citation - -// Print help message if needed -if (params.help) { - def String command = "nextflow run ${workflow.manifest.name} --input id.csv -profile docker" - log.info logo + paramsHelp(command) + citation + NfcoreTemplate.dashedLine(params.monochrome_logs) - System.exit(0) -} - -// Validate input parameters -if (params.validate_params) { - validateParameters() -} - // Check if --input file is empty ch_input = file(params.input, checkIfExists: true) if (ch_input.isEmpty()) { error("File provided with --input is empty: ${ch_input.getName()}!") } @@ -88,6 +68,7 @@ if (params.input_type == 'synapse') { include { MULTIQC_MAPPINGS_CONFIG } from './modules/local/multiqc_mappings_config' include { CUSTOM_DUMPSOFTWAREVERSIONS } from './modules/nf-core/custom/dumpsoftwareversions' +include { INITIALISE } from './subworkflows/nf-core/initialise/main' /* ======================================================================================== @@ -108,6 +89,7 @@ if (params.input_type == 'synapse') include { SYNAPSE } from './workflows/synaps // WORKFLOW: Run main nf-core/fetchngs analysis pipeline depending on type of identifier provided // workflow NFCORE_FETCHNGS { + INITIALISE(params.version, params.help, params.valid_params) ch_versions = Channel.empty() diff --git a/modules.json b/modules.json index ab610dfb..46dc80ef 100644 --- a/modules.json +++ b/modules.json @@ -33,6 +33,11 @@ "branch": "master", "git_sha": "6712754854ae2832abfff3f0800cdb4a6a60bfca", "installed_by": ["subworkflows"] + }, + "initialise": { + "branch": "master", + "git_sha": "7b55a4631bebd1cf827a448d0b70386681fea475", + "installed_by": ["subworkflows"] } } } diff --git a/subworkflows/nf-core/initialise/main.nf b/subworkflows/nf-core/initialise/main.nf new file mode 100644 index 00000000..0cbd3799 --- /dev/null +++ b/subworkflows/nf-core/initialise/main.nf @@ -0,0 +1,68 @@ +// This is a reimplementation of the basic initialise methods in the nf-core template +// The role of this subworkflow is to check the input parameters and print help messages +// Use this to start your nf-core pipeline + +include { paramsHelp; paramsSummaryLog; paramsSummaryMap; validateParameters } from 'plugin/nf-validation' + +workflow INITIALISE { + + take: + version // bool + help // bool + validate_params // bool + + main: + + // Print workflow version and exit on --version + if (version) { + String version_string = "" + + if (workflow.manifest.version) { + def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : '' + version_string += "${prefix_v}${workflow.manifest.version}" + } + + if (workflow.commitId) { + def git_shortsha = workflow.commitId.substring(0, 7) + version_string += "-g${git_shortsha}" + } + log.info "${workflow.manifest.name} ${version_string}" + System.exit(0) + } + + // Print citation for nf-core + def citation = "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" + + "* The nf-core framework\n" + + " https://doi.org/10.1038/s41587-020-0439-x\n\n" + + "* Software dependencies\n" + + " ${workflow.manifest.homePage}/blob/master/CITATIONS.md" + log.info citation + + // Print help message if needed + if (params.help) { + def String command = "nextflow run ${workflow.manifest.name} --input samplesheet.csv -profile docker" + log.info paramsHelp(command) + System.exit(0) + } + + if ( params.validate_params != false ){ + validateParameters() + } + + if (workflow.profile == 'standard' && workflow.configFiles.size() <= 1) { + log.warn "[$workflow.manifest.name] You are attempting to run the pipeline without any custom configuration!\n\n" + + "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" + + " (1) Using an existing pipeline profile e.g. `-profile docker` or `-profile singularity`\n" + + " (2) Using an existing nf-core/configs for your Institution e.g. `-profile crick` or `-profile uppmax`\n" + + " (3) Using your own local custom config e.g. `-c /path/to/your/custom.config`\n\n" + + "Please refer to the quick start section and usage docs for the pipeline.\n " + } + + log.info paramsSummaryLog(workflow) + + summary_params = paramsSummaryMap(workflow) + + emit: + summary_params + +} diff --git a/subworkflows/nf-core/initialise/meta.yml b/subworkflows/nf-core/initialise/meta.yml new file mode 100644 index 00000000..69596bb5 --- /dev/null +++ b/subworkflows/nf-core/initialise/meta.yml @@ -0,0 +1,33 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json +name: "initialise" +description: Validate input parameters and print help messages +keywords: + - admin + - check + - help + - version +modules: +input: + - version: + type: boolean + description: | + Structure: val(version) + Boolean to show the pipeline version and exit. + - help: + type: boolean + description: | + Structure: val(help) + Boolean to show the pipeline help message and exit. + - validate_params: + type: boolean + description: | + Structure: val(validate_params) + Whether to validate the parameters prior to starting the pipeline. +output: + - summary_params: + type: value + description: | + Structure: val(summary_params) + A map of the parameters used in the pipeline. +authors: + - "@adamrtalbot" From b8b15903aa71378d9357ab61c7e3c2f93a9d4d51 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 22 Sep 2023 12:00:32 +0200 Subject: [PATCH 13/25] move scripts --- workflows/sra/main.nf | 1 + 1 file changed, 1 insertion(+) diff --git a/workflows/sra/main.nf b/workflows/sra/main.nf index 8d5149d2..8b5f649e 100644 --- a/workflows/sra/main.nf +++ b/workflows/sra/main.nf @@ -9,6 +9,7 @@ include { SRA_RUNINFO_TO_FTP } from '../../modules/local/sra_runinfo_to_ftp include { SRA_FASTQ_FTP } from '../../modules/local/sra_fastq_ftp' include { SRA_TO_SAMPLESHEET } from '../../modules/local/sra_to_samplesheet' include { SRA_MERGE_SAMPLESHEET } from '../../modules/local/sra_merge_samplesheet' +include { MULTIQC_MAPPINGS_CONFIG } from '../../modules/local/multiqc_mappings_config' /* ======================================================================================== From b6c71a112e971d918c048bc4899dbfe131dab923 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 22 Sep 2023 17:59:55 +0200 Subject: [PATCH 14/25] no need to test on push on dev, pr are enough --- .nf-core.yml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.nf-core.yml b/.nf-core.yml index d617b3a3..78f1faff 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -2,7 +2,11 @@ repository_type: pipeline lint: actions_ci: false files_exist: + - .github/workflows/awsfulltest.yml + - .github/workflows/awstest.yml + - conf/igenomes.config - conf/modules.config + - lib/WorkflowFetchngs.groovy files_unchanged: - assets/sendmail_template.txt - lib/NfcoreTemplate.groovy From d6f8971a23c7432cc8a5655340ba627323b2410e Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 22 Sep 2023 18:08:35 +0200 Subject: [PATCH 15/25] more code polish --- main.nf | 12 +++--------- 1 file changed, 3 insertions(+), 9 deletions(-) diff --git a/main.nf b/main.nf index a5011951..aa24ed36 100644 --- a/main.nf +++ b/main.nf @@ -1,4 +1,5 @@ #!/usr/bin/env nextflow + /* ======================================================================================== nf-core/fetchngs @@ -66,7 +67,6 @@ if (params.input_type == 'synapse') { ======================================================================================== */ -include { MULTIQC_MAPPINGS_CONFIG } from './modules/local/multiqc_mappings_config' include { CUSTOM_DUMPSOFTWAREVERSIONS } from './modules/nf-core/custom/dumpsoftwareversions' include { INITIALISE } from './subworkflows/nf-core/initialise/main' @@ -98,12 +98,6 @@ workflow NFCORE_FETCHNGS { SRA(ch_ids) ch_versions = ch_versions.mix(SRA.out.versions) - // MODULE: Create a MultiQC config file with sample name mappings - if (params.sample_mapping_fields) { - MULTIQC_MAPPINGS_CONFIG(SRA.out.mappings) - ch_versions = ch_versions.mix(MULTIQC_MAPPINGS_CONFIG.out.versions) - } - // WORKFLOW: Download FastQ files for Synapse ids } else if (params.input_type == 'synapse') { SYNAPSE(ch_ids, ch_synapse_config) @@ -115,9 +109,9 @@ workflow NFCORE_FETCHNGS { } /* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +======================================================================================== RUN ALL WORKFLOWS -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +======================================================================================== */ // From a968fcb29bb5791199f921f2823f7f6c848539e3 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 25 Sep 2023 09:42:52 +0200 Subject: [PATCH 16/25] code polish --- main.nf | 21 ++++++++++++++------- 1 file changed, 14 insertions(+), 7 deletions(-) diff --git a/main.nf b/main.nf index aa24ed36..a67acf26 100644 --- a/main.nf +++ b/main.nf @@ -23,17 +23,24 @@ ch_input = file(params.input, checkIfExists: true) if (ch_input.isEmpty()) { error("File provided with --input is empty: ${ch_input.getName()}!") } // Read in ids from --input file -ch_ids = Channel.from(file(params.input, checkIfExists: true)) +Channel.from(file(params.input, checkIfExists: true)) .splitCsv(header:false, sep:'', strip:true) .map { it[0] } .unique() + .set { ch_ids } -// Auto-detect input type +// Auto-detect input id type def input_type = '' -if (WorkflowMain.isSraId(ch_input)) { input_type = 'sra' } -else if (WorkflowMain.isSynapseId(ch_input)) { input_type = 'synapse' } -else { error('Ids provided via --input not recognised please make sure they are either SRA / ENA / GEO / DDBJ or Synapse ids!') } -if (params.input_type != input_type) { error("Ids auto-detected as ${input_type}. Please provide '--input_type ${input_type}' as a parameter to the pipeline!") } +if (WorkflowMain.isSraId(ch_input)) { + input_type = 'sra' +} else if (WorkflowMain.isSynapseId(ch_input)) { + input_type = 'synapse' +} else { + error('Ids provided via --input not recognised please make sure they are either SRA / ENA / GEO / DDBJ or Synapse ids!') +} +if (params.input_type != input_type) { + error("Ids auto-detected as ${input_type}. Please provide '--input_type ${input_type}' as a parameter to the pipeline!") +} /* ======================================================================================== @@ -63,7 +70,7 @@ if (params.input_type == 'synapse') { /* ======================================================================================== - IMPORT MODULES + IMPORT MODULES/SUBWORKFLOWS ======================================================================================== */ From 58f92b086478fabcb1a106678c34e15f42a6e40d Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 25 Sep 2023 09:57:09 +0200 Subject: [PATCH 17/25] more code polish --- main.nf | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/main.nf b/main.nf index a67acf26..22977145 100644 --- a/main.nf +++ b/main.nf @@ -23,7 +23,8 @@ ch_input = file(params.input, checkIfExists: true) if (ch_input.isEmpty()) { error("File provided with --input is empty: ${ch_input.getName()}!") } // Read in ids from --input file -Channel.from(file(params.input, checkIfExists: true)) +Channel + .from(file(params.input, checkIfExists: true)) .splitCsv(header:false, sep:'', strip:true) .map { it[0] } .unique() @@ -55,9 +56,7 @@ if (params.input_type == 'sra') { // Validate input parameters WorkflowSra.initialise(params, valid_params) -} - -if (params.input_type == 'synapse') { +} else if (params.input_type == 'synapse') { // Create channel for synapse config if (params.synapse_config) { @@ -100,12 +99,16 @@ workflow NFCORE_FETCHNGS { ch_versions = Channel.empty() + // // WORKFLOW: Download FastQ files for SRA / ENA / GEO / DDBJ ids + // if (params.input_type == 'sra') { SRA(ch_ids) ch_versions = ch_versions.mix(SRA.out.versions) + // // WORKFLOW: Download FastQ files for Synapse ids + // } else if (params.input_type == 'synapse') { SYNAPSE(ch_ids, ch_synapse_config) ch_versions = ch_versions.mix(SYNAPSE.out.versions) From c98917663793ea5af43afcf85d8b75a7f83e16af Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 25 Sep 2023 10:00:34 +0200 Subject: [PATCH 18/25] params --- workflows/sra/main.nf | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/workflows/sra/main.nf b/workflows/sra/main.nf index 8b5f649e..de3eaf8b 100644 --- a/workflows/sra/main.nf +++ b/workflows/sra/main.nf @@ -130,6 +130,11 @@ workflow SRA { ) ch_versions = ch_versions.mix(SRA_MERGE_SAMPLESHEET.out.versions) + if (params.sample_mapping_fields) { + MULTIQC_MAPPINGS_CONFIG(SRA_MERGE_SAMPLESHEET.out.mappings) + ch_versions = ch_versions.mix(MULTIQC_MAPPINGS_CONFIG.out.versions) + } + emit: fastq = fastq_files samplesheet = SRA_MERGE_SAMPLESHEET.out.samplesheet From 131fd1b6fa42679d8cd779039e8f40de333d4e95 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 25 Sep 2023 10:27:52 +0200 Subject: [PATCH 19/25] more code polish --- lib/WorkflowMain.groovy | 111 +++++++++++++++++++++++++++++++++++++ lib/WorkflowSra.groovy | 33 ----------- lib/WorkflowSynapse.groovy | 92 ------------------------------ main.nf | 12 ++-- workflows/sra/main.nf | 14 +++-- workflows/synapse/main.nf | 6 +- 6 files changed, 128 insertions(+), 140 deletions(-) delete mode 100755 lib/WorkflowSra.groovy delete mode 100755 lib/WorkflowSynapse.groovy diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy index f9469941..4ec4029a 100755 --- a/lib/WorkflowMain.groovy +++ b/lib/WorkflowMain.groovy @@ -102,4 +102,115 @@ class WorkflowMain { } return is_synapse } + + // + // Check and validate parameters + // + public static void sraInitialise(params, valid_params) { + // Check minimal ENA fields are provided to download FastQ files + def ena_metadata_fields = params.ena_metadata_fields ? params.ena_metadata_fields.split(',').collect{ it.trim().toLowerCase() } : valid_params['ena_metadata_fields'] + if (!ena_metadata_fields.containsAll(valid_params['ena_metadata_fields'])) { + Nextflow.error("Invalid option: '${params.ena_metadata_fields}'. Minimally required fields for '--ena_metadata_fields': '${valid_params['ena_metadata_fields'].join(',')}'") + } + } + + // + // Print a warning after pipeline has completed + // + public static void sraCurateSamplesheetWarn(log) { + log.warn "=============================================================================\n" + + " Please double-check the samplesheet that has been auto-created by the pipeline.\n\n" + + " Public databases don't reliably hold information such as strandedness\n" + + " information, controls etc\n\n" + + " All of the sample metadata obtained from the ENA has been appended\n" + + " as additional columns to help you manually curate the samplesheet before\n" + + " running nf-core/other pipelines.\n" + + "===================================================================================" + } + + // + // Convert metadata obtained from the 'synapse show' command to a Groovy map + // + public static Map synapseShowToMap(synapse_file) { + def meta = [:] + def category = '' + synapse_file.eachLine { line -> + def entries = [null, null] + if (!line.startsWith(' ') && !line.trim().isEmpty()) { + category = line.tokenize(':')[0] + } else { + entries = line.trim().tokenize('=') + } + meta["${category}|${entries[0]}"] = entries[1] + } + meta.id = meta['properties|id'] + meta.name = meta['properties|name'] + meta.md5 = meta['File|md5'] + return meta.findAll{ it.value != null } + } + + // + // Print a warning after pipeline has completed + // + public static void synapseCurateSamplesheetWarn(log) { + log.warn "=============================================================================\n" + + " Please double-check the samplesheet that has been auto-created by the pipeline.\n\n" + + " Where applicable, default values will be used for sample-specific metadata\n" + + " such as strandedness, controls etc as this information is not provided\n" + + " in a standardised manner when uploading data to Synapse.\n" + + "===================================================================================" + } + + // + // Obtain Sample ID from File Name + // + public static String synapseSampleNameFromFastQ(input_file, pattern) { + + def sampleids = "" + + def filePattern = pattern.toString() + int p = filePattern.lastIndexOf('/') + if( p != -1 ) + filePattern = filePattern.substring(p+1) + + input_file.each { + String fileName = input_file.getFileName().toString() + + String indexOfWildcards = filePattern.findIndexOf { it=='*' || it=='?' } + String indexOfBrackets = filePattern.findIndexOf { it=='{' || it=='[' } + if( indexOfWildcards==-1 && indexOfBrackets==-1 ) { + if( fileName == filePattern ) + return actual.getSimpleName() + throw new IllegalArgumentException("Not a valid file pair globbing pattern: pattern=$filePattern file=$fileName") + } + + int groupCount = 0 + for( int i=0; i - def entries = [null, null] - if (!line.startsWith(' ') && !line.trim().isEmpty()) { - category = line.tokenize(':')[0] - } else { - entries = line.trim().tokenize('=') - } - meta["${category}|${entries[0]}"] = entries[1] - } - meta.id = meta['properties|id'] - meta.name = meta['properties|name'] - meta.md5 = meta['File|md5'] - return meta.findAll{ it.value != null } - } - - // - // Print a warning after pipeline has completed - // - public static void curateSamplesheetWarn(log) { - log.warn "=============================================================================\n" + - " Please double-check the samplesheet that has been auto-created by the pipeline.\n\n" + - " Where applicable, default values will be used for sample-specific metadata\n" + - " such as strandedness, controls etc as this information is not provided\n" + - " in a standardised manner when uploading data to Synapse.\n" + - "===================================================================================" - } - - // - // Obtain Sample ID from File Name - // - public static String sampleNameFromFastQ(input_file, pattern) { - - def sampleids = "" - - def filePattern = pattern.toString() - int p = filePattern.lastIndexOf('/') - if( p != -1 ) - filePattern = filePattern.substring(p+1) - - input_file.each { - String fileName = input_file.getFileName().toString() - - String indexOfWildcards = filePattern.findIndexOf { it=='*' || it=='?' } - String indexOfBrackets = filePattern.findIndexOf { it=='{' || it=='[' } - if( indexOfWildcards==-1 && indexOfBrackets==-1 ) { - if( fileName == filePattern ) - return actual.getSimpleName() - throw new IllegalArgumentException("Not a valid file pair globbing pattern: pattern=$filePattern file=$fileName") - } - - int groupCount = 0 - for( int i=0; i [ meta, [ meta.fastq_1, meta.fastq_2 ] ] @@ -76,6 +77,7 @@ workflow SRA { ftp: it[0].fastq_1 && !params.force_sratools_download sra: !it[0].fastq_1 || params.force_sratools_download } + .set { ch_sra_reads } // // MODULE: If FTP link is provided in run information then download FastQ directly via FTP and validate with md5sums @@ -95,12 +97,12 @@ workflow SRA { ch_versions = ch_versions.mix(FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS.out.versions.first()) // Isolate FASTQ channel which will be added to emit block - fastq_files = fastq_files.mix( + fastq_files.mix( SRA_FASTQ_FTP.out.fastq, FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS.out.reads - ) + ).set { fastq_files } - ch_sra_metadata = fastq_files.map { meta, fastq -> + fastq_files.map { meta, fastq -> def reads = fastq instanceof List ? fastq.flatten() : [ fastq ] def meta_clone = meta.clone() @@ -108,7 +110,7 @@ workflow SRA { meta_clone.fastq_2 = reads[1] && !meta.single_end ? "${params.outdir}/fastq/${reads[1].getName()}" : '' return meta_clone - } + }.set { ch_sra_metadata } } // diff --git a/workflows/synapse/main.nf b/workflows/synapse/main.nf index 30d05f4f..785877ac 100644 --- a/workflows/synapse/main.nf +++ b/workflows/synapse/main.nf @@ -56,7 +56,7 @@ workflow SYNAPSE { SYNAPSE_SHOW .out .metadata - .map { it -> WorkflowSynapse.synapseShowToMap(it) } + .map { it -> Workflow.synapseShowToMap(it) } .set { ch_samples_meta } // @@ -72,14 +72,14 @@ workflow SYNAPSE { SYNAPSE_GET .out .fastq - .map { meta, fastq -> [ WorkflowSynapse.sampleNameFromFastQ( fastq , "*{1,2}*"), fastq ] } + .map { meta, fastq -> [ Workflow.synapseSampleNameFromFastQ( fastq , "*{1,2}*"), fastq ] } .groupTuple(sort: { it -> it.baseName }) .set { ch_fastq } SYNAPSE_GET .out .fastq - .map { meta, fastq -> [ WorkflowSynapse.sampleNameFromFastQ( fastq , "*{1,2}*"), meta.id ] } + .map { meta, fastq -> [ Workflow.synapseSampleNameFromFastQ( fastq , "*{1,2}*"), meta.id ] } .groupTuple() .join(ch_fastq) .map { id, synids, fastq -> From 08d30eb30dad60108b780517a2bb70540b1090d8 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 25 Sep 2023 10:32:24 +0200 Subject: [PATCH 20/25] typo --- main.nf | 6 +++--- workflows/synapse/main.nf | 6 +++--- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/main.nf b/main.nf index 91aa6601..d74b62f8 100644 --- a/main.nf +++ b/main.nf @@ -55,7 +55,7 @@ if (params.input_type == 'sra') { ] // Validate input parameters - Workflow.sraInitialise(params, valid_params) + WorkflowMain.sraInitialise(params, valid_params) } else if (params.input_type == 'synapse') { // Create channel for synapse config @@ -143,8 +143,8 @@ workflow.onComplete { NfcoreTemplate.email(workflow, params, summary_params, projectDir, log) } NfcoreTemplate.summary(workflow, params, log) - if (params.input_type == 'sra') { Workflow.sraCurateSamplesheetWarn(log) } - if (params.input_type == 'synapse') { Workflow.synapseCurateSamplesheetWarn(log) } + if (params.input_type == 'sra') { WorkflowMain.sraCurateSamplesheetWarn(log) } + if (params.input_type == 'synapse') { WorkflowMain.synapseCurateSamplesheetWarn(log) } } /* diff --git a/workflows/synapse/main.nf b/workflows/synapse/main.nf index 785877ac..0fc46ed4 100644 --- a/workflows/synapse/main.nf +++ b/workflows/synapse/main.nf @@ -56,7 +56,7 @@ workflow SYNAPSE { SYNAPSE_SHOW .out .metadata - .map { it -> Workflow.synapseShowToMap(it) } + .map { it -> WorkflowMain.synapseShowToMap(it) } .set { ch_samples_meta } // @@ -72,14 +72,14 @@ workflow SYNAPSE { SYNAPSE_GET .out .fastq - .map { meta, fastq -> [ Workflow.synapseSampleNameFromFastQ( fastq , "*{1,2}*"), fastq ] } + .map { meta, fastq -> [ WorkflowMain.synapseSampleNameFromFastQ( fastq , "*{1,2}*"), fastq ] } .groupTuple(sort: { it -> it.baseName }) .set { ch_fastq } SYNAPSE_GET .out .fastq - .map { meta, fastq -> [ Workflow.synapseSampleNameFromFastQ( fastq , "*{1,2}*"), meta.id ] } + .map { meta, fastq -> [ WorkflowMain.synapseSampleNameFromFastQ( fastq , "*{1,2}*"), meta.id ] } .groupTuple() .join(ch_fastq) .map { id, synids, fastq -> From 034a52023931d1bcdd07cef94e1bff8fa1e2b0fe Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 25 Sep 2023 11:11:07 +0200 Subject: [PATCH 21/25] use rc2 --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 5642602b..30656e1a 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -15,7 +15,7 @@ on: env: NXF_ANSI_LOG: false - NFTEST_VER: "0.8.0-rc1" + NFTEST_VER: "0.8.0-rc2" concurrency: group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" From 45c9020c2d24e669ed2f9b8a5e30dbb56018bc51 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 25 Sep 2023 11:11:25 +0200 Subject: [PATCH 22/25] regenerate tests and snapshots --- .../sra_custom_ena_metadata_fields.nf.test | 2 +- ...ra_custom_ena_metadata_fields.nf.test.snap | 62 ++-------- .../sra/tests/sra_default_parameters.nf.test | 2 +- .../tests/sra_default_parameters.nf.test.snap | 114 ++---------------- .../tests/sra_force_sratools_download.nf.test | 2 +- .../sra_force_sratools_download.nf.test.snap | 110 ++--------------- .../sra_nf_core_pipeline_atacseq.nf.test | 2 +- .../sra_nf_core_pipeline_atacseq.nf.test.snap | 114 ++---------------- .../tests/sra_nf_core_pipeline_rnaseq.nf.test | 2 +- .../sra_nf_core_pipeline_rnaseq.nf.test.snap | 114 ++---------------- .../sra_nf_core_pipeline_taxprofiler.nf.test | 2 +- ..._nf_core_pipeline_taxprofiler.nf.test.snap | 114 ++---------------- .../sra_nf_core_pipeline_viralrecon.nf.test | 2 +- ...a_nf_core_pipeline_viralrecon.nf.test.snap | 114 ++---------------- .../sra/tests/sra_skip_fastq_download.nf.test | 2 +- .../sra_skip_fastq_download.nf.test.snap | 20 +-- 16 files changed, 108 insertions(+), 670 deletions(-) diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test index 45280ab0..7c9df9d9 100644 --- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test +++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test @@ -12,7 +12,7 @@ nextflow_workflow { when { workflow { """ - input[0] = Channel.from('DRR026872','DRR028935','ERR1109373','ERR1160846','GSE214215','GSM4907283','SRR12848126','SRR13191702','SRR14593545','SRR14709033','SRR9984183') + input[0] = Channel.from('DRR026872', 'DRR028935', 'ERR1160846', 'GSE214215', 'GSM4907283', 'SRR12848126', 'SRR13191702', 'SRR14593545', 'SRR14709033', 'SRR9984183') """ } params { diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap index a2537a95..29feb896 100644 --- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap +++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap @@ -38,25 +38,6 @@ "DRX026011_DRR028935_2.fastq.gz:md5,941c9998d746416dad53c94c480ddf30" ] ], - [ - { - "id": "ERX1188904_ERR1109373", - "run_accession": "ERR1109373", - "experiment_accession": "ERX1188904", - "library_layout": "PAIRED", - "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9", - "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz", - "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "md5_1": "9fd57225d6c07a31843276d6df9b15c0", - "md5_2": "5a62e8f785687dce890cfb4fe3e607f9", - "single_end": false - }, - [ - "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0", - "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9" - ] - ], [ { "id": "ERX1234253_ERR1160846", @@ -272,17 +253,18 @@ ] ], "1": [ - "samplesheet.csv:md5,be5465f34924356e136c804d63e1b562" + "samplesheet.csv:md5,d161b1a26b415a61064d8c558c9695c5" ], "2": [ - "id_mappings.csv:md5,8473773df806859c6af7acafcfe5aa6f" + "id_mappings.csv:md5,e8a7d8effe4af1d999dc26cf92cf6621" ], "3": [ + "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8", - "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", - "versions.yml:md5,e977678bd13a54fc9c31addf135be15e", - "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd" + "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd", + "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", + "versions.yml:md5,e977678bd13a54fc9c31addf135be15e" ], "fastq": [ [ @@ -320,25 +302,6 @@ "DRX026011_DRR028935_2.fastq.gz:md5,941c9998d746416dad53c94c480ddf30" ] ], - [ - { - "id": "ERX1188904_ERR1109373", - "run_accession": "ERR1109373", - "experiment_accession": "ERX1188904", - "library_layout": "PAIRED", - "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9", - "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz", - "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "md5_1": "9fd57225d6c07a31843276d6df9b15c0", - "md5_2": "5a62e8f785687dce890cfb4fe3e607f9", - "single_end": false - }, - [ - "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0", - "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9" - ] - ], [ { "id": "ERX1234253_ERR1160846", @@ -554,20 +517,21 @@ ] ], "mappings": [ - "id_mappings.csv:md5,8473773df806859c6af7acafcfe5aa6f" + "id_mappings.csv:md5,e8a7d8effe4af1d999dc26cf92cf6621" ], "samplesheet": [ - "samplesheet.csv:md5,be5465f34924356e136c804d63e1b562" + "samplesheet.csv:md5,d161b1a26b415a61064d8c558c9695c5" ], "versions": [ + "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8", - "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", - "versions.yml:md5,e977678bd13a54fc9c31addf135be15e", - "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd" + "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd", + "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", + "versions.yml:md5,e977678bd13a54fc9c31addf135be15e" ] } ], - "timestamp": "2023-09-11T18:48:18.757655" + "timestamp": "2023-09-25T10:51:46.450639" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_default_parameters.nf.test b/workflows/sra/tests/sra_default_parameters.nf.test index ef35c80a..b525bec5 100644 --- a/workflows/sra/tests/sra_default_parameters.nf.test +++ b/workflows/sra/tests/sra_default_parameters.nf.test @@ -12,7 +12,7 @@ nextflow_workflow { when { workflow { """ - input[0] = Channel.from('DRR026872','DRR028935','ERR1109373','ERR1160846','GSE214215','GSM4907283','SRR12848126','SRR13191702','SRR14593545','SRR14709033','SRR9984183') + input[0] = Channel.from('DRR026872', 'DRR028935', 'ERR1160846', 'GSE214215', 'GSM4907283', 'SRR12848126', 'SRR13191702', 'SRR14593545', 'SRR14709033', 'SRR9984183') """ } params { diff --git a/workflows/sra/tests/sra_default_parameters.nf.test.snap b/workflows/sra/tests/sra_default_parameters.nf.test.snap index b8dc88ca..ea2b868a 100644 --- a/workflows/sra/tests/sra_default_parameters.nf.test.snap +++ b/workflows/sra/tests/sra_default_parameters.nf.test.snap @@ -90,51 +90,6 @@ "DRX026011_DRR028935_2.fastq.gz:md5,941c9998d746416dad53c94c480ddf30" ] ], - [ - { - "id": "ERX1188904_ERR1109373", - "run_accession": "ERR1109373", - "experiment_accession": "ERX1188904", - "sample_accession": "SAMEA3643867", - "secondary_sample_accession": "ERS951016", - "study_accession": "PRJEB11633", - "secondary_study_accession": "ERP013030", - "submission_accession": "ERA528939", - "run_alias": "ena-RUN-CAM-03-11-2015-17:01:52:847-7", - "experiment_alias": "ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7", - "sample_alias": "sample_56", - "study_alias": "ena-STUDY-CAM-02-11-2015-17:42:24:189-13", - "library_layout": "PAIRED", - "library_selection": "RT-PCR", - "library_source": "TRANSCRIPTOMIC", - "library_strategy": "RNA-Seq", - "library_name": "unspecified", - "instrument_model": "Illumina HiSeq 2500", - "instrument_platform": "ILLUMINA", - "base_count": "29700", - "read_count": "169", - "tax_id": "63433", - "scientific_name": "Leptopilina boulardi", - "sample_title": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", - "experiment_title": "Illumina HiSeq 2500 paired end sequencing", - "study_title": "Total RNA from abdomen and head of L. boulardi females and alignment of the RNA-Seq reads against the genome of L. boulardi Toti-like Virus.", - "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", - "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9", - "fastq_bytes": "3221;8151;8118", - "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz", - "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "md5_1": "9fd57225d6c07a31843276d6df9b15c0", - "md5_2": "5a62e8f785687dce890cfb4fe3e607f9", - "single_end": false - }, - [ - "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0", - "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9" - ] - ], [ { "id": "ERX1234253_ERR1160846", @@ -662,17 +617,18 @@ ] ], "1": [ - "samplesheet.csv:md5,4aec9029e063bae998b3fa3dc3481556" + "samplesheet.csv:md5,c1104c2edfc663b103f79b0551450192" ], "2": [ - "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565" + "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342" ], "3": [ - "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", + "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8", "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", - "versions.yml:md5,e977678bd13a54fc9c31addf135be15e", - "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd" + "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd", + "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", + "versions.yml:md5,e977678bd13a54fc9c31addf135be15e" ], "fastq": [ [ @@ -762,51 +718,6 @@ "DRX026011_DRR028935_2.fastq.gz:md5,941c9998d746416dad53c94c480ddf30" ] ], - [ - { - "id": "ERX1188904_ERR1109373", - "run_accession": "ERR1109373", - "experiment_accession": "ERX1188904", - "sample_accession": "SAMEA3643867", - "secondary_sample_accession": "ERS951016", - "study_accession": "PRJEB11633", - "secondary_study_accession": "ERP013030", - "submission_accession": "ERA528939", - "run_alias": "ena-RUN-CAM-03-11-2015-17:01:52:847-7", - "experiment_alias": "ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7", - "sample_alias": "sample_56", - "study_alias": "ena-STUDY-CAM-02-11-2015-17:42:24:189-13", - "library_layout": "PAIRED", - "library_selection": "RT-PCR", - "library_source": "TRANSCRIPTOMIC", - "library_strategy": "RNA-Seq", - "library_name": "unspecified", - "instrument_model": "Illumina HiSeq 2500", - "instrument_platform": "ILLUMINA", - "base_count": "29700", - "read_count": "169", - "tax_id": "63433", - "scientific_name": "Leptopilina boulardi", - "sample_title": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", - "experiment_title": "Illumina HiSeq 2500 paired end sequencing", - "study_title": "Total RNA from abdomen and head of L. boulardi females and alignment of the RNA-Seq reads against the genome of L. boulardi Toti-like Virus.", - "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", - "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9", - "fastq_bytes": "3221;8151;8118", - "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz", - "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "md5_1": "9fd57225d6c07a31843276d6df9b15c0", - "md5_2": "5a62e8f785687dce890cfb4fe3e607f9", - "single_end": false - }, - [ - "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0", - "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9" - ] - ], [ { "id": "ERX1234253_ERR1160846", @@ -1334,20 +1245,21 @@ ] ], "mappings": [ - "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565" + "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342" ], "samplesheet": [ - "samplesheet.csv:md5,4aec9029e063bae998b3fa3dc3481556" + "samplesheet.csv:md5,c1104c2edfc663b103f79b0551450192" ], "versions": [ - "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", + "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8", "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", - "versions.yml:md5,e977678bd13a54fc9c31addf135be15e", - "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd" + "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd", + "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", + "versions.yml:md5,e977678bd13a54fc9c31addf135be15e" ] } ], - "timestamp": "2023-09-11T18:56:05.693225" + "timestamp": "2023-09-25T10:59:42.069791" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test b/workflows/sra/tests/sra_force_sratools_download.nf.test index 76ce7cd3..2548689d 100644 --- a/workflows/sra/tests/sra_force_sratools_download.nf.test +++ b/workflows/sra/tests/sra_force_sratools_download.nf.test @@ -12,7 +12,7 @@ nextflow_workflow { when { workflow { """ - input[0] = Channel.from('DRR026872','DRR028935','ERR1109373','ERR1160846','GSE214215','GSM4907283','SRR12848126','SRR13191702','SRR14593545','SRR14709033','SRR9984183') + input[0] = Channel.from('DRR026872', 'DRR028935', 'ERR1160846', 'GSE214215', 'GSM4907283', 'SRR12848126', 'SRR13191702', 'SRR14593545', 'SRR14709033', 'SRR9984183') """ } params { diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test.snap b/workflows/sra/tests/sra_force_sratools_download.nf.test.snap index 4e1b8aaf..7fdbbf66 100644 --- a/workflows/sra/tests/sra_force_sratools_download.nf.test.snap +++ b/workflows/sra/tests/sra_force_sratools_download.nf.test.snap @@ -90,51 +90,6 @@ "DRX026011_DRR028935_2.fastq.gz:md5,b97b1e0e806bcae10a7443e2f22d6ca2" ] ], - [ - { - "id": "ERX1188904_ERR1109373", - "run_accession": "ERR1109373", - "experiment_accession": "ERX1188904", - "sample_accession": "SAMEA3643867", - "secondary_sample_accession": "ERS951016", - "study_accession": "PRJEB11633", - "secondary_study_accession": "ERP013030", - "submission_accession": "ERA528939", - "run_alias": "ena-RUN-CAM-03-11-2015-17:01:52:847-7", - "experiment_alias": "ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7", - "sample_alias": "sample_56", - "study_alias": "ena-STUDY-CAM-02-11-2015-17:42:24:189-13", - "library_layout": "PAIRED", - "library_selection": "RT-PCR", - "library_source": "TRANSCRIPTOMIC", - "library_strategy": "RNA-Seq", - "library_name": "unspecified", - "instrument_model": "Illumina HiSeq 2500", - "instrument_platform": "ILLUMINA", - "base_count": "29700", - "read_count": "169", - "tax_id": "63433", - "scientific_name": "Leptopilina boulardi", - "sample_title": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", - "experiment_title": "Illumina HiSeq 2500 paired end sequencing", - "study_title": "Total RNA from abdomen and head of L. boulardi females and alignment of the RNA-Seq reads against the genome of L. boulardi Toti-like Virus.", - "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", - "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9", - "fastq_bytes": "3221;8151;8118", - "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz", - "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "md5_1": "9fd57225d6c07a31843276d6df9b15c0", - "md5_2": "5a62e8f785687dce890cfb4fe3e607f9", - "single_end": false - }, - [ - "ERX1188904_ERR1109373_1.fastq.gz:md5,e7edae2715dfaf4c318d37959fd9ae22", - "ERX1188904_ERR1109373_2.fastq.gz:md5,34ab048c92201a5ec4ab36d8dc1c5732" - ] - ], [ { "id": "ERX1234253_ERR1160846", @@ -662,16 +617,17 @@ ] ], "1": [ - "samplesheet.csv:md5,4aec9029e063bae998b3fa3dc3481556" + "samplesheet.csv:md5,c1104c2edfc663b103f79b0551450192" ], "2": [ - "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565" + "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342" ], "3": [ + "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8", - "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", - "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd" + "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd", + "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47" ], "fastq": [ [ @@ -761,51 +717,6 @@ "DRX026011_DRR028935_2.fastq.gz:md5,b97b1e0e806bcae10a7443e2f22d6ca2" ] ], - [ - { - "id": "ERX1188904_ERR1109373", - "run_accession": "ERR1109373", - "experiment_accession": "ERX1188904", - "sample_accession": "SAMEA3643867", - "secondary_sample_accession": "ERS951016", - "study_accession": "PRJEB11633", - "secondary_study_accession": "ERP013030", - "submission_accession": "ERA528939", - "run_alias": "ena-RUN-CAM-03-11-2015-17:01:52:847-7", - "experiment_alias": "ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7", - "sample_alias": "sample_56", - "study_alias": "ena-STUDY-CAM-02-11-2015-17:42:24:189-13", - "library_layout": "PAIRED", - "library_selection": "RT-PCR", - "library_source": "TRANSCRIPTOMIC", - "library_strategy": "RNA-Seq", - "library_name": "unspecified", - "instrument_model": "Illumina HiSeq 2500", - "instrument_platform": "ILLUMINA", - "base_count": "29700", - "read_count": "169", - "tax_id": "63433", - "scientific_name": "Leptopilina boulardi", - "sample_title": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", - "experiment_title": "Illumina HiSeq 2500 paired end sequencing", - "study_title": "Total RNA from abdomen and head of L. boulardi females and alignment of the RNA-Seq reads against the genome of L. boulardi Toti-like Virus.", - "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", - "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9", - "fastq_bytes": "3221;8151;8118", - "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz", - "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "md5_1": "9fd57225d6c07a31843276d6df9b15c0", - "md5_2": "5a62e8f785687dce890cfb4fe3e607f9", - "single_end": false - }, - [ - "ERX1188904_ERR1109373_1.fastq.gz:md5,e7edae2715dfaf4c318d37959fd9ae22", - "ERX1188904_ERR1109373_2.fastq.gz:md5,34ab048c92201a5ec4ab36d8dc1c5732" - ] - ], [ { "id": "ERX1234253_ERR1160846", @@ -1333,19 +1244,20 @@ ] ], "mappings": [ - "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565" + "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342" ], "samplesheet": [ - "samplesheet.csv:md5,4aec9029e063bae998b3fa3dc3481556" + "samplesheet.csv:md5,c1104c2edfc663b103f79b0551450192" ], "versions": [ + "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8", - "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", - "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd" + "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd", + "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47" ] } ], - "timestamp": "2023-09-11T19:02:05.556134" + "timestamp": "2023-09-25T11:09:38.27192" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test index 0ce0c230..ad60725c 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test @@ -12,7 +12,7 @@ nextflow_workflow { when { workflow { """ - input[0] = Channel.from('DRR026872','DRR028935','ERR1109373','ERR1160846','GSE214215','GSM4907283','SRR12848126','SRR13191702','SRR14593545','SRR14709033','SRR9984183') + input[0] = Channel.from('DRR026872', 'DRR028935', 'ERR1160846', 'GSE214215', 'GSM4907283', 'SRR12848126', 'SRR13191702', 'SRR14593545', 'SRR14709033', 'SRR9984183') """ } params { diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap index f6528e52..0cbec631 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap +++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap @@ -90,51 +90,6 @@ "DRX026011_DRR028935_2.fastq.gz:md5,941c9998d746416dad53c94c480ddf30" ] ], - [ - { - "id": "ERX1188904_ERR1109373", - "run_accession": "ERR1109373", - "experiment_accession": "ERX1188904", - "sample_accession": "SAMEA3643867", - "secondary_sample_accession": "ERS951016", - "study_accession": "PRJEB11633", - "secondary_study_accession": "ERP013030", - "submission_accession": "ERA528939", - "run_alias": "ena-RUN-CAM-03-11-2015-17:01:52:847-7", - "experiment_alias": "ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7", - "sample_alias": "sample_56", - "study_alias": "ena-STUDY-CAM-02-11-2015-17:42:24:189-13", - "library_layout": "PAIRED", - "library_selection": "RT-PCR", - "library_source": "TRANSCRIPTOMIC", - "library_strategy": "RNA-Seq", - "library_name": "unspecified", - "instrument_model": "Illumina HiSeq 2500", - "instrument_platform": "ILLUMINA", - "base_count": "29700", - "read_count": "169", - "tax_id": "63433", - "scientific_name": "Leptopilina boulardi", - "sample_title": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", - "experiment_title": "Illumina HiSeq 2500 paired end sequencing", - "study_title": "Total RNA from abdomen and head of L. boulardi females and alignment of the RNA-Seq reads against the genome of L. boulardi Toti-like Virus.", - "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", - "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9", - "fastq_bytes": "3221;8151;8118", - "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz", - "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "md5_1": "9fd57225d6c07a31843276d6df9b15c0", - "md5_2": "5a62e8f785687dce890cfb4fe3e607f9", - "single_end": false - }, - [ - "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0", - "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9" - ] - ], [ { "id": "ERX1234253_ERR1160846", @@ -662,17 +617,18 @@ ] ], "1": [ - "samplesheet.csv:md5,16e5161103702777b2d763c1ed660d3c" + "samplesheet.csv:md5,46752dd6abac80b59573910f7ce4babe" ], "2": [ - "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565" + "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342" ], "3": [ - "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", + "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8", "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", - "versions.yml:md5,e977678bd13a54fc9c31addf135be15e", - "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd" + "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd", + "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", + "versions.yml:md5,e977678bd13a54fc9c31addf135be15e" ], "fastq": [ [ @@ -762,51 +718,6 @@ "DRX026011_DRR028935_2.fastq.gz:md5,941c9998d746416dad53c94c480ddf30" ] ], - [ - { - "id": "ERX1188904_ERR1109373", - "run_accession": "ERR1109373", - "experiment_accession": "ERX1188904", - "sample_accession": "SAMEA3643867", - "secondary_sample_accession": "ERS951016", - "study_accession": "PRJEB11633", - "secondary_study_accession": "ERP013030", - "submission_accession": "ERA528939", - "run_alias": "ena-RUN-CAM-03-11-2015-17:01:52:847-7", - "experiment_alias": "ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7", - "sample_alias": "sample_56", - "study_alias": "ena-STUDY-CAM-02-11-2015-17:42:24:189-13", - "library_layout": "PAIRED", - "library_selection": "RT-PCR", - "library_source": "TRANSCRIPTOMIC", - "library_strategy": "RNA-Seq", - "library_name": "unspecified", - "instrument_model": "Illumina HiSeq 2500", - "instrument_platform": "ILLUMINA", - "base_count": "29700", - "read_count": "169", - "tax_id": "63433", - "scientific_name": "Leptopilina boulardi", - "sample_title": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", - "experiment_title": "Illumina HiSeq 2500 paired end sequencing", - "study_title": "Total RNA from abdomen and head of L. boulardi females and alignment of the RNA-Seq reads against the genome of L. boulardi Toti-like Virus.", - "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", - "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9", - "fastq_bytes": "3221;8151;8118", - "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz", - "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "md5_1": "9fd57225d6c07a31843276d6df9b15c0", - "md5_2": "5a62e8f785687dce890cfb4fe3e607f9", - "single_end": false - }, - [ - "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0", - "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9" - ] - ], [ { "id": "ERX1234253_ERR1160846", @@ -1334,20 +1245,21 @@ ] ], "mappings": [ - "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565" + "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342" ], "samplesheet": [ - "samplesheet.csv:md5,16e5161103702777b2d763c1ed660d3c" + "samplesheet.csv:md5,46752dd6abac80b59573910f7ce4babe" ], "versions": [ - "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", + "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8", "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", - "versions.yml:md5,e977678bd13a54fc9c31addf135be15e", - "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd" + "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd", + "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", + "versions.yml:md5,e977678bd13a54fc9c31addf135be15e" ] } ], - "timestamp": "2023-09-11T18:37:54.607231" + "timestamp": "2023-09-25T10:45:48.713699" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test index 67c0fbe4..993590ff 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test @@ -12,7 +12,7 @@ nextflow_workflow { when { workflow { """ - input[0] = Channel.from('DRR026872','DRR028935','ERR1109373','ERR1160846','GSE214215','GSM4907283','SRR12848126','SRR13191702','SRR14593545','SRR14709033','SRR9984183') + input[0] = Channel.from('DRR026872', 'DRR028935', 'ERR1160846', 'GSE214215', 'GSM4907283', 'SRR12848126', 'SRR13191702', 'SRR14593545', 'SRR14709033', 'SRR9984183') """ } params { diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap index 124877ae..c6bd2d32 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap +++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap @@ -90,51 +90,6 @@ "DRX026011_DRR028935_2.fastq.gz:md5,941c9998d746416dad53c94c480ddf30" ] ], - [ - { - "id": "ERX1188904_ERR1109373", - "run_accession": "ERR1109373", - "experiment_accession": "ERX1188904", - "sample_accession": "SAMEA3643867", - "secondary_sample_accession": "ERS951016", - "study_accession": "PRJEB11633", - "secondary_study_accession": "ERP013030", - "submission_accession": "ERA528939", - "run_alias": "ena-RUN-CAM-03-11-2015-17:01:52:847-7", - "experiment_alias": "ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7", - "sample_alias": "sample_56", - "study_alias": "ena-STUDY-CAM-02-11-2015-17:42:24:189-13", - "library_layout": "PAIRED", - "library_selection": "RT-PCR", - "library_source": "TRANSCRIPTOMIC", - "library_strategy": "RNA-Seq", - "library_name": "unspecified", - "instrument_model": "Illumina HiSeq 2500", - "instrument_platform": "ILLUMINA", - "base_count": "29700", - "read_count": "169", - "tax_id": "63433", - "scientific_name": "Leptopilina boulardi", - "sample_title": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", - "experiment_title": "Illumina HiSeq 2500 paired end sequencing", - "study_title": "Total RNA from abdomen and head of L. boulardi females and alignment of the RNA-Seq reads against the genome of L. boulardi Toti-like Virus.", - "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", - "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9", - "fastq_bytes": "3221;8151;8118", - "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz", - "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "md5_1": "9fd57225d6c07a31843276d6df9b15c0", - "md5_2": "5a62e8f785687dce890cfb4fe3e607f9", - "single_end": false - }, - [ - "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0", - "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9" - ] - ], [ { "id": "ERX1234253_ERR1160846", @@ -662,17 +617,18 @@ ] ], "1": [ - "samplesheet.csv:md5,fcbb1fbe56dc14561ec83e5f6a70ee80" + "samplesheet.csv:md5,69117245b73776d6e4daecdbfdff9767" ], "2": [ - "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565" + "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342" ], "3": [ + "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8", - "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", - "versions.yml:md5,e977678bd13a54fc9c31addf135be15e", - "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd" + "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd", + "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", + "versions.yml:md5,e977678bd13a54fc9c31addf135be15e" ], "fastq": [ [ @@ -762,51 +718,6 @@ "DRX026011_DRR028935_2.fastq.gz:md5,941c9998d746416dad53c94c480ddf30" ] ], - [ - { - "id": "ERX1188904_ERR1109373", - "run_accession": "ERR1109373", - "experiment_accession": "ERX1188904", - "sample_accession": "SAMEA3643867", - "secondary_sample_accession": "ERS951016", - "study_accession": "PRJEB11633", - "secondary_study_accession": "ERP013030", - "submission_accession": "ERA528939", - "run_alias": "ena-RUN-CAM-03-11-2015-17:01:52:847-7", - "experiment_alias": "ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7", - "sample_alias": "sample_56", - "study_alias": "ena-STUDY-CAM-02-11-2015-17:42:24:189-13", - "library_layout": "PAIRED", - "library_selection": "RT-PCR", - "library_source": "TRANSCRIPTOMIC", - "library_strategy": "RNA-Seq", - "library_name": "unspecified", - "instrument_model": "Illumina HiSeq 2500", - "instrument_platform": "ILLUMINA", - "base_count": "29700", - "read_count": "169", - "tax_id": "63433", - "scientific_name": "Leptopilina boulardi", - "sample_title": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", - "experiment_title": "Illumina HiSeq 2500 paired end sequencing", - "study_title": "Total RNA from abdomen and head of L. boulardi females and alignment of the RNA-Seq reads against the genome of L. boulardi Toti-like Virus.", - "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", - "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9", - "fastq_bytes": "3221;8151;8118", - "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz", - "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "md5_1": "9fd57225d6c07a31843276d6df9b15c0", - "md5_2": "5a62e8f785687dce890cfb4fe3e607f9", - "single_end": false - }, - [ - "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0", - "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9" - ] - ], [ { "id": "ERX1234253_ERR1160846", @@ -1334,20 +1245,21 @@ ] ], "mappings": [ - "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565" + "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342" ], "samplesheet": [ - "samplesheet.csv:md5,fcbb1fbe56dc14561ec83e5f6a70ee80" + "samplesheet.csv:md5,69117245b73776d6e4daecdbfdff9767" ], "versions": [ + "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8", - "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", - "versions.yml:md5,e977678bd13a54fc9c31addf135be15e", - "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd" + "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd", + "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", + "versions.yml:md5,e977678bd13a54fc9c31addf135be15e" ] } ], - "timestamp": "2023-09-11T18:51:38.198125" + "timestamp": "2023-09-25T11:02:54.001279" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test index e00793cd..a5e69da1 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test @@ -12,7 +12,7 @@ nextflow_workflow { when { workflow { """ - input[0] = Channel.from('DRR026872','DRR028935','ERR1109373','ERR1160846','GSE214215','GSM4907283','SRR12848126','SRR13191702','SRR14593545','SRR14709033','SRR9984183') + input[0] = Channel.from('DRR026872', 'DRR028935', 'ERR1160846', 'GSE214215', 'GSM4907283', 'SRR12848126', 'SRR13191702', 'SRR14593545', 'SRR14709033', 'SRR9984183') """ } params { diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap index b63ad4b7..4d57827d 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap +++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap @@ -90,51 +90,6 @@ "DRX026011_DRR028935_2.fastq.gz:md5,941c9998d746416dad53c94c480ddf30" ] ], - [ - { - "id": "ERX1188904_ERR1109373", - "run_accession": "ERR1109373", - "experiment_accession": "ERX1188904", - "sample_accession": "SAMEA3643867", - "secondary_sample_accession": "ERS951016", - "study_accession": "PRJEB11633", - "secondary_study_accession": "ERP013030", - "submission_accession": "ERA528939", - "run_alias": "ena-RUN-CAM-03-11-2015-17:01:52:847-7", - "experiment_alias": "ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7", - "sample_alias": "sample_56", - "study_alias": "ena-STUDY-CAM-02-11-2015-17:42:24:189-13", - "library_layout": "PAIRED", - "library_selection": "RT-PCR", - "library_source": "TRANSCRIPTOMIC", - "library_strategy": "RNA-Seq", - "library_name": "unspecified", - "instrument_model": "Illumina HiSeq 2500", - "instrument_platform": "ILLUMINA", - "base_count": "29700", - "read_count": "169", - "tax_id": "63433", - "scientific_name": "Leptopilina boulardi", - "sample_title": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", - "experiment_title": "Illumina HiSeq 2500 paired end sequencing", - "study_title": "Total RNA from abdomen and head of L. boulardi females and alignment of the RNA-Seq reads against the genome of L. boulardi Toti-like Virus.", - "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", - "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9", - "fastq_bytes": "3221;8151;8118", - "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz", - "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "md5_1": "9fd57225d6c07a31843276d6df9b15c0", - "md5_2": "5a62e8f785687dce890cfb4fe3e607f9", - "single_end": false - }, - [ - "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0", - "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9" - ] - ], [ { "id": "ERX1234253_ERR1160846", @@ -662,17 +617,18 @@ ] ], "1": [ - "samplesheet.csv:md5,0df1f60a9b5bc94f8a85e96edcc90f5c" + "samplesheet.csv:md5,0705e78609390cc464c2fb10051178bc" ], "2": [ - "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565" + "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342" ], "3": [ + "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8", - "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", - "versions.yml:md5,e977678bd13a54fc9c31addf135be15e", - "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd" + "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd", + "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", + "versions.yml:md5,e977678bd13a54fc9c31addf135be15e" ], "fastq": [ [ @@ -762,51 +718,6 @@ "DRX026011_DRR028935_2.fastq.gz:md5,941c9998d746416dad53c94c480ddf30" ] ], - [ - { - "id": "ERX1188904_ERR1109373", - "run_accession": "ERR1109373", - "experiment_accession": "ERX1188904", - "sample_accession": "SAMEA3643867", - "secondary_sample_accession": "ERS951016", - "study_accession": "PRJEB11633", - "secondary_study_accession": "ERP013030", - "submission_accession": "ERA528939", - "run_alias": "ena-RUN-CAM-03-11-2015-17:01:52:847-7", - "experiment_alias": "ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7", - "sample_alias": "sample_56", - "study_alias": "ena-STUDY-CAM-02-11-2015-17:42:24:189-13", - "library_layout": "PAIRED", - "library_selection": "RT-PCR", - "library_source": "TRANSCRIPTOMIC", - "library_strategy": "RNA-Seq", - "library_name": "unspecified", - "instrument_model": "Illumina HiSeq 2500", - "instrument_platform": "ILLUMINA", - "base_count": "29700", - "read_count": "169", - "tax_id": "63433", - "scientific_name": "Leptopilina boulardi", - "sample_title": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", - "experiment_title": "Illumina HiSeq 2500 paired end sequencing", - "study_title": "Total RNA from abdomen and head of L. boulardi females and alignment of the RNA-Seq reads against the genome of L. boulardi Toti-like Virus.", - "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", - "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9", - "fastq_bytes": "3221;8151;8118", - "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz", - "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "md5_1": "9fd57225d6c07a31843276d6df9b15c0", - "md5_2": "5a62e8f785687dce890cfb4fe3e607f9", - "single_end": false - }, - [ - "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0", - "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9" - ] - ], [ { "id": "ERX1234253_ERR1160846", @@ -1334,20 +1245,21 @@ ] ], "mappings": [ - "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565" + "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342" ], "samplesheet": [ - "samplesheet.csv:md5,0df1f60a9b5bc94f8a85e96edcc90f5c" + "samplesheet.csv:md5,0705e78609390cc464c2fb10051178bc" ], "versions": [ + "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8", - "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", - "versions.yml:md5,e977678bd13a54fc9c31addf135be15e", - "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd" + "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd", + "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", + "versions.yml:md5,e977678bd13a54fc9c31addf135be15e" ] } ], - "timestamp": "2023-09-11T18:44:02.293186" + "timestamp": "2023-09-25T10:48:46.519896" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test index 045e0363..f64cf92e 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test +++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test @@ -12,7 +12,7 @@ nextflow_workflow { when { workflow { """ - input[0] = Channel.from('DRR026872','DRR028935','ERR1109373','ERR1160846','GSE214215','GSM4907283','SRR12848126','SRR13191702','SRR14593545','SRR14709033','SRR9984183') + input[0] = Channel.from('DRR026872', 'DRR028935', 'ERR1160846', 'GSE214215', 'GSM4907283', 'SRR12848126', 'SRR13191702', 'SRR14593545', 'SRR14709033', 'SRR9984183') """ } params { diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap index 1387f422..3520d5bf 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap +++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap @@ -90,51 +90,6 @@ "DRX026011_DRR028935_2.fastq.gz:md5,941c9998d746416dad53c94c480ddf30" ] ], - [ - { - "id": "ERX1188904_ERR1109373", - "run_accession": "ERR1109373", - "experiment_accession": "ERX1188904", - "sample_accession": "SAMEA3643867", - "secondary_sample_accession": "ERS951016", - "study_accession": "PRJEB11633", - "secondary_study_accession": "ERP013030", - "submission_accession": "ERA528939", - "run_alias": "ena-RUN-CAM-03-11-2015-17:01:52:847-7", - "experiment_alias": "ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7", - "sample_alias": "sample_56", - "study_alias": "ena-STUDY-CAM-02-11-2015-17:42:24:189-13", - "library_layout": "PAIRED", - "library_selection": "RT-PCR", - "library_source": "TRANSCRIPTOMIC", - "library_strategy": "RNA-Seq", - "library_name": "unspecified", - "instrument_model": "Illumina HiSeq 2500", - "instrument_platform": "ILLUMINA", - "base_count": "29700", - "read_count": "169", - "tax_id": "63433", - "scientific_name": "Leptopilina boulardi", - "sample_title": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", - "experiment_title": "Illumina HiSeq 2500 paired end sequencing", - "study_title": "Total RNA from abdomen and head of L. boulardi females and alignment of the RNA-Seq reads against the genome of L. boulardi Toti-like Virus.", - "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", - "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9", - "fastq_bytes": "3221;8151;8118", - "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz", - "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "md5_1": "9fd57225d6c07a31843276d6df9b15c0", - "md5_2": "5a62e8f785687dce890cfb4fe3e607f9", - "single_end": false - }, - [ - "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0", - "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9" - ] - ], [ { "id": "ERX1234253_ERR1160846", @@ -662,17 +617,18 @@ ] ], "1": [ - "samplesheet.csv:md5,4aec9029e063bae998b3fa3dc3481556" + "samplesheet.csv:md5,c1104c2edfc663b103f79b0551450192" ], "2": [ - "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565" + "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342" ], "3": [ - "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", + "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8", "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", - "versions.yml:md5,e977678bd13a54fc9c31addf135be15e", - "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd" + "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd", + "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", + "versions.yml:md5,e977678bd13a54fc9c31addf135be15e" ], "fastq": [ [ @@ -762,51 +718,6 @@ "DRX026011_DRR028935_2.fastq.gz:md5,941c9998d746416dad53c94c480ddf30" ] ], - [ - { - "id": "ERX1188904_ERR1109373", - "run_accession": "ERR1109373", - "experiment_accession": "ERX1188904", - "sample_accession": "SAMEA3643867", - "secondary_sample_accession": "ERS951016", - "study_accession": "PRJEB11633", - "secondary_study_accession": "ERP013030", - "submission_accession": "ERA528939", - "run_alias": "ena-RUN-CAM-03-11-2015-17:01:52:847-7", - "experiment_alias": "ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7", - "sample_alias": "sample_56", - "study_alias": "ena-STUDY-CAM-02-11-2015-17:42:24:189-13", - "library_layout": "PAIRED", - "library_selection": "RT-PCR", - "library_source": "TRANSCRIPTOMIC", - "library_strategy": "RNA-Seq", - "library_name": "unspecified", - "instrument_model": "Illumina HiSeq 2500", - "instrument_platform": "ILLUMINA", - "base_count": "29700", - "read_count": "169", - "tax_id": "63433", - "scientific_name": "Leptopilina boulardi", - "sample_title": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", - "experiment_title": "Illumina HiSeq 2500 paired end sequencing", - "study_title": "Total RNA from abdomen and head of L. boulardi females and alignment of the RNA-Seq reads against the genome of L. boulardi Toti-like Virus.", - "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", - "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9", - "fastq_bytes": "3221;8151;8118", - "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz", - "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "md5_1": "9fd57225d6c07a31843276d6df9b15c0", - "md5_2": "5a62e8f785687dce890cfb4fe3e607f9", - "single_end": false - }, - [ - "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0", - "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9" - ] - ], [ { "id": "ERX1234253_ERR1160846", @@ -1334,20 +1245,21 @@ ] ], "mappings": [ - "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565" + "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342" ], "samplesheet": [ - "samplesheet.csv:md5,4aec9029e063bae998b3fa3dc3481556" + "samplesheet.csv:md5,c1104c2edfc663b103f79b0551450192" ], "versions": [ - "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", + "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8", "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", - "versions.yml:md5,e977678bd13a54fc9c31addf135be15e", - "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd" + "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd", + "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", + "versions.yml:md5,e977678bd13a54fc9c31addf135be15e" ] } ], - "timestamp": "2023-09-11T18:34:25.049818" + "timestamp": "2023-09-25T10:42:52.035768" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test b/workflows/sra/tests/sra_skip_fastq_download.nf.test index 67abee3b..aa290c68 100644 --- a/workflows/sra/tests/sra_skip_fastq_download.nf.test +++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test @@ -12,7 +12,7 @@ nextflow_workflow { when { workflow { """ - input[0] = Channel.from('DRR026872','DRR028935','ERR1109373','ERR1160846','GSE214215','GSM4907283','SRR12848126','SRR13191702','SRR14593545','SRR14709033','SRR9984183') + input[0] = Channel.from('DRR026872', 'DRR028935', 'ERR1160846', 'GSE214215', 'GSM4907283', 'SRR12848126', 'SRR13191702', 'SRR14593545', 'SRR14709033', 'SRR9984183') """ } params { diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap b/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap index 3b04b917..91a10c87 100644 --- a/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap +++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap @@ -6,32 +6,34 @@ ], "1": [ - "samplesheet.csv:md5,7cf3503b651fe016bc1e5fb3c2e996d5" + "samplesheet.csv:md5,b1636e896008b96044d352a0757a390b" ], "2": [ - "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565" + "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342" ], "3": [ - "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", + "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", - "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd" + "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd", + "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47" ], "fastq": [ ], "mappings": [ - "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565" + "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342" ], "samplesheet": [ - "samplesheet.csv:md5,7cf3503b651fe016bc1e5fb3c2e996d5" + "samplesheet.csv:md5,b1636e896008b96044d352a0757a390b" ], "versions": [ - "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", + "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", - "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd" + "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd", + "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47" ] } ], - "timestamp": "2023-09-11T18:56:34.175665" + "timestamp": "2023-09-25T11:03:28.968158" } } \ No newline at end of file From 191a8e724285471f8d698ce15eebac3fbdeeb95f Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Mon, 25 Sep 2023 10:45:28 +0200 Subject: [PATCH 23/25] Apply suggestions from code review --- workflows/sra/main.nf | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/workflows/sra/main.nf b/workflows/sra/main.nf index 46a2c809..43beb51d 100644 --- a/workflows/sra/main.nf +++ b/workflows/sra/main.nf @@ -60,7 +60,7 @@ workflow SRA { return meta_clone } .unique() - .set{ ch_sra_metadata } + .set { ch_sra_metadata } ch_versions = ch_versions.mix(SRA_RUNINFO_TO_FTP.out.versions.first()) @@ -100,9 +100,7 @@ workflow SRA { fastq_files.mix( SRA_FASTQ_FTP.out.fastq, FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS.out.reads - ).set { fastq_files } - - fastq_files.map { meta, fastq -> + ).map { meta, fastq -> def reads = fastq instanceof List ? fastq.flatten() : [ fastq ] def meta_clone = meta.clone() @@ -133,7 +131,9 @@ workflow SRA { ch_versions = ch_versions.mix(SRA_MERGE_SAMPLESHEET.out.versions) if (params.sample_mapping_fields) { - MULTIQC_MAPPINGS_CONFIG(SRA_MERGE_SAMPLESHEET.out.mappings) + MULTIQC_MAPPINGS_CONFIG ( + SRA_MERGE_SAMPLESHEET.out.mappings + ) ch_versions = ch_versions.mix(MULTIQC_MAPPINGS_CONFIG.out.versions) } From 6cf3085c08ab4654cba21ac3bdfccd6d3e7745b5 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 25 Sep 2023 12:12:16 +0200 Subject: [PATCH 24/25] update snapshots --- ...ra_custom_ena_metadata_fields.nf.test.snap | 500 +------ .../tests/sra_default_parameters.nf.test.snap | 1228 +---------------- .../sra_force_sratools_download.nf.test.snap | 1228 +---------------- .../sra_nf_core_pipeline_atacseq.nf.test.snap | 1228 +---------------- .../sra_nf_core_pipeline_rnaseq.nf.test.snap | 1228 +---------------- ..._nf_core_pipeline_taxprofiler.nf.test.snap | 1228 +---------------- ...a_nf_core_pipeline_viralrecon.nf.test.snap | 1228 +---------------- 7 files changed, 21 insertions(+), 7847 deletions(-) diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap index 29feb896..7a7df129 100644 --- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap +++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap @@ -3,254 +3,7 @@ "content": [ { "0": [ - 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"timestamp": "2023-09-25T10:42:52.035768" + "timestamp": "2023-09-25T11:50:52.373496" } } \ No newline at end of file From 56e5143fbf3d14b944183df461e5c0903ac7faea Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 6 Oct 2023 12:25:48 +0200 Subject: [PATCH 25/25] update snapshots --- .github/workflows/ci.yml | 2 +- ...sra_default_parameters.nf.test => main.nf.test} | 0 ...t_parameters.nf.test.snap => main.nf.test.snap} | 14 +++++++++++++- .../sra_custom_ena_metadata_fields.nf.test.snap | 14 +++++++++++++- .../tests/sra_force_sratools_download.nf.test.snap | 14 +++++++++++++- .../sra_nf_core_pipeline_atacseq.nf.test.snap | 14 +++++++++++++- .../tests/sra_nf_core_pipeline_rnaseq.nf.test.snap | 14 +++++++++++++- .../sra_nf_core_pipeline_taxprofiler.nf.test.snap | 14 +++++++++++++- .../sra_nf_core_pipeline_viralrecon.nf.test.snap | 14 +++++++++++++- .../sra/tests/sra_skip_fastq_download.nf.test.snap | 14 +++++++++++++- 10 files changed, 105 insertions(+), 9 deletions(-) rename workflows/sra/tests/{sra_default_parameters.nf.test => main.nf.test} (100%) rename workflows/sra/tests/{sra_default_parameters.nf.test.snap => main.nf.test.snap} (75%) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 30656e1a..68e2773c 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -15,7 +15,7 @@ on: env: NXF_ANSI_LOG: false - NFTEST_VER: "0.8.0-rc2" + NFTEST_VER: "0.8.0" concurrency: group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" diff --git a/workflows/sra/tests/sra_default_parameters.nf.test b/workflows/sra/tests/main.nf.test similarity index 100% rename from workflows/sra/tests/sra_default_parameters.nf.test rename to workflows/sra/tests/main.nf.test diff --git a/workflows/sra/tests/sra_default_parameters.nf.test.snap b/workflows/sra/tests/main.nf.test.snap similarity index 75% rename from workflows/sra/tests/sra_default_parameters.nf.test.snap rename to workflows/sra/tests/main.nf.test.snap index edb662a2..955dd72a 100644 --- a/workflows/sra/tests/sra_default_parameters.nf.test.snap +++ b/workflows/sra/tests/main.nf.test.snap @@ -12,6 +12,12 @@ "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342" ], "3": [ + [ + "multiqc_config.yml:md5,bb99e81ddd360988338c10ecbdbce65a", + "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9" + ] + ], + "4": [ "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8", "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", @@ -25,6 +31,12 @@ "mappings": [ "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342" ], + "sample_mappings": [ + [ + "multiqc_config.yml:md5,bb99e81ddd360988338c10ecbdbce65a", + "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9" + ] + ], "samplesheet": [ "samplesheet.csv:md5,c1104c2edfc663b103f79b0551450192" ], @@ -38,6 +50,6 @@ ] } ], - "timestamp": "2023-09-25T12:00:37.501679" + "timestamp": "2023-10-06T12:18:32.149462" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap index 7a7df129..143375ac 100644 --- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap +++ b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap @@ -12,6 +12,12 @@ "id_mappings.csv:md5,e8a7d8effe4af1d999dc26cf92cf6621" ], "3": [ + [ + "multiqc_config.yml:md5,b1c25951b237552448e878f7c9dc4235", + "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9" + ] + ], + "4": [ "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8", "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", @@ -25,6 +31,12 @@ "mappings": [ "id_mappings.csv:md5,e8a7d8effe4af1d999dc26cf92cf6621" ], + "sample_mappings": [ + [ + "multiqc_config.yml:md5,b1c25951b237552448e878f7c9dc4235", + "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9" + ] + ], "samplesheet": [ "samplesheet.csv:md5,d161b1a26b415a61064d8c558c9695c5" ], @@ -38,6 +50,6 @@ ] } ], - "timestamp": "2023-09-25T11:58:11.85816" + "timestamp": "2023-10-06T12:10:32.762201" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test.snap b/workflows/sra/tests/sra_force_sratools_download.nf.test.snap index 91eec432..5cb1876c 100644 --- a/workflows/sra/tests/sra_force_sratools_download.nf.test.snap +++ b/workflows/sra/tests/sra_force_sratools_download.nf.test.snap @@ -12,6 +12,12 @@ "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342" ], "3": [ + [ + "multiqc_config.yml:md5,bb99e81ddd360988338c10ecbdbce65a", + "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9" + ] + ], + "4": [ "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8", "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", @@ -24,6 +30,12 @@ "mappings": [ "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342" ], + "sample_mappings": [ + [ + "multiqc_config.yml:md5,bb99e81ddd360988338c10ecbdbce65a", + "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9" + ] + ], "samplesheet": [ "samplesheet.csv:md5,c1104c2edfc663b103f79b0551450192" ], @@ -36,6 +48,6 @@ ] } ], - "timestamp": "2023-09-25T12:08:28.465466" + "timestamp": "2023-10-06T12:24:57.695874" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap index 4560b05b..60cd3444 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap +++ b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap @@ -12,6 +12,12 @@ "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342" ], "3": [ + [ + "multiqc_config.yml:md5,bb99e81ddd360988338c10ecbdbce65a", + "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9" + ] + ], + "4": [ "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8", "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", @@ -25,6 +31,12 @@ "mappings": [ "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342" ], + "sample_mappings": [ + [ + "multiqc_config.yml:md5,bb99e81ddd360988338c10ecbdbce65a", + "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9" + ] + ], "samplesheet": [ "samplesheet.csv:md5,46752dd6abac80b59573910f7ce4babe" ], @@ -38,6 +50,6 @@ ] } ], - "timestamp": "2023-09-25T11:53:25.411769" + "timestamp": "2023-10-06T12:03:19.401141" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap index 26357aa5..a0c20a40 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap +++ b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap @@ -12,6 +12,12 @@ "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342" ], "3": [ + [ + "multiqc_config.yml:md5,bb99e81ddd360988338c10ecbdbce65a", + "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9" + ] + ], + "4": [ "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8", "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", @@ -25,6 +31,12 @@ "mappings": [ "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342" ], + "sample_mappings": [ + [ + "multiqc_config.yml:md5,bb99e81ddd360988338c10ecbdbce65a", + "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9" + ] + ], "samplesheet": [ "samplesheet.csv:md5,69117245b73776d6e4daecdbfdff9767" ], @@ -38,6 +50,6 @@ ] } ], - "timestamp": "2023-09-25T12:03:02.485911" + "timestamp": "2023-10-06T12:14:02.500312" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap index ff4b27df..d9d6ddee 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap +++ b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap @@ -12,6 +12,12 @@ "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342" ], "3": [ + [ + "multiqc_config.yml:md5,bb99e81ddd360988338c10ecbdbce65a", + "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9" + ] + ], + "4": [ "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8", "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", @@ -25,6 +31,12 @@ "mappings": [ "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342" ], + "sample_mappings": [ + [ + "multiqc_config.yml:md5,bb99e81ddd360988338c10ecbdbce65a", + "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9" + ] + ], "samplesheet": [ "samplesheet.csv:md5,0705e78609390cc464c2fb10051178bc" ], @@ -38,6 +50,6 @@ ] } ], - "timestamp": "2023-09-25T11:55:48.759498" + "timestamp": "2023-10-06T12:07:01.184728" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap index 4b38d6a1..c3e9ae8b 100644 --- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap +++ b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap @@ -12,6 +12,12 @@ "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342" ], "3": [ + [ + "multiqc_config.yml:md5,bb99e81ddd360988338c10ecbdbce65a", + "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9" + ] + ], + "4": [ "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8", "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", @@ -25,6 +31,12 @@ "mappings": [ "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342" ], + "sample_mappings": [ + [ + "multiqc_config.yml:md5,bb99e81ddd360988338c10ecbdbce65a", + "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9" + ] + ], "samplesheet": [ "samplesheet.csv:md5,c1104c2edfc663b103f79b0551450192" ], @@ -38,6 +50,6 @@ ] } ], - "timestamp": "2023-09-25T11:50:52.373496" + "timestamp": "2023-10-06T11:59:31.7356" } } \ No newline at end of file diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap b/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap index 91a10c87..c137d853 100644 --- a/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap +++ b/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap @@ -12,6 +12,12 @@ "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342" ], "3": [ + [ + "multiqc_config.yml:md5,bb99e81ddd360988338c10ecbdbce65a", + "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9" + ] + ], + "4": [ "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9", "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd", @@ -23,6 +29,12 @@ "mappings": [ "id_mappings.csv:md5,a18766d39f6b2239163b4ef00eeaf342" ], + "sample_mappings": [ + [ + "multiqc_config.yml:md5,bb99e81ddd360988338c10ecbdbce65a", + "versions.yml:md5,1496d1cbc9041e07ab8a0c25f0b054d9" + ] + ], "samplesheet": [ "samplesheet.csv:md5,b1636e896008b96044d352a0757a390b" ], @@ -34,6 +46,6 @@ ] } ], - "timestamp": "2023-09-25T11:03:28.968158" + "timestamp": "2023-10-06T12:18:48.477246" } } \ No newline at end of file