From dfdd7653a0a04db5e6006d8236b0a1e9970b851c Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Thu, 5 Sep 2024 10:58:17 +0100 Subject: [PATCH 01/17] Bump versions for next release --- CHANGELOG.md | 8 ++++++++ nextflow.config | 2 +- tests/default.nf.test.snap | 4 ++-- tests/featurecounts_group_type.nf.test.snap | 4 ++-- tests/hisat2.nf.test.snap | 4 ++-- tests/kallisto.nf.test.snap | 4 ++-- tests/min_mapped_reads.nf.test.snap | 4 ++-- tests/remove_ribo_rna.nf.test.snap | 4 ++-- tests/salmon.nf.test.snap | 4 ++-- tests/skip_qc.nf.test.snap | 4 ++-- tests/skip_trimming.nf.test.snap | 2 +- tests/star_rsem.nf.test.snap | 4 ++-- workflows/rnaseq/assets/multiqc/multiqc_config.yml | 2 +- 13 files changed, 29 insertions(+), 21 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 2c3d147f3..161f09878 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,14 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). +## v3.16.0dev - [date] + +### Credits + +Special thanks to the following for their contributions to the release: + +### Enhancements & fixes + ## [[3.15.0](https://github.com/nf-core/rnaseq/releases/tag/3.15.0)] - 2024-09-04 ### Credits diff --git a/nextflow.config b/nextflow.config index 1771272d4..d5e00c6f4 100644 --- a/nextflow.config +++ b/nextflow.config @@ -340,7 +340,7 @@ manifest { description = """RNA sequencing analysis pipeline for gene/isoform quantification and extensive quality control.""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '3.15.0' + version = '3.16.0dev' doi = 'https://doi.org/10.5281/zenodo.1400710' } diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 9be7dfb04..79b3ca290 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -266,7 +266,7 @@ }, "Params: default - stub": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, FASTQC={fastqc=0.12.1}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.0}}", + "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, FASTQC={fastqc=0.12.1}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0dev}}", "genome_transcriptome.fasta", "genome_transcriptome.gtf", "RAP1_IAA_30M_REP1_raw.html", @@ -932,7 +932,7 @@ }, "versions": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV_FW={bedtools=2.31.1}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, DESEQ2_QC_PSEUDO={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DESEQ2_QC_STAR_SALMON={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DUPRADAR={bioconductor-dupradar=1.32.0}, FASTQC={fastqc=0.12.1}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, MULTIQC_CUSTOM_BIOTYPE={python=3.9.5}, PICARD_MARKDUPLICATES={picard=3.1.1}, QUALIMAP_RNASEQ={qualimap=2.3}, RSEQC_BAMSTAT={rseqc=5.0.2}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_INNERDISTANCE={rseqc=5.0.2}, RSEQC_JUNCTIONANNOTATION={rseqc=5.0.2}, RSEQC_JUNCTIONSATURATION={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, STAR_ALIGN={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.0}}" + "{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV_FW={bedtools=2.31.1}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, DESEQ2_QC_PSEUDO={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DESEQ2_QC_STAR_SALMON={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DUPRADAR={bioconductor-dupradar=1.32.0}, FASTQC={fastqc=0.12.1}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, MULTIQC_CUSTOM_BIOTYPE={python=3.9.5}, PICARD_MARKDUPLICATES={picard=3.1.1}, QUALIMAP_RNASEQ={qualimap=2.3}, RSEQC_BAMSTAT={rseqc=5.0.2}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_INNERDISTANCE={rseqc=5.0.2}, RSEQC_JUNCTIONANNOTATION={rseqc=5.0.2}, RSEQC_JUNCTIONSATURATION={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, STAR_ALIGN={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0dev}}" ], "meta": { "nf-test": "0.9.0", diff --git a/tests/featurecounts_group_type.nf.test.snap b/tests/featurecounts_group_type.nf.test.snap index a7e6910dd..3a08ab907 100644 --- a/tests/featurecounts_group_type.nf.test.snap +++ b/tests/featurecounts_group_type.nf.test.snap @@ -747,7 +747,7 @@ }, "versions": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV_FW={bedtools=2.31.1}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, DESEQ2_QC_PSEUDO={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DESEQ2_QC_STAR_SALMON={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DUPRADAR={bioconductor-dupradar=1.32.0}, FASTQC={fastqc=0.12.1}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, PICARD_MARKDUPLICATES={picard=3.1.1}, QUALIMAP_RNASEQ={qualimap=2.3}, RSEQC_BAMSTAT={rseqc=5.0.2}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_INNERDISTANCE={rseqc=5.0.2}, RSEQC_JUNCTIONANNOTATION={rseqc=5.0.2}, RSEQC_JUNCTIONSATURATION={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, STAR_ALIGN={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.0}}" + "{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV_FW={bedtools=2.31.1}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, DESEQ2_QC_PSEUDO={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DESEQ2_QC_STAR_SALMON={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DUPRADAR={bioconductor-dupradar=1.32.0}, FASTQC={fastqc=0.12.1}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, PICARD_MARKDUPLICATES={picard=3.1.1}, QUALIMAP_RNASEQ={qualimap=2.3}, RSEQC_BAMSTAT={rseqc=5.0.2}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_INNERDISTANCE={rseqc=5.0.2}, RSEQC_JUNCTIONANNOTATION={rseqc=5.0.2}, RSEQC_JUNCTIONSATURATION={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, STAR_ALIGN={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0dev}}" ], "meta": { "nf-test": "0.9.0", @@ -757,7 +757,7 @@ }, "Params: --featurecounts_group_type false - stub": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, FASTQC={fastqc=0.12.1}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.0}}", + "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, FASTQC={fastqc=0.12.1}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0dev}}", "genome_transcriptome.fasta", "genome_transcriptome.gtf", "RAP1_IAA_30M_REP1_raw.html", diff --git a/tests/hisat2.nf.test.snap b/tests/hisat2.nf.test.snap index db5ac14e1..1a15dd9a4 100644 --- a/tests/hisat2.nf.test.snap +++ b/tests/hisat2.nf.test.snap @@ -631,7 +631,7 @@ }, "Params: --aligner hisat2 - stub": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, FASTQC={fastqc=0.12.1}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, HISAT2_EXTRACTSPLICESITES={hisat2=2.2.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_HISAT2_INDEX={untar=1.34}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.0}}", + "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, FASTQC={fastqc=0.12.1}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, HISAT2_EXTRACTSPLICESITES={hisat2=2.2.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_HISAT2_INDEX={untar=1.34}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0dev}}", "genome_transcriptome.fasta", "genome_transcriptome.gtf", "RAP1_IAA_30M_REP1_raw.html", @@ -726,7 +726,7 @@ }, "versions": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV_FW={bedtools=2.31.1}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, DESEQ2_QC_PSEUDO={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DUPRADAR={bioconductor-dupradar=1.32.0}, FASTQC={fastqc=0.12.1}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, HISAT2_ALIGN={hisat2=2.2.1, samtools=1.16.1}, HISAT2_EXTRACTSPLICESITES={hisat2=2.2.1}, MULTIQC_CUSTOM_BIOTYPE={python=3.9.5}, PICARD_MARKDUPLICATES={picard=3.1.1}, QUALIMAP_RNASEQ={qualimap=2.3}, RSEQC_BAMSTAT={rseqc=5.0.2}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_INNERDISTANCE={rseqc=5.0.2}, RSEQC_JUNCTIONANNOTATION={rseqc=5.0.2}, RSEQC_JUNCTIONSATURATION={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_HISAT2_INDEX={untar=1.34}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.0}}" + "{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV_FW={bedtools=2.31.1}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, DESEQ2_QC_PSEUDO={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DUPRADAR={bioconductor-dupradar=1.32.0}, FASTQC={fastqc=0.12.1}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, HISAT2_ALIGN={hisat2=2.2.1, samtools=1.16.1}, HISAT2_EXTRACTSPLICESITES={hisat2=2.2.1}, MULTIQC_CUSTOM_BIOTYPE={python=3.9.5}, PICARD_MARKDUPLICATES={picard=3.1.1}, QUALIMAP_RNASEQ={qualimap=2.3}, RSEQC_BAMSTAT={rseqc=5.0.2}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_INNERDISTANCE={rseqc=5.0.2}, RSEQC_JUNCTIONANNOTATION={rseqc=5.0.2}, RSEQC_JUNCTIONSATURATION={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_HISAT2_INDEX={untar=1.34}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0dev}}" ], "meta": { "nf-test": "0.9.0", diff --git a/tests/kallisto.nf.test.snap b/tests/kallisto.nf.test.snap index 809f4e0f2..a431f33fc 100644 --- a/tests/kallisto.nf.test.snap +++ b/tests/kallisto.nf.test.snap @@ -103,7 +103,7 @@ }, "versions": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, KALLISTO_INDEX={kallisto=0.48.0}, KALLISTO_QUANT={kallisto=0.48.0}, SALMON_QUANT={salmon=1.10.1}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.0}}" + "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, KALLISTO_INDEX={kallisto=0.48.0}, KALLISTO_QUANT={kallisto=0.48.0}, SALMON_QUANT={salmon=1.10.1}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0dev}}" ], "meta": { "nf-test": "0.9.0", @@ -219,7 +219,7 @@ }, "Params: --pseudo_aligner kallisto --skip_qc --skip_alignment - stub": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, KALLISTO_INDEX={kallisto=0.48.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.0}}", + "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, KALLISTO_INDEX={kallisto=0.48.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0dev}}", "genome_transcriptome.fasta", "genome_transcriptome.gtf", "multiqc_report.html", diff --git a/tests/min_mapped_reads.nf.test.snap b/tests/min_mapped_reads.nf.test.snap index 941a21a58..c68828368 100644 --- a/tests/min_mapped_reads.nf.test.snap +++ b/tests/min_mapped_reads.nf.test.snap @@ -447,7 +447,7 @@ }, "Params: --min_mapped_reads 90 - stub": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, FASTQC={fastqc=0.12.1}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.0}}", + "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, FASTQC={fastqc=0.12.1}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0dev}}", "genome_transcriptome.fasta", "genome_transcriptome.gtf", "RAP1_IAA_30M_REP1_raw.html", @@ -854,7 +854,7 @@ }, "versions": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV_FW={bedtools=2.31.1}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, DESEQ2_QC_PSEUDO={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DESEQ2_QC_STAR_SALMON={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DUPRADAR={bioconductor-dupradar=1.32.0}, FASTQC={fastqc=0.12.1}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, MULTIQC_CUSTOM_BIOTYPE={python=3.9.5}, PICARD_MARKDUPLICATES={picard=3.1.1}, QUALIMAP_RNASEQ={qualimap=2.3}, RSEQC_BAMSTAT={rseqc=5.0.2}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_INNERDISTANCE={rseqc=5.0.2}, RSEQC_JUNCTIONANNOTATION={rseqc=5.0.2}, RSEQC_JUNCTIONSATURATION={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, STAR_ALIGN={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.0}}" + "{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV_FW={bedtools=2.31.1}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, DESEQ2_QC_PSEUDO={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DESEQ2_QC_STAR_SALMON={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DUPRADAR={bioconductor-dupradar=1.32.0}, FASTQC={fastqc=0.12.1}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, MULTIQC_CUSTOM_BIOTYPE={python=3.9.5}, PICARD_MARKDUPLICATES={picard=3.1.1}, QUALIMAP_RNASEQ={qualimap=2.3}, RSEQC_BAMSTAT={rseqc=5.0.2}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_INNERDISTANCE={rseqc=5.0.2}, RSEQC_JUNCTIONANNOTATION={rseqc=5.0.2}, RSEQC_JUNCTIONSATURATION={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, STAR_ALIGN={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0dev}}" ], "meta": { "nf-test": "0.9.0", diff --git a/tests/remove_ribo_rna.nf.test.snap b/tests/remove_ribo_rna.nf.test.snap index 73cd09c7c..a6e841b08 100644 --- a/tests/remove_ribo_rna.nf.test.snap +++ b/tests/remove_ribo_rna.nf.test.snap @@ -498,7 +498,7 @@ }, "Params: --remove_ribo_rna - stub": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, FASTQC={fastqc=0.12.1}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, SORTMERNA_INDEX={sortmerna=4.3.6}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.0}}", + "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, FASTQC={fastqc=0.12.1}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, SORTMERNA_INDEX={sortmerna=4.3.6}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0dev}}", "genome_transcriptome.fasta", "genome_transcriptome.gtf", "RAP1_IAA_30M_REP1_raw.html", @@ -954,7 +954,7 @@ }, "versions": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV_FW={bedtools=2.31.1}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, DESEQ2_QC_PSEUDO={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DESEQ2_QC_STAR_SALMON={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DUPRADAR={bioconductor-dupradar=1.32.0}, FASTQC={fastqc=0.12.1}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, MULTIQC_CUSTOM_BIOTYPE={python=3.9.5}, PICARD_MARKDUPLICATES={picard=3.1.1}, QUALIMAP_RNASEQ={qualimap=2.3}, RSEQC_BAMSTAT={rseqc=5.0.2}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_INNERDISTANCE={rseqc=5.0.2}, RSEQC_JUNCTIONANNOTATION={rseqc=5.0.2}, RSEQC_JUNCTIONSATURATION={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, SORTMERNA={sortmerna=4.3.6}, SORTMERNA_INDEX={sortmerna=4.3.6}, STAR_ALIGN={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.0}}" + "{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV_FW={bedtools=2.31.1}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, DESEQ2_QC_PSEUDO={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DESEQ2_QC_STAR_SALMON={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DUPRADAR={bioconductor-dupradar=1.32.0}, FASTQC={fastqc=0.12.1}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, MULTIQC_CUSTOM_BIOTYPE={python=3.9.5}, PICARD_MARKDUPLICATES={picard=3.1.1}, QUALIMAP_RNASEQ={qualimap=2.3}, RSEQC_BAMSTAT={rseqc=5.0.2}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_INNERDISTANCE={rseqc=5.0.2}, RSEQC_JUNCTIONANNOTATION={rseqc=5.0.2}, RSEQC_JUNCTIONSATURATION={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, SORTMERNA={sortmerna=4.3.6}, SORTMERNA_INDEX={sortmerna=4.3.6}, STAR_ALIGN={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0dev}}" ], "meta": { "nf-test": "0.9.0", diff --git a/tests/salmon.nf.test.snap b/tests/salmon.nf.test.snap index 93f7cc786..004c15ad4 100644 --- a/tests/salmon.nf.test.snap +++ b/tests/salmon.nf.test.snap @@ -61,7 +61,7 @@ }, "versions": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, SALMON_QUANT={salmon=1.10.1}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.0}}" + "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, SALMON_QUANT={salmon=1.10.1}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0dev}}" ], "meta": { "nf-test": "0.9.0", @@ -265,7 +265,7 @@ }, "Params: --pseudo_aligner salmon --skip_qc --skip_alignment - stub": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.0}}", + "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0dev}}", "genome_transcriptome.fasta", "genome_transcriptome.gtf", "RAP1_IAA_30M_REP1_raw.html", diff --git a/tests/skip_qc.nf.test.snap b/tests/skip_qc.nf.test.snap index 563f4913e..7a1eaccf3 100644 --- a/tests/skip_qc.nf.test.snap +++ b/tests/skip_qc.nf.test.snap @@ -157,7 +157,7 @@ }, "Params: --skip_qc - stub": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.0}}", + "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0dev}}", "genome_transcriptome.fasta", "genome_transcriptome.gtf", "RAP1_IAA_30M_REP1_raw.html", @@ -477,7 +477,7 @@ }, "versions": { "content": [ - 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"{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV_FW={bedtools=2.31.1}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, DESEQ2_QC_PSEUDO={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DESEQ2_QC_STAR_SALMON={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DUPRADAR={bioconductor-dupradar=1.32.0}, FASTQC={fastqc=0.12.1}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, MULTIQC_CUSTOM_BIOTYPE={python=3.9.5}, PICARD_MARKDUPLICATES={picard=3.1.1}, QUALIMAP_RNASEQ={qualimap=2.3}, RSEQC_BAMSTAT={rseqc=5.0.2}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_INNERDISTANCE={rseqc=5.0.2}, RSEQC_JUNCTIONANNOTATION={rseqc=5.0.2}, RSEQC_JUNCTIONSATURATION={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, STAR_ALIGN={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.0}}" + "{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV_FW={bedtools=2.31.1}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, DESEQ2_QC_PSEUDO={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DESEQ2_QC_STAR_SALMON={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DUPRADAR={bioconductor-dupradar=1.32.0}, FASTQC={fastqc=0.12.1}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, MULTIQC_CUSTOM_BIOTYPE={python=3.9.5}, PICARD_MARKDUPLICATES={picard=3.1.1}, QUALIMAP_RNASEQ={qualimap=2.3}, RSEQC_BAMSTAT={rseqc=5.0.2}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_INNERDISTANCE={rseqc=5.0.2}, RSEQC_JUNCTIONANNOTATION={rseqc=5.0.2}, RSEQC_JUNCTIONSATURATION={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, STAR_ALIGN={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0dev}}" ], "meta": { "nf-test": "0.9.0", diff --git a/tests/star_rsem.nf.test.snap b/tests/star_rsem.nf.test.snap index 945d18f11..a6a804341 100644 --- a/tests/star_rsem.nf.test.snap +++ b/tests/star_rsem.nf.test.snap @@ -766,7 +766,7 @@ }, "Params: --aligner star_rsem - stub": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, FASTQC={fastqc=0.12.1}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_RSEM_INDEX={untar=1.34}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.0}}", + "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, FASTQC={fastqc=0.12.1}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_RSEM_INDEX={untar=1.34}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0dev}}", "genome_transcriptome.fasta", "genome_transcriptome.gtf", "RAP1_IAA_30M_REP1_raw.html", @@ -797,7 +797,7 @@ }, "versions": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV_FW={bedtools=2.31.1}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, DESEQ2_QC_PSEUDO={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DESEQ2_QC_RSEM={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DUPRADAR={bioconductor-dupradar=1.32.0}, FASTQC={fastqc=0.12.1}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, MULTIQC_CUSTOM_BIOTYPE={python=3.9.5}, PICARD_MARKDUPLICATES={picard=3.1.1}, QUALIMAP_RNASEQ={qualimap=2.3}, RSEM_CALCULATEEXPRESSION={rsem=1.3.1, star=2.7.10a}, RSEM_MERGE_COUNTS={sed=4.7}, RSEQC_BAMSTAT={rseqc=5.0.2}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_INNERDISTANCE={rseqc=5.0.2}, RSEQC_JUNCTIONANNOTATION={rseqc=5.0.2}, RSEQC_JUNCTIONSATURATION={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_RSEM_INDEX={untar=1.34}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.0}}" + "{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV_FW={bedtools=2.31.1}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, DESEQ2_QC_PSEUDO={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DESEQ2_QC_RSEM={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DUPRADAR={bioconductor-dupradar=1.32.0}, FASTQC={fastqc=0.12.1}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, MULTIQC_CUSTOM_BIOTYPE={python=3.9.5}, PICARD_MARKDUPLICATES={picard=3.1.1}, QUALIMAP_RNASEQ={qualimap=2.3}, RSEM_CALCULATEEXPRESSION={rsem=1.3.1, star=2.7.10a}, RSEM_MERGE_COUNTS={sed=4.7}, RSEQC_BAMSTAT={rseqc=5.0.2}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_INNERDISTANCE={rseqc=5.0.2}, RSEQC_JUNCTIONANNOTATION={rseqc=5.0.2}, RSEQC_JUNCTIONSATURATION={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_RSEM_INDEX={untar=1.34}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0dev}}" ], "meta": { "nf-test": "0.9.0", diff --git a/workflows/rnaseq/assets/multiqc/multiqc_config.yml b/workflows/rnaseq/assets/multiqc/multiqc_config.yml index 136e03f1c..49d3939e2 100644 --- a/workflows/rnaseq/assets/multiqc/multiqc_config.yml +++ b/workflows/rnaseq/assets/multiqc/multiqc_config.yml @@ -1,5 +1,5 @@ report_comment: > - This report has been generated by the nf-core/rnaseq analysis pipeline. For information about how to interpret these results, please see the documentation. + This report has been generated by the nf-core/rnaseq analysis pipeline. For information about how to interpret these results, please see the documentation. report_section_order: # Important checks and failures sample-status: From ad85ab2b1c7fe07a8508124db2bdfdccc6ff5bdd Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Thu, 5 Sep 2024 10:59:33 +0100 Subject: [PATCH 02/17] Bump CI --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 161f09878..7e6598e67 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,6 +5,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## v3.16.0dev - [date] + ### Credits Special thanks to the following for their contributions to the release: From 169318d162fd1b22564bd061ffd220e892216780 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Thu, 5 Sep 2024 11:03:03 +0100 Subject: [PATCH 03/17] Update CHANGELOG.md Co-authored-by: Maxime U Garcia --- CHANGELOG.md | 1 - 1 file changed, 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 7e6598e67..161f09878 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,7 +5,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## v3.16.0dev - [date] - ### Credits Special thanks to the following for their contributions to the release: From 4896bd00a5bbdbf58e3adf7411f5bc8f6b411e2c Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Thu, 5 Sep 2024 11:07:06 +0100 Subject: [PATCH 04/17] Update changelog --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 161f09878..e1976f761 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,6 +5,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## v3.16.0dev - [date] +- [PR #1374](https://github.com/nf-core/rnaseq/pull/1374) - Bump pipeline version to 3.16.0dev + ### Credits Special thanks to the following for their contributions to the release: From 457bdd992a86116dc6b3e5278e381b59024919e7 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Fri, 13 Sep 2024 11:29:53 +0100 Subject: [PATCH 05/17] Fix R module name-mangling issues --- modules.json | 4 ++-- .../summarizedexperiment/summarizedexperiment/environment.yml | 2 -- .../summarizedexperiment/templates/summarizedexperiment.r | 2 +- modules/nf-core/tximeta/tximport/environment.yml | 2 -- modules/nf-core/tximeta/tximport/templates/tximport.r | 2 +- 5 files changed, 4 insertions(+), 8 deletions(-) diff --git a/modules.json b/modules.json index 6e266bc86..fc53bd567 100644 --- a/modules.json +++ b/modules.json @@ -227,7 +227,7 @@ }, "summarizedexperiment/summarizedexperiment": { "branch": "master", - "git_sha": "4e5f4687318f24ba944a13609d3ea6ebd890737d", + "git_sha": "625fbbc0531fb1717349c7f1b1c677a3b8619767", "installed_by": ["modules", "quantify_pseudo_alignment"] }, "trimgalore": { @@ -237,7 +237,7 @@ }, "tximeta/tximport": { "branch": "master", - "git_sha": "d612c281cf2fae62cdd79c70a22fc6349108570c", + "git_sha": "625fbbc0531fb1717349c7f1b1c677a3b8619767", "installed_by": ["modules", "quantify_pseudo_alignment"] }, "ucsc/bedclip": { diff --git a/modules/nf-core/summarizedexperiment/summarizedexperiment/environment.yml b/modules/nf-core/summarizedexperiment/summarizedexperiment/environment.yml index 252ace791..dc4e6c936 100644 --- a/modules/nf-core/summarizedexperiment/summarizedexperiment/environment.yml +++ b/modules/nf-core/summarizedexperiment/summarizedexperiment/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "summarizedexperiment_summarizedexperiment" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::bioconductor-summarizedexperiment=1.32.0" diff --git a/modules/nf-core/summarizedexperiment/summarizedexperiment/templates/summarizedexperiment.r b/modules/nf-core/summarizedexperiment/summarizedexperiment/templates/summarizedexperiment.r index 6c705350a..60ea3179f 100644 --- a/modules/nf-core/summarizedexperiment/summarizedexperiment/templates/summarizedexperiment.r +++ b/modules/nf-core/summarizedexperiment/summarizedexperiment/templates/summarizedexperiment.r @@ -13,7 +13,7 @@ library(SummarizedExperiment) #' #' @return output Data frame -read_delim_flexible <- function(file, header = TRUE, row.names = NULL, check.names = TRUE, stringsAsFactors = FALSE){ +read_delim_flexible <- function(file, header = TRUE, row.names = NULL, check.names = FALSE, stringsAsFactors = FALSE){ ext <- tolower(tail(strsplit(basename(file), split = "\\\\.")[[1]], 1)) diff --git a/modules/nf-core/tximeta/tximport/environment.yml b/modules/nf-core/tximeta/tximport/environment.yml index 24b202222..4b6df0cfe 100644 --- a/modules/nf-core/tximeta/tximport/environment.yml +++ b/modules/nf-core/tximeta/tximport/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "tximeta_tximport" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::bioconductor-tximeta=1.20.1" diff --git a/modules/nf-core/tximeta/tximport/templates/tximport.r b/modules/nf-core/tximeta/tximport/templates/tximport.r index e8235c8b0..5986c05d9 100755 --- a/modules/nf-core/tximeta/tximport/templates/tximport.r +++ b/modules/nf-core/tximeta/tximport/templates/tximport.r @@ -26,7 +26,7 @@ library(tximport) #' @return A data frame combining the first two columns of the rowData with the assay data from the specified slot. build_table <- function(se.obj, slot) { - cbind(rowData(se.obj)[,1:2], assays(se.obj)[[slot]]) + data.frame(cbind(rowData(se.obj)[,1:2], assays(se.obj)[[slot]]), check.names = FALSE) } #' Write a table to a file from a SummarizedExperiment object with given parameters From 765e67df300d2399d45efcf95271a87d4d598e41 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Fri, 13 Sep 2024 11:35:44 +0100 Subject: [PATCH 06/17] Bump changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index e1976f761..76a96cf3a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -6,6 +6,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## v3.16.0dev - [date] - [PR #1374](https://github.com/nf-core/rnaseq/pull/1374) - Bump pipeline version to 3.16.0dev +- [PR #1380](https://github.com/nf-core/rnaseq/pull/1380) - Fix issues with R modules changing sample names ### Credits From 7534d14a3af3d5a7404a2b30dd610fcb7f466950 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 13 Sep 2024 13:45:02 +0200 Subject: [PATCH 07/17] update all modules --- modules.json | 100 +++++++++--------- modules/nf-core/bbmap/bbsplit/environment.yml | 2 - .../bedtools/genomecov/environment.yml | 2 - modules/nf-core/cat/fastq/environment.yml | 2 - .../custom/catadditionalfasta/environment.yml | 2 - .../catadditionalfasta/templates/fasta2gtf.py | 16 ++- .../custom/getchromsizes/environment.yml | 2 - .../nf-core/custom/tx2gene/environment.yml | 2 - .../custom/tx2gene/templates/tx2gene.py | 7 +- modules/nf-core/dupradar/environment.yml | 2 - modules/nf-core/fastp/environment.yml | 2 - modules/nf-core/fastqc/environment.yml | 2 - modules/nf-core/fq/subsample/environment.yml | 2 - modules/nf-core/gffread/environment.yml | 2 - modules/nf-core/gunzip/environment.yml | 2 - modules/nf-core/hisat2/align/environment.yml | 2 - modules/nf-core/hisat2/align/main.nf | 9 +- modules/nf-core/hisat2/build/environment.yml | 2 - modules/nf-core/hisat2/build/main.nf | 7 +- .../hisat2/build/tests/main.nf.test.snap | 29 +---- .../hisat2/extractsplicesites/environment.yml | 2 - .../nf-core/hisat2/extractsplicesites/main.nf | 7 +- .../nf-core/kallisto/index/environment.yml | 2 - .../nf-core/kallisto/quant/environment.yml | 2 - modules/nf-core/multiqc/environment.yml | 2 - .../picard/markduplicates/environment.yml | 2 - .../markduplicates/picard-markduplicates.diff | 11 +- .../nf-core/preseq/lcextrap/environment.yml | 2 - .../nf-core/qualimap/rnaseq/environment.yml | 2 - .../rsem/calculateexpression/environment.yml | 2 - .../rsem/preparereference/environment.yml | 2 - modules/nf-core/rseqc/bamstat/environment.yml | 2 - .../rseqc/inferexperiment/environment.yml | 2 - .../rseqc/innerdistance/environment.yml | 2 - .../rseqc/junctionannotation/environment.yml | 2 - .../rseqc/junctionsaturation/environment.yml | 2 - .../rseqc/readdistribution/environment.yml | 2 - .../rseqc/readduplication/environment.yml | 2 - modules/nf-core/rseqc/tin/environment.yml | 2 - modules/nf-core/salmon/index/environment.yml | 2 - modules/nf-core/salmon/quant/environment.yml | 2 - .../nf-core/samtools/flagstat/environment.yml | 2 - .../nf-core/samtools/idxstats/environment.yml | 2 - .../nf-core/samtools/index/environment.yml | 2 - modules/nf-core/samtools/sort/environment.yml | 2 - .../nf-core/samtools/stats/environment.yml | 2 - modules/nf-core/sortmerna/environment.yml | 2 - modules/nf-core/star/align/environment.yml | 2 - .../star/genomegenerate/environment.yml | 2 - .../stringtie/stringtie/environment.yml | 2 - .../subread/featurecounts/environment.yml | 2 - modules/nf-core/trimgalore/environment.yml | 3 - modules/nf-core/ucsc/bedclip/environment.yml | 2 - .../ucsc/bedgraphtobigwig/environment.yml | 2 - .../nf-core/umitools/dedup/environment.yml | 2 - .../nf-core/umitools/extract/environment.yml | 2 - .../umitools/prepareforrsem/environment.yml | 2 - modules/nf-core/untar/environment.yml | 2 - 58 files changed, 84 insertions(+), 203 deletions(-) diff --git a/modules.json b/modules.json index fc53bd567..01eed863b 100644 --- a/modules.json +++ b/modules.json @@ -7,183 +7,183 @@ "nf-core": { "bbmap/bbsplit": { "branch": "master", - "git_sha": "1ceaa8ba4d0fd886dbca0e545815d905b7407de7", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["fastq_qc_trim_filter_setstrandedness", "modules"] }, "bedtools/genomecov": { "branch": "master", - "git_sha": "9ba6b02bbcb322ff4265cc51fca0ee5d8420b929", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["modules"] }, "cat/fastq": { "branch": "master", - "git_sha": "1ceaa8ba4d0fd886dbca0e545815d905b7407de7", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["fastq_qc_trim_filter_setstrandedness", "modules"] }, "custom/catadditionalfasta": { "branch": "master", - "git_sha": "1ceaa8ba4d0fd886dbca0e545815d905b7407de7", + "git_sha": "e743b2dea725bcfc4b76a209981808987332013a", "installed_by": ["modules"] }, "custom/getchromsizes": { "branch": "master", - "git_sha": "1ceaa8ba4d0fd886dbca0e545815d905b7407de7", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["modules"] }, "custom/tx2gene": { "branch": "master", - "git_sha": "4e5f4687318f24ba944a13609d3ea6ebd890737d", + "git_sha": "e743b2dea725bcfc4b76a209981808987332013a", "installed_by": ["modules", "quantify_pseudo_alignment"] }, "dupradar": { "branch": "master", - "git_sha": "055416736dcb4955960ecc17dea61eb41b68c024", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["modules"] }, "fastp": { "branch": "master", - "git_sha": "1ceaa8ba4d0fd886dbca0e545815d905b7407de7", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["fastq_fastqc_umitools_fastp", "modules"] }, "fastqc": { "branch": "master", - "git_sha": "b49b8992e5271ce427f3a7cdb29628fc58400eb5", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["fastq_fastqc_umitools_fastp", "fastq_fastqc_umitools_trimgalore"] }, "fq/subsample": { "branch": "master", - "git_sha": "2c6b1144ed58b6184ad58fc4e6b6a90219b4bf4f", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["fastq_subsample_fq_salmon", "modules"] }, "gffread": { "branch": "master", - "git_sha": "6c996d7fbe0816dcbb68ce587ad5f873313682a1", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["modules"] }, "gunzip": { "branch": "master", - "git_sha": "4e5f4687318f24ba944a13609d3ea6ebd890737d", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["modules"] }, "hisat2/align": { "branch": "master", - "git_sha": "2c6b1144ed58b6184ad58fc4e6b6a90219b4bf4f", + "git_sha": "ad30f90cfc383dfaa505771d24f9e292c53157ab", "installed_by": ["fastq_align_hisat2"] }, "hisat2/build": { "branch": "master", - "git_sha": "2c6b1144ed58b6184ad58fc4e6b6a90219b4bf4f", + "git_sha": "ad30f90cfc383dfaa505771d24f9e292c53157ab", "installed_by": ["modules"] }, "hisat2/extractsplicesites": { "branch": "master", - "git_sha": "2c6b1144ed58b6184ad58fc4e6b6a90219b4bf4f", + "git_sha": "ad30f90cfc383dfaa505771d24f9e292c53157ab", "installed_by": ["modules"] }, "kallisto/index": { "branch": "master", - "git_sha": "fbe341e9af0bb98533757f536b26d38507d31724", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["modules"] }, "kallisto/quant": { "branch": "master", - "git_sha": "fbe341e9af0bb98533757f536b26d38507d31724", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["modules", "quantify_pseudo_alignment"] }, "multiqc": { "branch": "master", - "git_sha": "19ca321db5d8bd48923262c2eca6422359633491", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["modules"] }, "picard/markduplicates": { "branch": "master", - "git_sha": "46eca555142d6e597729fcb682adcc791796f514", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["bam_markduplicates_picard"], "patch": "modules/nf-core/picard/markduplicates/picard-markduplicates.diff" }, "preseq/lcextrap": { "branch": "master", - "git_sha": "2c6b1144ed58b6184ad58fc4e6b6a90219b4bf4f", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["modules"] }, "qualimap/rnaseq": { "branch": "master", - "git_sha": "46eca555142d6e597729fcb682adcc791796f514", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["modules"] }, "rsem/calculateexpression": { "branch": "master", - "git_sha": "b4919e9a2b4d8b71061e601633db4600a3858fa1", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["modules"] }, "rsem/preparereference": { "branch": "master", - "git_sha": "b4919e9a2b4d8b71061e601633db4600a3858fa1", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["modules"] }, "rseqc/bamstat": { "branch": "master", - "git_sha": "b4919e9a2b4d8b71061e601633db4600a3858fa1", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["bam_rseqc"] }, "rseqc/inferexperiment": { "branch": "master", - "git_sha": "b4919e9a2b4d8b71061e601633db4600a3858fa1", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["bam_rseqc"] }, "rseqc/innerdistance": { "branch": "master", - "git_sha": "b4919e9a2b4d8b71061e601633db4600a3858fa1", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["bam_rseqc"] }, "rseqc/junctionannotation": { "branch": "master", - "git_sha": "b4919e9a2b4d8b71061e601633db4600a3858fa1", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["bam_rseqc"] }, "rseqc/junctionsaturation": { "branch": "master", - "git_sha": "b4919e9a2b4d8b71061e601633db4600a3858fa1", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["bam_rseqc"] }, "rseqc/readdistribution": { "branch": "master", - "git_sha": "b4919e9a2b4d8b71061e601633db4600a3858fa1", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["bam_rseqc"] }, "rseqc/readduplication": { "branch": "master", - "git_sha": "b4919e9a2b4d8b71061e601633db4600a3858fa1", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["bam_rseqc"] }, "rseqc/tin": { "branch": "master", - "git_sha": "b4919e9a2b4d8b71061e601633db4600a3858fa1", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["bam_rseqc"] }, "salmon/index": { "branch": "master", - "git_sha": "cb6b2b94fc40dea58f0b1e3dd095f3dd24f2ac8a", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["fastq_subsample_fq_salmon"] }, "salmon/quant": { "branch": "master", - "git_sha": "727232afb8294b53dd9d05bfe469b70cce1675bb", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["fastq_subsample_fq_salmon", "modules", "quantify_pseudo_alignment"] }, "samtools/flagstat": { "branch": "master", - "git_sha": "46eca555142d6e597729fcb682adcc791796f514", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["bam_stats_samtools"] }, "samtools/idxstats": { "branch": "master", - "git_sha": "46eca555142d6e597729fcb682adcc791796f514", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["bam_stats_samtools"] }, "samtools/index": { "branch": "master", - "git_sha": "46eca555142d6e597729fcb682adcc791796f514", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": [ "bam_dedup_stats_samtools_umitools", "bam_markduplicates_picard", @@ -192,37 +192,37 @@ }, "samtools/sort": { "branch": "master", - "git_sha": "46eca555142d6e597729fcb682adcc791796f514", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["bam_sort_stats_samtools"] }, "samtools/stats": { "branch": "master", - "git_sha": "1fe379cf6e6c1e6fa5e32bcbeefea0f1e874dac6", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["bam_stats_samtools"] }, "sortmerna": { "branch": "master", - "git_sha": "df05c8db5195867c0bc7b92c1788115b66f0d17d", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["fastq_qc_trim_filter_setstrandedness", "modules"] }, "star/align": { "branch": "master", - "git_sha": "46eca555142d6e597729fcb682adcc791796f514", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["modules"] }, "star/genomegenerate": { "branch": "master", - "git_sha": "46eca555142d6e597729fcb682adcc791796f514", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["modules"] }, "stringtie/stringtie": { "branch": "master", - "git_sha": "c789476080a150f87066ca3ed42a622339a26c0b", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["modules"] }, "subread/featurecounts": { "branch": "master", - "git_sha": "b4919e9a2b4d8b71061e601633db4600a3858fa1", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["modules"] }, "summarizedexperiment/summarizedexperiment": { @@ -232,7 +232,7 @@ }, "trimgalore": { "branch": "master", - "git_sha": "b4919e9a2b4d8b71061e601633db4600a3858fa1", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["fastq_fastqc_umitools_trimgalore"] }, "tximeta/tximport": { @@ -242,32 +242,32 @@ }, "ucsc/bedclip": { "branch": "master", - "git_sha": "b4919e9a2b4d8b71061e601633db4600a3858fa1", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["bedgraph_bedclip_bedgraphtobigwig"] }, "ucsc/bedgraphtobigwig": { "branch": "master", - "git_sha": "46eca555142d6e597729fcb682adcc791796f514", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["bedgraph_bedclip_bedgraphtobigwig"] }, "umitools/dedup": { "branch": "master", - "git_sha": "0eacd714effe5aac1c1de26593873960b3346cab", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["bam_dedup_stats_samtools_umitools"] }, "umitools/extract": { "branch": "master", - "git_sha": "b4919e9a2b4d8b71061e601633db4600a3858fa1", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["fastq_fastqc_umitools_fastp", "fastq_fastqc_umitools_trimgalore"] }, "umitools/prepareforrsem": { "branch": "master", - "git_sha": "fac6cc9b2bc4042225bd9247ec03b413f764b47f", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["modules"] }, "untar": { "branch": "master", - "git_sha": "4e5f4687318f24ba944a13609d3ea6ebd890737d", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["modules"] } } diff --git a/modules/nf-core/bbmap/bbsplit/environment.yml b/modules/nf-core/bbmap/bbsplit/environment.yml index 4c6db6276..dfd8936e1 100644 --- a/modules/nf-core/bbmap/bbsplit/environment.yml +++ b/modules/nf-core/bbmap/bbsplit/environment.yml @@ -1,7 +1,5 @@ -name: bbmap_bbsplit channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bbmap=39.01 diff --git a/modules/nf-core/bedtools/genomecov/environment.yml b/modules/nf-core/bedtools/genomecov/environment.yml index 8fbe20c31..5683bc05f 100644 --- a/modules/nf-core/bedtools/genomecov/environment.yml +++ b/modules/nf-core/bedtools/genomecov/environment.yml @@ -1,7 +1,5 @@ -name: bedtools_genomecov channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bedtools=2.31.1 diff --git a/modules/nf-core/cat/fastq/environment.yml b/modules/nf-core/cat/fastq/environment.yml index 8c69b121f..c7eb9bd1c 100644 --- a/modules/nf-core/cat/fastq/environment.yml +++ b/modules/nf-core/cat/fastq/environment.yml @@ -1,7 +1,5 @@ -name: cat_fastq channels: - conda-forge - bioconda - - defaults dependencies: - conda-forge::coreutils=8.30 diff --git a/modules/nf-core/custom/catadditionalfasta/environment.yml b/modules/nf-core/custom/catadditionalfasta/environment.yml index e587338b5..1d80d11a9 100644 --- a/modules/nf-core/custom/catadditionalfasta/environment.yml +++ b/modules/nf-core/custom/catadditionalfasta/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "custom_catadditionalfasta" channels: - conda-forge - bioconda - - defaults dependencies: - conda-forge::python=3.9.5 diff --git a/modules/nf-core/custom/catadditionalfasta/templates/fasta2gtf.py b/modules/nf-core/custom/catadditionalfasta/templates/fasta2gtf.py index 194a04160..06b4c253a 100755 --- a/modules/nf-core/custom/catadditionalfasta/templates/fasta2gtf.py +++ b/modules/nf-core/custom/catadditionalfasta/templates/fasta2gtf.py @@ -2,11 +2,11 @@ # Written by Pranathi Vemuri, later modified by Jonathan Manning and released under the MIT license. -import os import logging +import os import platform -from typing import Iterator, Tuple from itertools import groupby +from typing import Iterator, Tuple def setup_logging() -> logging.Logger: @@ -114,8 +114,16 @@ def main() -> None: fasta_to_gtf("$add_fasta", f"{add_name}.gtf", "$biotype") # Concatenate new fasta to existing fasta, and the GTF we just generated to the GTF - genome_name = "$params.genome" if "$params.genome" != "null" else os.path.splitext(os.path.basename("$fasta"))[0] - output_prefix = "$task.ext.prefix" if "$task.ext.prefix" != "null" else f"{genome_name}_{add_name}" + genome_name = ( + "$params.genome" + if "$params.genome" != "null" + else os.path.splitext(os.path.basename("$fasta"))[0] + ) + output_prefix = ( + "$task.ext.prefix" + if "$task.ext.prefix" != "null" + else f"{genome_name}_{add_name}" + ) os.mkdir("out") os.system(f"cat $fasta $add_fasta > out/{output_prefix}.fasta") diff --git a/modules/nf-core/custom/getchromsizes/environment.yml b/modules/nf-core/custom/getchromsizes/environment.yml index 2ecd0128f..da2df5e43 100644 --- a/modules/nf-core/custom/getchromsizes/environment.yml +++ b/modules/nf-core/custom/getchromsizes/environment.yml @@ -1,8 +1,6 @@ -name: custom_getchromsizes channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::samtools=1.20 - bioconda::htslib=1.20 diff --git a/modules/nf-core/custom/tx2gene/environment.yml b/modules/nf-core/custom/tx2gene/environment.yml index a859dc881..9f5f9fb9b 100644 --- a/modules/nf-core/custom/tx2gene/environment.yml +++ b/modules/nf-core/custom/tx2gene/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "custom_tx2gene" channels: - conda-forge - bioconda - - defaults dependencies: - python=3.9.5 diff --git a/modules/nf-core/custom/tx2gene/templates/tx2gene.py b/modules/nf-core/custom/tx2gene/templates/tx2gene.py index 8c2e3b1f4..4d769513d 100755 --- a/modules/nf-core/custom/tx2gene/templates/tx2gene.py +++ b/modules/nf-core/custom/tx2gene/templates/tx2gene.py @@ -2,13 +2,12 @@ # Written by Lorena Pantano with subsequent reworking by Jonathan Manning. Released under the MIT license. -import logging -import argparse import glob +import logging import os import platform import re -from collections import Counter, defaultdict, OrderedDict +from collections import Counter, OrderedDict from collections.abc import Set from typing import Dict @@ -52,7 +51,7 @@ def read_top_transcripts(quant_dir: str, file_pattern: str) -> Set[str]: try: # Find the quantification file within the directory quant_file_path = glob.glob(os.path.join(quant_dir, "*", file_pattern))[0] - with open(quant_file_path, "r") as file_handle: + with open(quant_file_path) as file_handle: # Read the file and extract the top 100 transcripts return {line.split()[0] for i, line in enumerate(file_handle) if i > 0 and i <= 100} except IndexError: diff --git a/modules/nf-core/dupradar/environment.yml b/modules/nf-core/dupradar/environment.yml index 58b2bf11d..fb16938d2 100644 --- a/modules/nf-core/dupradar/environment.yml +++ b/modules/nf-core/dupradar/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "dupradar" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::bioconductor-dupradar=1.32.0" diff --git a/modules/nf-core/fastp/environment.yml b/modules/nf-core/fastp/environment.yml index 70389e664..26d4aca5d 100644 --- a/modules/nf-core/fastp/environment.yml +++ b/modules/nf-core/fastp/environment.yml @@ -1,7 +1,5 @@ -name: fastp channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::fastp=0.23.4 diff --git a/modules/nf-core/fastqc/environment.yml b/modules/nf-core/fastqc/environment.yml index 1787b38a9..691d4c763 100644 --- a/modules/nf-core/fastqc/environment.yml +++ b/modules/nf-core/fastqc/environment.yml @@ -1,7 +1,5 @@ -name: fastqc channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::fastqc=0.12.1 diff --git a/modules/nf-core/fq/subsample/environment.yml b/modules/nf-core/fq/subsample/environment.yml index c588de38a..eaba9339b 100644 --- a/modules/nf-core/fq/subsample/environment.yml +++ b/modules/nf-core/fq/subsample/environment.yml @@ -1,7 +1,5 @@ -name: fq_subsample channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::fq=0.9.1 diff --git a/modules/nf-core/gffread/environment.yml b/modules/nf-core/gffread/environment.yml index c6df58ad0..ee2398416 100644 --- a/modules/nf-core/gffread/environment.yml +++ b/modules/nf-core/gffread/environment.yml @@ -1,7 +1,5 @@ -name: gffread channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gffread=0.12.7 diff --git a/modules/nf-core/gunzip/environment.yml b/modules/nf-core/gunzip/environment.yml index dfc02a7b5..c7794856d 100644 --- a/modules/nf-core/gunzip/environment.yml +++ b/modules/nf-core/gunzip/environment.yml @@ -1,8 +1,6 @@ -name: gunzip channels: - conda-forge - bioconda - - defaults dependencies: - conda-forge::grep=3.11 - conda-forge::sed=4.8 diff --git a/modules/nf-core/hisat2/align/environment.yml b/modules/nf-core/hisat2/align/environment.yml index 0c1415f94..26c62a3bf 100644 --- a/modules/nf-core/hisat2/align/environment.yml +++ b/modules/nf-core/hisat2/align/environment.yml @@ -1,8 +1,6 @@ -name: hisat2_align channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::hisat2=2.2.1 - bioconda::samtools=1.16.1 diff --git a/modules/nf-core/hisat2/align/main.nf b/modules/nf-core/hisat2/align/main.nf index ea186f62a..f45f9bccb 100644 --- a/modules/nf-core/hisat2/align/main.nf +++ b/modules/nf-core/hisat2/align/main.nf @@ -2,7 +2,6 @@ process HISAT2_ALIGN { tag "$meta.id" label 'process_high' - // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1:2cdf6bf1e92acbeb9b2834b1c58754167173a410-0' : @@ -25,7 +24,6 @@ process HISAT2_ALIGN { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def VERSION = '2.2.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. def strandedness = '' if (meta.strandedness == 'forward') { @@ -53,7 +51,7 @@ process HISAT2_ALIGN { cat <<-END_VERSIONS > versions.yml "${task.process}": - hisat2: $VERSION + hisat2: \$(hisat2 --version | grep -o 'version [^ ]*' | cut -d ' ' -f 2) samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') END_VERSIONS """ @@ -85,7 +83,7 @@ process HISAT2_ALIGN { cat <<-END_VERSIONS > versions.yml "${task.process}": - hisat2: $VERSION + hisat2: \$(hisat2 --version | grep -o 'version [^ ]*' | cut -d ' ' -f 2) samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') END_VERSIONS """ @@ -94,7 +92,6 @@ process HISAT2_ALIGN { stub: def prefix = task.ext.prefix ?: "${meta.id}" def unaligned = params.save_unaligned ? "echo '' | gzip > ${prefix}.unmapped_1.fastq.gz \n echo '' | gzip > ${prefix}.unmapped_2.fastq.gz" : '' - def VERSION = '2.2.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. """ ${unaligned} @@ -103,7 +100,7 @@ process HISAT2_ALIGN { cat <<-END_VERSIONS > versions.yml "${task.process}": - hisat2: $VERSION + hisat2: \$(hisat2 --version | grep -o 'version [^ ]*' | cut -d ' ' -f 2) samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') END_VERSIONS """ diff --git a/modules/nf-core/hisat2/build/environment.yml b/modules/nf-core/hisat2/build/environment.yml index 2e67cd3ea..afced7338 100644 --- a/modules/nf-core/hisat2/build/environment.yml +++ b/modules/nf-core/hisat2/build/environment.yml @@ -1,7 +1,5 @@ -name: hisat2_build channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::hisat2=2.2.1 diff --git a/modules/nf-core/hisat2/build/main.nf b/modules/nf-core/hisat2/build/main.nf index 17d8fdd5b..37a3e4565 100644 --- a/modules/nf-core/hisat2/build/main.nf +++ b/modules/nf-core/hisat2/build/main.nf @@ -3,7 +3,6 @@ process HISAT2_BUILD { label 'process_high' label 'process_high_memory' - // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hisat2:2.2.1--h1b792b2_3' : @@ -44,7 +43,6 @@ process HISAT2_BUILD { log.info "[HISAT2 index build] Less than ${hisat2_build_memory} GB available, so NOT using splice sites and exons to build HISAT2 index." log.info "[HISAT2 index build] Use --hisat2_build_memory [small number] to skip this check." } - def VERSION = '2.2.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. """ mkdir hisat2 $extract_exons @@ -58,18 +56,17 @@ process HISAT2_BUILD { cat <<-END_VERSIONS > versions.yml "${task.process}": - hisat2: $VERSION + hisat2: \$(hisat2 --version | grep -o 'version [^ ]*' | cut -d ' ' -f 2) END_VERSIONS """ stub: - def VERSION = '2.2.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. """ mkdir hisat2 cat <<-END_VERSIONS > versions.yml "${task.process}": - hisat2: $VERSION + hisat2: \$(hisat2 --version | grep -o 'version [^ ]*' | cut -d ' ' -f 2) END_VERSIONS """ } diff --git a/modules/nf-core/hisat2/build/tests/main.nf.test.snap b/modules/nf-core/hisat2/build/tests/main.nf.test.snap index 0e3b5c57f..68fc7ffba 100644 --- a/modules/nf-core/hisat2/build/tests/main.nf.test.snap +++ b/modules/nf-core/hisat2/build/tests/main.nf.test.snap @@ -1,27 +1,4 @@ { - "test - stub": { - "content": [ - { - "0": [ - - ], - "1": [ - - ], - "index": [ - - ], - "versions": [ - - ] - } - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-06-20T17:29:31.567024" - }, "Should run without failures - stub": { "content": [ { @@ -31,7 +8,7 @@ "id": "genome" }, [ - + ] ] ], @@ -44,7 +21,7 @@ "id": "genome" }, [ - + ] ] ], @@ -110,4 +87,4 @@ }, "timestamp": "2023-10-16T14:42:22.381609786" } -} +} \ No newline at end of file diff --git a/modules/nf-core/hisat2/extractsplicesites/environment.yml b/modules/nf-core/hisat2/extractsplicesites/environment.yml index 4b03e5e46..afced7338 100644 --- a/modules/nf-core/hisat2/extractsplicesites/environment.yml +++ b/modules/nf-core/hisat2/extractsplicesites/environment.yml @@ -1,7 +1,5 @@ -name: hisat2_extractsplicesites channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::hisat2=2.2.1 diff --git a/modules/nf-core/hisat2/extractsplicesites/main.nf b/modules/nf-core/hisat2/extractsplicesites/main.nf index 588a9947a..82d2cfbac 100644 --- a/modules/nf-core/hisat2/extractsplicesites/main.nf +++ b/modules/nf-core/hisat2/extractsplicesites/main.nf @@ -2,7 +2,6 @@ process HISAT2_EXTRACTSPLICESITES { tag "$gtf" label 'process_medium' - // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hisat2:2.2.1--h1b792b2_3' : @@ -20,23 +19,21 @@ process HISAT2_EXTRACTSPLICESITES { script: def args = task.ext.args ?: '' - def VERSION = '2.2.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. """ hisat2_extract_splice_sites.py $gtf > ${gtf.baseName}.splice_sites.txt cat <<-END_VERSIONS > versions.yml "${task.process}": - hisat2: $VERSION + hisat2: \$(hisat2 --version | grep -o 'version [^ ]*' | cut -d ' ' -f 2) END_VERSIONS """ stub: - def VERSION = '2.2.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. """ touch ${gtf.baseName}.splice_sites.txt cat <<-END_VERSIONS > versions.yml "${task.process}": - hisat2: $VERSION + hisat2: \$(hisat2 --version | grep -o 'version [^ ]*' | cut -d ' ' -f 2) END_VERSIONS """ } diff --git a/modules/nf-core/kallisto/index/environment.yml b/modules/nf-core/kallisto/index/environment.yml index 471b006a8..27be64918 100644 --- a/modules/nf-core/kallisto/index/environment.yml +++ b/modules/nf-core/kallisto/index/environment.yml @@ -1,7 +1,5 @@ -name: kallisto_index channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::kallisto=0.48.0 diff --git a/modules/nf-core/kallisto/quant/environment.yml b/modules/nf-core/kallisto/quant/environment.yml index c2d6306bb..27be64918 100644 --- a/modules/nf-core/kallisto/quant/environment.yml +++ b/modules/nf-core/kallisto/quant/environment.yml @@ -1,7 +1,5 @@ -name: kallisto_quant channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::kallisto=0.48.0 diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml index a31464c97..f1cd99b07 100644 --- a/modules/nf-core/multiqc/environment.yml +++ b/modules/nf-core/multiqc/environment.yml @@ -1,7 +1,5 @@ -name: multiqc channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::multiqc=1.24.1 diff --git a/modules/nf-core/picard/markduplicates/environment.yml b/modules/nf-core/picard/markduplicates/environment.yml index 58b795f54..5f919a9a9 100644 --- a/modules/nf-core/picard/markduplicates/environment.yml +++ b/modules/nf-core/picard/markduplicates/environment.yml @@ -1,7 +1,5 @@ -name: picard_markduplicates channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::picard=3.1.1 diff --git a/modules/nf-core/picard/markduplicates/picard-markduplicates.diff b/modules/nf-core/picard/markduplicates/picard-markduplicates.diff index bf684640d..5a2cf0007 100644 --- a/modules/nf-core/picard/markduplicates/picard-markduplicates.diff +++ b/modules/nf-core/picard/markduplicates/picard-markduplicates.diff @@ -1,4 +1,5 @@ Changes in module 'nf-core/picard/markduplicates' +Changes in 'picard/markduplicates/main.nf': --- modules/nf-core/picard/markduplicates/main.nf +++ modules/nf-core/picard/markduplicates/main.nf @@ -4,8 +4,8 @@ @@ -13,13 +14,19 @@ Changes in module 'nf-core/picard/markduplicates' input: tuple val(meta), path(reads) +'modules/nf-core/picard/markduplicates/meta.yml' is unchanged +Changes in 'picard/markduplicates/environment.yml': --- modules/nf-core/picard/markduplicates/environment.yml +++ modules/nf-core/picard/markduplicates/environment.yml -@@ -4,4 +4,4 @@ +@@ -2,4 +2,4 @@ + - conda-forge - bioconda - - defaults dependencies: - - bioconda::picard=3.2.0 + - bioconda::picard=3.1.1 +'modules/nf-core/picard/markduplicates/tests/main.nf.test.snap' is unchanged +'modules/nf-core/picard/markduplicates/tests/nextflow.config' is unchanged +'modules/nf-core/picard/markduplicates/tests/main.nf.test' is unchanged +'modules/nf-core/picard/markduplicates/tests/tags.yml' was removed ************************************************************ diff --git a/modules/nf-core/preseq/lcextrap/environment.yml b/modules/nf-core/preseq/lcextrap/environment.yml index 57b8b9c67..926d7aece 100644 --- a/modules/nf-core/preseq/lcextrap/environment.yml +++ b/modules/nf-core/preseq/lcextrap/environment.yml @@ -1,7 +1,5 @@ -name: preseq_lcextrap channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::preseq=3.1.2 diff --git a/modules/nf-core/qualimap/rnaseq/environment.yml b/modules/nf-core/qualimap/rnaseq/environment.yml index 590ae85f7..4fa5f4e8e 100644 --- a/modules/nf-core/qualimap/rnaseq/environment.yml +++ b/modules/nf-core/qualimap/rnaseq/environment.yml @@ -1,7 +1,5 @@ -name: qualimap_rnaseq channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::qualimap=2.3 diff --git a/modules/nf-core/rsem/calculateexpression/environment.yml b/modules/nf-core/rsem/calculateexpression/environment.yml index b811fa6fe..bcf70fa9a 100644 --- a/modules/nf-core/rsem/calculateexpression/environment.yml +++ b/modules/nf-core/rsem/calculateexpression/environment.yml @@ -1,8 +1,6 @@ -name: rsem_calculateexpression channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::rsem=1.3.3 - bioconda::star=2.7.10a diff --git a/modules/nf-core/rsem/preparereference/environment.yml b/modules/nf-core/rsem/preparereference/environment.yml index c80e69106..bcf70fa9a 100644 --- a/modules/nf-core/rsem/preparereference/environment.yml +++ b/modules/nf-core/rsem/preparereference/environment.yml @@ -1,8 +1,6 @@ -name: rsem_preparereference channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::rsem=1.3.3 - bioconda::star=2.7.10a diff --git a/modules/nf-core/rseqc/bamstat/environment.yml b/modules/nf-core/rseqc/bamstat/environment.yml index e960c9943..304e38fcf 100644 --- a/modules/nf-core/rseqc/bamstat/environment.yml +++ b/modules/nf-core/rseqc/bamstat/environment.yml @@ -1,8 +1,6 @@ -name: rseqc_bamstat channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::rseqc=5.0.3 - conda-forge::r-base>=3.5 diff --git a/modules/nf-core/rseqc/inferexperiment/environment.yml b/modules/nf-core/rseqc/inferexperiment/environment.yml index 78215985a..304e38fcf 100644 --- a/modules/nf-core/rseqc/inferexperiment/environment.yml +++ b/modules/nf-core/rseqc/inferexperiment/environment.yml @@ -1,8 +1,6 @@ -name: rseqc_inferexperiment channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::rseqc=5.0.3 - conda-forge::r-base>=3.5 diff --git a/modules/nf-core/rseqc/innerdistance/environment.yml b/modules/nf-core/rseqc/innerdistance/environment.yml index fb6e9e925..304e38fcf 100644 --- a/modules/nf-core/rseqc/innerdistance/environment.yml +++ b/modules/nf-core/rseqc/innerdistance/environment.yml @@ -1,8 +1,6 @@ -name: rseqc_innerdistance channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::rseqc=5.0.3 - conda-forge::r-base>=3.5 diff --git a/modules/nf-core/rseqc/junctionannotation/environment.yml b/modules/nf-core/rseqc/junctionannotation/environment.yml index 35276b715..304e38fcf 100644 --- a/modules/nf-core/rseqc/junctionannotation/environment.yml +++ b/modules/nf-core/rseqc/junctionannotation/environment.yml @@ -1,8 +1,6 @@ -name: rseqc_junctionannotation channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::rseqc=5.0.3 - conda-forge::r-base>=3.5 diff --git a/modules/nf-core/rseqc/junctionsaturation/environment.yml b/modules/nf-core/rseqc/junctionsaturation/environment.yml index 7b9cc4fa7..304e38fcf 100644 --- a/modules/nf-core/rseqc/junctionsaturation/environment.yml +++ b/modules/nf-core/rseqc/junctionsaturation/environment.yml @@ -1,8 +1,6 @@ -name: rseqc_junctionsaturation channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::rseqc=5.0.3 - conda-forge::r-base>=3.5 diff --git a/modules/nf-core/rseqc/readdistribution/environment.yml b/modules/nf-core/rseqc/readdistribution/environment.yml index 59be9fa88..304e38fcf 100644 --- a/modules/nf-core/rseqc/readdistribution/environment.yml +++ b/modules/nf-core/rseqc/readdistribution/environment.yml @@ -1,8 +1,6 @@ -name: rseqc_readdistribution channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::rseqc=5.0.3 - conda-forge::r-base>=3.5 diff --git a/modules/nf-core/rseqc/readduplication/environment.yml b/modules/nf-core/rseqc/readduplication/environment.yml index c99f107a1..304e38fcf 100644 --- a/modules/nf-core/rseqc/readduplication/environment.yml +++ b/modules/nf-core/rseqc/readduplication/environment.yml @@ -1,8 +1,6 @@ -name: rseqc_readduplication channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::rseqc=5.0.3 - conda-forge::r-base>=3.5 diff --git a/modules/nf-core/rseqc/tin/environment.yml b/modules/nf-core/rseqc/tin/environment.yml index 288da4300..304e38fcf 100644 --- a/modules/nf-core/rseqc/tin/environment.yml +++ b/modules/nf-core/rseqc/tin/environment.yml @@ -1,8 +1,6 @@ -name: rseqc_tin channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::rseqc=5.0.3 - conda-forge::r-base>=3.5 diff --git a/modules/nf-core/salmon/index/environment.yml b/modules/nf-core/salmon/index/environment.yml index a6607d964..471164faa 100644 --- a/modules/nf-core/salmon/index/environment.yml +++ b/modules/nf-core/salmon/index/environment.yml @@ -1,7 +1,5 @@ -name: salmon_index channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::salmon=1.10.1 diff --git a/modules/nf-core/salmon/quant/environment.yml b/modules/nf-core/salmon/quant/environment.yml index 862667241..471164faa 100644 --- a/modules/nf-core/salmon/quant/environment.yml +++ b/modules/nf-core/salmon/quant/environment.yml @@ -1,7 +1,5 @@ -name: salmon_quant channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::salmon=1.10.1 diff --git a/modules/nf-core/samtools/flagstat/environment.yml b/modules/nf-core/samtools/flagstat/environment.yml index 68b81558e..da2df5e43 100644 --- a/modules/nf-core/samtools/flagstat/environment.yml +++ b/modules/nf-core/samtools/flagstat/environment.yml @@ -1,8 +1,6 @@ -name: samtools_flagstat channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::samtools=1.20 - bioconda::htslib=1.20 diff --git a/modules/nf-core/samtools/idxstats/environment.yml b/modules/nf-core/samtools/idxstats/environment.yml index eb6c88099..da2df5e43 100644 --- a/modules/nf-core/samtools/idxstats/environment.yml +++ b/modules/nf-core/samtools/idxstats/environment.yml @@ -1,8 +1,6 @@ -name: samtools_idxstats channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::samtools=1.20 - bioconda::htslib=1.20 diff --git a/modules/nf-core/samtools/index/environment.yml b/modules/nf-core/samtools/index/environment.yml index 260d516be..da2df5e43 100644 --- a/modules/nf-core/samtools/index/environment.yml +++ b/modules/nf-core/samtools/index/environment.yml @@ -1,8 +1,6 @@ -name: samtools_index channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::samtools=1.20 - bioconda::htslib=1.20 diff --git a/modules/nf-core/samtools/sort/environment.yml b/modules/nf-core/samtools/sort/environment.yml index 36a12eab0..da2df5e43 100644 --- a/modules/nf-core/samtools/sort/environment.yml +++ b/modules/nf-core/samtools/sort/environment.yml @@ -1,8 +1,6 @@ -name: samtools_sort channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::samtools=1.20 - bioconda::htslib=1.20 diff --git a/modules/nf-core/samtools/stats/environment.yml b/modules/nf-core/samtools/stats/environment.yml index 1cc83bd95..da2df5e43 100644 --- a/modules/nf-core/samtools/stats/environment.yml +++ b/modules/nf-core/samtools/stats/environment.yml @@ -1,8 +1,6 @@ -name: samtools_stats channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::samtools=1.20 - bioconda::htslib=1.20 diff --git a/modules/nf-core/sortmerna/environment.yml b/modules/nf-core/sortmerna/environment.yml index f40f9958d..fab44081f 100644 --- a/modules/nf-core/sortmerna/environment.yml +++ b/modules/nf-core/sortmerna/environment.yml @@ -1,7 +1,5 @@ -name: sortmerna channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::sortmerna=4.3.6 diff --git a/modules/nf-core/star/align/environment.yml b/modules/nf-core/star/align/environment.yml index 8bd58cff5..e3d1c714d 100644 --- a/modules/nf-core/star/align/environment.yml +++ b/modules/nf-core/star/align/environment.yml @@ -1,8 +1,6 @@ -name: star_align channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::star=2.7.10a - bioconda::samtools=1.18 diff --git a/modules/nf-core/star/genomegenerate/environment.yml b/modules/nf-core/star/genomegenerate/environment.yml index 791f255e5..38611dfa2 100644 --- a/modules/nf-core/star/genomegenerate/environment.yml +++ b/modules/nf-core/star/genomegenerate/environment.yml @@ -1,8 +1,6 @@ -name: star_genomegenerate channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::samtools=1.18 - bioconda::htslib=1.18 diff --git a/modules/nf-core/stringtie/stringtie/environment.yml b/modules/nf-core/stringtie/stringtie/environment.yml index 7a0eccdb8..0556de41a 100644 --- a/modules/nf-core/stringtie/stringtie/environment.yml +++ b/modules/nf-core/stringtie/stringtie/environment.yml @@ -1,7 +1,5 @@ -name: stringtie_stringtie channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::stringtie=2.2.1 diff --git a/modules/nf-core/subread/featurecounts/environment.yml b/modules/nf-core/subread/featurecounts/environment.yml index ca19439d7..7e919aa31 100644 --- a/modules/nf-core/subread/featurecounts/environment.yml +++ b/modules/nf-core/subread/featurecounts/environment.yml @@ -1,7 +1,5 @@ -name: subread_featurecounts channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::subread=2.0.1 diff --git a/modules/nf-core/trimgalore/environment.yml b/modules/nf-core/trimgalore/environment.yml index 0981320c1..f172c1b39 100644 --- a/modules/nf-core/trimgalore/environment.yml +++ b/modules/nf-core/trimgalore/environment.yml @@ -1,9 +1,6 @@ -name: trimgalore - channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::cutadapt=3.4 diff --git a/modules/nf-core/ucsc/bedclip/environment.yml b/modules/nf-core/ucsc/bedclip/environment.yml index 571dc2749..94e825f03 100644 --- a/modules/nf-core/ucsc/bedclip/environment.yml +++ b/modules/nf-core/ucsc/bedclip/environment.yml @@ -1,7 +1,5 @@ -name: ucsc_bedclip channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::ucsc-bedclip=377 diff --git a/modules/nf-core/ucsc/bedgraphtobigwig/environment.yml b/modules/nf-core/ucsc/bedgraphtobigwig/environment.yml index f91e216f5..a54fb8f16 100644 --- a/modules/nf-core/ucsc/bedgraphtobigwig/environment.yml +++ b/modules/nf-core/ucsc/bedgraphtobigwig/environment.yml @@ -1,7 +1,5 @@ -name: ucsc_bedgraphtobigwig channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::ucsc-bedgraphtobigwig=445 diff --git a/modules/nf-core/umitools/dedup/environment.yml b/modules/nf-core/umitools/dedup/environment.yml index bc497824f..9f9e03c49 100644 --- a/modules/nf-core/umitools/dedup/environment.yml +++ b/modules/nf-core/umitools/dedup/environment.yml @@ -1,7 +1,5 @@ -name: umitools_dedup channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::umi_tools=1.1.5 diff --git a/modules/nf-core/umitools/extract/environment.yml b/modules/nf-core/umitools/extract/environment.yml index aab452d1e..9f9e03c49 100644 --- a/modules/nf-core/umitools/extract/environment.yml +++ b/modules/nf-core/umitools/extract/environment.yml @@ -1,7 +1,5 @@ -name: umitools_extract channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::umi_tools=1.1.5 diff --git a/modules/nf-core/umitools/prepareforrsem/environment.yml b/modules/nf-core/umitools/prepareforrsem/environment.yml index dbb1bde77..9f9e03c49 100644 --- a/modules/nf-core/umitools/prepareforrsem/environment.yml +++ b/modules/nf-core/umitools/prepareforrsem/environment.yml @@ -1,7 +1,5 @@ -name: umitools_prepareforrsem channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::umi_tools=1.1.5 diff --git a/modules/nf-core/untar/environment.yml b/modules/nf-core/untar/environment.yml index 4f498244a..c7794856d 100644 --- a/modules/nf-core/untar/environment.yml +++ b/modules/nf-core/untar/environment.yml @@ -1,8 +1,6 @@ -name: untar channels: - conda-forge - bioconda - - defaults dependencies: - conda-forge::grep=3.11 - conda-forge::sed=4.8 From d1ca557f92b5696594843875f9b8f9675caf14aa Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 13 Sep 2024 13:46:19 +0200 Subject: [PATCH 08/17] update CHANGELOG --- CHANGELOG.md | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 76a96cf3a..f35bf876c 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,15 +5,16 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## v3.16.0dev - [date] -- [PR #1374](https://github.com/nf-core/rnaseq/pull/1374) - Bump pipeline version to 3.16.0dev -- [PR #1380](https://github.com/nf-core/rnaseq/pull/1380) - Fix issues with R modules changing sample names - ### Credits Special thanks to the following for their contributions to the release: ### Enhancements & fixes +- [PR #1374](https://github.com/nf-core/rnaseq/pull/1374) - Bump pipeline version to 3.16.0dev +- [PR #1380](https://github.com/nf-core/rnaseq/pull/1380) - Fix issues with R modules changing sample names +- [PR #1381](https://github.com/nf-core/rnaseq/pull/1381) - Update all modules following massive conda usage update in nf-core modules + ## [[3.15.0](https://github.com/nf-core/rnaseq/releases/tag/3.15.0)] - 2024-09-04 ### Credits From 48077f8bdf02edfe5bf160c28e1ee91fcb774dc4 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 13 Sep 2024 13:53:21 +0200 Subject: [PATCH 09/17] better patch of picard md --- .../markduplicates/picard-markduplicates.diff | 163 +++++++++++++++++- 1 file changed, 161 insertions(+), 2 deletions(-) diff --git a/modules/nf-core/picard/markduplicates/picard-markduplicates.diff b/modules/nf-core/picard/markduplicates/picard-markduplicates.diff index 5a2cf0007..0daa9399e 100644 --- a/modules/nf-core/picard/markduplicates/picard-markduplicates.diff +++ b/modules/nf-core/picard/markduplicates/picard-markduplicates.diff @@ -25,8 +25,167 @@ Changes in 'picard/markduplicates/environment.yml': - - bioconda::picard=3.2.0 + - bioconda::picard=3.1.1 -'modules/nf-core/picard/markduplicates/tests/main.nf.test.snap' is unchanged +Changes in 'picard/markduplicates/tests/main.nf.test.snap': +--- modules/nf-core/picard/markduplicates/tests/main.nf.test.snap ++++ modules/nf-core/picard/markduplicates/tests/main.nf.test.snap +@@ -27,7 +27,7 @@ + ] + ], + "4": [ +- "versions.yml:md5,33dd4b32140e801e0d2e50aeefd0788d" ++ "versions.yml:md5,b699af51b1956f3810f8a7c066e0ab17" + ], + "bai": [ + +@@ -54,7 +54,7 @@ + ] + ], + "versions": [ +- "versions.yml:md5,33dd4b32140e801e0d2e50aeefd0788d" ++ "versions.yml:md5,b699af51b1956f3810f8a7c066e0ab17" + ] + } + ], +@@ -62,7 +62,7 @@ + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, +- "timestamp": "2024-07-22T11:56:32.025869" ++ "timestamp": "2024-07-22T19:34:20.663558" + }, + "sarscov2 [unsorted bam] - stub": { + "content": [ +@@ -92,7 +92,7 @@ + ] + ], + "4": [ +- "versions.yml:md5,33dd4b32140e801e0d2e50aeefd0788d" ++ "versions.yml:md5,b699af51b1956f3810f8a7c066e0ab17" + ], + "bai": [ + +@@ -119,7 +119,7 @@ + ] + ], + "versions": [ +- "versions.yml:md5,33dd4b32140e801e0d2e50aeefd0788d" ++ "versions.yml:md5,b699af51b1956f3810f8a7c066e0ab17" + ] + } + ], +@@ -127,61 +127,61 @@ + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, +- "timestamp": "2024-07-22T11:56:20.497105" ++ "timestamp": "2024-07-22T19:34:01.021052" + }, + "sarscov2 [unsorted bam]": { + "content": [ + "test.marked.bam", + [ + "## htsjdk.samtools.metrics.StringHeader", +- "# MarkDuplicates --INPUT test.paired_end.bam --OUTPUT test.marked.bam --METRICS_FILE test.marked.MarkDuplicates.metrics.txt --ASSUME_SORT_ORDER queryname --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_UNCERTAINTY 0 --UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false", ++ "# MarkDuplicates --INPUT test.paired_end.bam --OUTPUT test.marked.bam --METRICS_FILE test.marked.MarkDuplicates.metrics.txt --ASSUME_SORT_ORDER queryname --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_QUALITY_SUM_STRATEGY false --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false", + "## htsjdk.samtools.metrics.StringHeader" + ], + [ +- "versions.yml:md5,33dd4b32140e801e0d2e50aeefd0788d" ++ "versions.yml:md5,b699af51b1956f3810f8a7c066e0ab17" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, +- "timestamp": "2024-07-22T11:50:14.881666" ++ "timestamp": "2024-07-22T19:32:49.777427" + }, + "sarscov2 [sorted bam]": { + "content": [ + "test.marked.bam", + [ + "## htsjdk.samtools.metrics.StringHeader", +- "# MarkDuplicates --INPUT test.paired_end.sorted.bam --OUTPUT test.marked.bam --METRICS_FILE test.marked.MarkDuplicates.metrics.txt --ASSUME_SORT_ORDER queryname --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_UNCERTAINTY 0 --UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false", ++ "# MarkDuplicates --INPUT test.paired_end.sorted.bam --OUTPUT test.marked.bam --METRICS_FILE test.marked.MarkDuplicates.metrics.txt --ASSUME_SORT_ORDER queryname --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_QUALITY_SUM_STRATEGY false --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false", + "## htsjdk.samtools.metrics.StringHeader" + ], + [ +- "versions.yml:md5,33dd4b32140e801e0d2e50aeefd0788d" ++ "versions.yml:md5,b699af51b1956f3810f8a7c066e0ab17" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, +- "timestamp": "2024-07-22T11:52:03.11428" ++ "timestamp": "2024-07-22T19:33:14.462596" + }, + "homo_sapiens [cram]": { + "content": [ + "test.marked.cram", + [ + "## htsjdk.samtools.metrics.StringHeader", +- "# MarkDuplicates --INPUT test.paired_end.sorted.cram --OUTPUT test.marked.cram --METRICS_FILE test.marked.MarkDuplicates.metrics.txt --ASSUME_SORT_ORDER queryname --REFERENCE_SEQUENCE genome.fasta --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_UNCERTAINTY 0 --UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false", ++ "# MarkDuplicates --INPUT test.paired_end.sorted.cram --OUTPUT test.marked.cram --METRICS_FILE test.marked.MarkDuplicates.metrics.txt --ASSUME_SORT_ORDER queryname --REFERENCE_SEQUENCE genome.fasta --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_QUALITY_SUM_STRATEGY false --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false", + "## htsjdk.samtools.metrics.StringHeader" + ], + [ +- "versions.yml:md5,33dd4b32140e801e0d2e50aeefd0788d" ++ "versions.yml:md5,b699af51b1956f3810f8a7c066e0ab17" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, +- "timestamp": "2024-07-22T11:53:05.403139" ++ "timestamp": "2024-07-22T19:33:40.215159" + }, + "homo_sapiens [cram] - stub": { + "content": [ +@@ -211,7 +211,7 @@ + ] + ], + "4": [ +- "versions.yml:md5,33dd4b32140e801e0d2e50aeefd0788d" ++ "versions.yml:md5,b699af51b1956f3810f8a7c066e0ab17" + ], + "bai": [ + +@@ -238,7 +238,7 @@ + ] + ], + "versions": [ +- "versions.yml:md5,33dd4b32140e801e0d2e50aeefd0788d" ++ "versions.yml:md5,b699af51b1956f3810f8a7c066e0ab17" + ] + } + ], +@@ -246,6 +246,6 @@ + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, +- "timestamp": "2024-07-22T11:56:43.438188" ++ "timestamp": "2024-07-22T19:34:51.753515" + } + } 'modules/nf-core/picard/markduplicates/tests/nextflow.config' is unchanged -'modules/nf-core/picard/markduplicates/tests/main.nf.test' is unchanged +Changes in 'picard/markduplicates/tests/main.nf.test': +--- modules/nf-core/picard/markduplicates/tests/main.nf.test ++++ modules/nf-core/picard/markduplicates/tests/main.nf.test +@@ -4,10 +4,6 @@ + script "../main.nf" + process "PICARD_MARKDUPLICATES" + config "./nextflow.config" +- tag "modules" +- tag "modules_nfcore" +- tag "picard" +- tag "picard/markduplicates" + + test("sarscov2 [unsorted bam]") { + + 'modules/nf-core/picard/markduplicates/tests/tags.yml' was removed ************************************************************ From f6425c5c2634b9fe04684572c38a8c8be24c24c8 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 13 Sep 2024 13:58:06 +0200 Subject: [PATCH 10/17] include conda changes to local modules too --- modules/local/deseq2_qc/environment.yml | 2 -- modules/local/gtf2bed/environment.yml | 2 -- modules/local/gtf_filter/environment.yml | 2 -- modules/local/multiqc_custom_biotype/environment.yml | 2 -- .../local/preprocess_transcripts_fasta_gencode/environment.yml | 2 -- modules/local/rsem_merge_counts/environment.yml | 2 -- modules/local/star_align_igenomes/environment.yml | 2 -- modules/local/star_genomegenerate_igenomes/environment.yml | 2 -- 8 files changed, 16 deletions(-) diff --git a/modules/local/deseq2_qc/environment.yml b/modules/local/deseq2_qc/environment.yml index 9daad310d..1f424690c 100644 --- a/modules/local/deseq2_qc/environment.yml +++ b/modules/local/deseq2_qc/environment.yml @@ -1,8 +1,6 @@ -name: deseq2_qc channels: - conda-forge - bioconda - - defaults dependencies: - conda-forge::r-base - conda-forge::r-optparse diff --git a/modules/local/gtf2bed/environment.yml b/modules/local/gtf2bed/environment.yml index 3c009b31b..99d32b942 100644 --- a/modules/local/gtf2bed/environment.yml +++ b/modules/local/gtf2bed/environment.yml @@ -1,7 +1,5 @@ -name: gtf2bed channels: - conda-forge - bioconda - - defaults dependencies: - conda-forge::perl=5.26.2 diff --git a/modules/local/gtf_filter/environment.yml b/modules/local/gtf_filter/environment.yml index c8b5ca202..eb4030692 100644 --- a/modules/local/gtf_filter/environment.yml +++ b/modules/local/gtf_filter/environment.yml @@ -1,7 +1,5 @@ -name: gtf_filter channels: - conda-forge - bioconda - - defaults dependencies: - conda-forge::python=3.9.5 diff --git a/modules/local/multiqc_custom_biotype/environment.yml b/modules/local/multiqc_custom_biotype/environment.yml index 7a6b5722e..eb4030692 100644 --- a/modules/local/multiqc_custom_biotype/environment.yml +++ b/modules/local/multiqc_custom_biotype/environment.yml @@ -1,7 +1,5 @@ -name: multiqc_custom_biotype channels: - conda-forge - bioconda - - defaults dependencies: - conda-forge::python=3.9.5 diff --git a/modules/local/preprocess_transcripts_fasta_gencode/environment.yml b/modules/local/preprocess_transcripts_fasta_gencode/environment.yml index 06e4d9658..b7c48640f 100644 --- a/modules/local/preprocess_transcripts_fasta_gencode/environment.yml +++ b/modules/local/preprocess_transcripts_fasta_gencode/environment.yml @@ -1,7 +1,5 @@ -name: preprocess_transcripts_fasta_gencode channels: - conda-forge - bioconda - - defaults dependencies: - conda-forge::sed=4.7 diff --git a/modules/local/rsem_merge_counts/environment.yml b/modules/local/rsem_merge_counts/environment.yml index eeeb3329a..b7c48640f 100644 --- a/modules/local/rsem_merge_counts/environment.yml +++ b/modules/local/rsem_merge_counts/environment.yml @@ -1,7 +1,5 @@ -name: rsem_merge_counts channels: - conda-forge - bioconda - - defaults dependencies: - conda-forge::sed=4.7 diff --git a/modules/local/star_align_igenomes/environment.yml b/modules/local/star_align_igenomes/environment.yml index 0d92f8dd5..97745a29e 100644 --- a/modules/local/star_align_igenomes/environment.yml +++ b/modules/local/star_align_igenomes/environment.yml @@ -1,8 +1,6 @@ -name: star_align_igenomes channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::star=2.6.1d - bioconda::samtools=1.10 diff --git a/modules/local/star_genomegenerate_igenomes/environment.yml b/modules/local/star_genomegenerate_igenomes/environment.yml index c3c6c2481..97745a29e 100644 --- a/modules/local/star_genomegenerate_igenomes/environment.yml +++ b/modules/local/star_genomegenerate_igenomes/environment.yml @@ -1,8 +1,6 @@ -name: star_genomegenerate_igenomes channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::star=2.6.1d - bioconda::samtools=1.10 From 262672cbfcdc22aac5b067d1d53d4a18b746b0e4 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Fri, 13 Sep 2024 16:47:38 +0100 Subject: [PATCH 11/17] slight fixes for rnaseq prepro --- .../nf-core/fastq_qc_trim_filter_setstrandedness/main.nf | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/main.nf b/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/main.nf index 4c7b25f8e..14da422eb 100644 --- a/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/main.nf +++ b/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/main.nf @@ -181,7 +181,7 @@ workflow FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS { ch_versions = ch_versions.mix(FASTQ_FASTQC_UMITOOLS_FASTP.out.versions) ch_multiqc_files = FASTQ_FASTQC_UMITOOLS_FASTP.out.fastqc_raw_zip .mix(FASTQ_FASTQC_UMITOOLS_FASTP.out.fastqc_trim_zip) - .mix(FASTQ_FASTQC_UMITOOLS_FASTP.out.trim_json.map{tuple(it[0], [it[1]])}) + .mix(FASTQ_FASTQC_UMITOOLS_FASTP.out.trim_json) .mix(ch_multiqc_files) } @@ -209,6 +209,7 @@ workflow FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS { ch_multiqc_files = ch_multiqc_files .mix( ch_fail_trimming_multiqc.collectFile(name: 'fail_trimmed_samples_mqc.tsv') + .map { [[], it] } ) // From 3701544623b6de1a56cc27a44466b749bb7417bf Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Fri, 13 Sep 2024 16:57:47 +0000 Subject: [PATCH 12/17] Remove chunk duplicated from subworkflow --- workflows/rnaseq/main.nf | 19 ------------------- 1 file changed, 19 deletions(-) diff --git a/workflows/rnaseq/main.nf b/workflows/rnaseq/main.nf index 0b702e641..2ee8384f4 100755 --- a/workflows/rnaseq/main.nf +++ b/workflows/rnaseq/main.nf @@ -167,25 +167,6 @@ workflow RNASEQ { meta, num_reads -> return [ meta.id, num_reads > params.min_trimmed_reads.toFloat() ] } - // - // Get list of samples that failed trimming threshold for MultiQC report - // - ch_trim_read_count - .map { - meta, num_reads -> - if (num_reads <= params.min_trimmed_reads.toFloat()) { - return [ "$meta.id\t$num_reads" ] - } - } - .collect() - .map { - tsv_data -> - def header = ["Sample", "Reads after trimming"] - sample_status_header_multiqc.text + multiqcTsvFromList(tsv_data, header) - } - .set { ch_fail_trimming_multiqc } - - ch_multiqc_files = ch_multiqc_files.mix(ch_fail_trimming_multiqc.collectFile(name: 'fail_trimmed_samples_mqc.tsv')) // // SUBWORKFLOW: Alignment with STAR and gene/transcript quantification with Salmon From 5c6982c145699dd1651cf06d3f2140ac5755d8a5 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Fri, 13 Sep 2024 17:00:28 +0000 Subject: [PATCH 13/17] Try from branch --- modules.json | 4 ++-- .../nf-core/fastq_qc_trim_filter_setstrandedness/main.nf | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/modules.json b/modules.json index fc53bd567..bb42dadd3 100644 --- a/modules.json +++ b/modules.json @@ -324,8 +324,8 @@ "installed_by": ["fastq_qc_trim_filter_setstrandedness", "subworkflows"] }, "fastq_qc_trim_filter_setstrandedness": { - "branch": "master", - "git_sha": "8c47be6a114b82a6e6d2f5320b3b5c67579956c0", + "branch": "fastq_prepro_trimfail_fix", + "git_sha": "5ccbeafc08c38098a5eae0583f97ea56518278ab", "installed_by": ["subworkflows"] }, "fastq_subsample_fq_salmon": { diff --git a/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/main.nf b/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/main.nf index 14da422eb..4ed073efc 100644 --- a/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/main.nf +++ b/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/main.nf @@ -209,7 +209,7 @@ workflow FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS { ch_multiqc_files = ch_multiqc_files .mix( ch_fail_trimming_multiqc.collectFile(name: 'fail_trimmed_samples_mqc.tsv') - .map { [[], it] } + .map { [[:], it] } ) // From 3e9af61bd3fb9f931c5a7058cb17be5240fdfb6f Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Mon, 16 Sep 2024 12:35:22 +0100 Subject: [PATCH 14/17] install subworkflow from master --- modules.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/modules.json b/modules.json index df4c6d69d..30090ab26 100644 --- a/modules.json +++ b/modules.json @@ -324,8 +324,8 @@ "installed_by": ["fastq_qc_trim_filter_setstrandedness", "subworkflows"] }, "fastq_qc_trim_filter_setstrandedness": { - "branch": "fastq_prepro_trimfail_fix", - "git_sha": "5ccbeafc08c38098a5eae0583f97ea56518278ab", + "branch": "master", + "git_sha": "ee3b8b84da02320fff5f3f2dc1d6f9b72d7cd5af", "installed_by": ["subworkflows"] }, "fastq_subsample_fq_salmon": { From 5703690c59aab36988374c045e07adbd6da42754 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Mon, 16 Sep 2024 12:41:15 +0100 Subject: [PATCH 15/17] Update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index f35bf876c..9ba7510ff 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -14,6 +14,7 @@ Special thanks to the following for their contributions to the release: - [PR #1374](https://github.com/nf-core/rnaseq/pull/1374) - Bump pipeline version to 3.16.0dev - [PR #1380](https://github.com/nf-core/rnaseq/pull/1380) - Fix issues with R modules changing sample names - [PR #1381](https://github.com/nf-core/rnaseq/pull/1381) - Update all modules following massive conda usage update in nf-core modules +- [PR #1382](https://github.com/nf-core/rnaseq/pull/1381) - Slight fixes for rnaseq preprocessing ## [[3.15.0](https://github.com/nf-core/rnaseq/releases/tag/3.15.0)] - 2024-09-04 From ec187a8b6e21be9c7122e11ce25c4425cb10c721 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Mon, 16 Sep 2024 14:34:09 +0100 Subject: [PATCH 16/17] Bump versions --- CHANGELOG.md | 6 +----- nextflow.config | 2 +- tests/default.nf.test.snap | 4 ++-- tests/featurecounts_group_type.nf.test.snap | 4 ++-- tests/hisat2.nf.test.snap | 4 ++-- tests/kallisto.nf.test.snap | 4 ++-- tests/min_mapped_reads.nf.test.snap | 4 ++-- tests/remove_ribo_rna.nf.test.snap | 4 ++-- tests/salmon.nf.test.snap | 4 ++-- tests/skip_qc.nf.test.snap | 4 ++-- tests/skip_trimming.nf.test.snap | 2 +- tests/star_rsem.nf.test.snap | 4 ++-- workflows/rnaseq/assets/multiqc/multiqc_config.yml | 2 +- 13 files changed, 22 insertions(+), 26 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 9ba7510ff..05bfbd17f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,11 +3,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## v3.16.0dev - [date] - -### Credits - -Special thanks to the following for their contributions to the release: +## [[3.15.1](https://github.com/nf-core/rnaseq/releases/tag/3.15.1)] - 2024-09-16 ### Enhancements & fixes diff --git a/nextflow.config b/nextflow.config index d5e00c6f4..d4bd05ca3 100644 --- a/nextflow.config +++ b/nextflow.config @@ -340,7 +340,7 @@ manifest { description = """RNA sequencing analysis pipeline for gene/isoform quantification and extensive quality control.""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '3.16.0dev' + version = '3.15.1' doi = 'https://doi.org/10.5281/zenodo.1400710' } diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 79b3ca290..eb727b082 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -266,7 +266,7 @@ }, "Params: default - stub": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, FASTQC={fastqc=0.12.1}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0dev}}", + "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, FASTQC={fastqc=0.12.1}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.1}}", "genome_transcriptome.fasta", "genome_transcriptome.gtf", "RAP1_IAA_30M_REP1_raw.html", @@ -932,7 +932,7 @@ }, "versions": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV_FW={bedtools=2.31.1}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, DESEQ2_QC_PSEUDO={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DESEQ2_QC_STAR_SALMON={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DUPRADAR={bioconductor-dupradar=1.32.0}, FASTQC={fastqc=0.12.1}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, MULTIQC_CUSTOM_BIOTYPE={python=3.9.5}, PICARD_MARKDUPLICATES={picard=3.1.1}, QUALIMAP_RNASEQ={qualimap=2.3}, RSEQC_BAMSTAT={rseqc=5.0.2}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_INNERDISTANCE={rseqc=5.0.2}, RSEQC_JUNCTIONANNOTATION={rseqc=5.0.2}, RSEQC_JUNCTIONSATURATION={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, STAR_ALIGN={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0dev}}" + "{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV_FW={bedtools=2.31.1}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, DESEQ2_QC_PSEUDO={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DESEQ2_QC_STAR_SALMON={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DUPRADAR={bioconductor-dupradar=1.32.0}, FASTQC={fastqc=0.12.1}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, MULTIQC_CUSTOM_BIOTYPE={python=3.9.5}, PICARD_MARKDUPLICATES={picard=3.1.1}, QUALIMAP_RNASEQ={qualimap=2.3}, RSEQC_BAMSTAT={rseqc=5.0.2}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_INNERDISTANCE={rseqc=5.0.2}, RSEQC_JUNCTIONANNOTATION={rseqc=5.0.2}, RSEQC_JUNCTIONSATURATION={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, STAR_ALIGN={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.1}}" ], "meta": { "nf-test": "0.9.0", diff --git a/tests/featurecounts_group_type.nf.test.snap b/tests/featurecounts_group_type.nf.test.snap index 3a08ab907..4bb12f76b 100644 --- a/tests/featurecounts_group_type.nf.test.snap +++ b/tests/featurecounts_group_type.nf.test.snap @@ -747,7 +747,7 @@ }, "versions": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV_FW={bedtools=2.31.1}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, DESEQ2_QC_PSEUDO={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DESEQ2_QC_STAR_SALMON={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DUPRADAR={bioconductor-dupradar=1.32.0}, FASTQC={fastqc=0.12.1}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, PICARD_MARKDUPLICATES={picard=3.1.1}, QUALIMAP_RNASEQ={qualimap=2.3}, RSEQC_BAMSTAT={rseqc=5.0.2}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_INNERDISTANCE={rseqc=5.0.2}, RSEQC_JUNCTIONANNOTATION={rseqc=5.0.2}, RSEQC_JUNCTIONSATURATION={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, STAR_ALIGN={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0dev}}" + "{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV_FW={bedtools=2.31.1}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, DESEQ2_QC_PSEUDO={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DESEQ2_QC_STAR_SALMON={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DUPRADAR={bioconductor-dupradar=1.32.0}, FASTQC={fastqc=0.12.1}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, PICARD_MARKDUPLICATES={picard=3.1.1}, QUALIMAP_RNASEQ={qualimap=2.3}, RSEQC_BAMSTAT={rseqc=5.0.2}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_INNERDISTANCE={rseqc=5.0.2}, RSEQC_JUNCTIONANNOTATION={rseqc=5.0.2}, RSEQC_JUNCTIONSATURATION={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, STAR_ALIGN={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.1}}" ], "meta": { "nf-test": "0.9.0", @@ -757,7 +757,7 @@ }, "Params: --featurecounts_group_type false - stub": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, FASTQC={fastqc=0.12.1}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0dev}}", + "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, FASTQC={fastqc=0.12.1}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.1}}", "genome_transcriptome.fasta", "genome_transcriptome.gtf", "RAP1_IAA_30M_REP1_raw.html", diff --git a/tests/hisat2.nf.test.snap b/tests/hisat2.nf.test.snap index 1a15dd9a4..734ca3040 100644 --- a/tests/hisat2.nf.test.snap +++ b/tests/hisat2.nf.test.snap @@ -631,7 +631,7 @@ }, "Params: --aligner hisat2 - stub": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, FASTQC={fastqc=0.12.1}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, HISAT2_EXTRACTSPLICESITES={hisat2=2.2.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_HISAT2_INDEX={untar=1.34}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0dev}}", + "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, FASTQC={fastqc=0.12.1}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, HISAT2_EXTRACTSPLICESITES={hisat2=2.2.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_HISAT2_INDEX={untar=1.34}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.1}}", "genome_transcriptome.fasta", "genome_transcriptome.gtf", "RAP1_IAA_30M_REP1_raw.html", @@ -726,7 +726,7 @@ }, "versions": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV_FW={bedtools=2.31.1}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, DESEQ2_QC_PSEUDO={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DUPRADAR={bioconductor-dupradar=1.32.0}, FASTQC={fastqc=0.12.1}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, HISAT2_ALIGN={hisat2=2.2.1, samtools=1.16.1}, HISAT2_EXTRACTSPLICESITES={hisat2=2.2.1}, MULTIQC_CUSTOM_BIOTYPE={python=3.9.5}, PICARD_MARKDUPLICATES={picard=3.1.1}, QUALIMAP_RNASEQ={qualimap=2.3}, RSEQC_BAMSTAT={rseqc=5.0.2}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_INNERDISTANCE={rseqc=5.0.2}, RSEQC_JUNCTIONANNOTATION={rseqc=5.0.2}, RSEQC_JUNCTIONSATURATION={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, 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RSEQC_BAMSTAT={rseqc=5.0.2}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_INNERDISTANCE={rseqc=5.0.2}, RSEQC_JUNCTIONANNOTATION={rseqc=5.0.2}, RSEQC_JUNCTIONSATURATION={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_HISAT2_INDEX={untar=1.34}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.1}}" ], "meta": { "nf-test": "0.9.0", diff --git a/tests/kallisto.nf.test.snap b/tests/kallisto.nf.test.snap index a431f33fc..b0ff0b3fb 100644 --- a/tests/kallisto.nf.test.snap +++ b/tests/kallisto.nf.test.snap @@ -103,7 +103,7 @@ }, "versions": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, KALLISTO_INDEX={kallisto=0.48.0}, KALLISTO_QUANT={kallisto=0.48.0}, SALMON_QUANT={salmon=1.10.1}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0dev}}" + "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, KALLISTO_INDEX={kallisto=0.48.0}, KALLISTO_QUANT={kallisto=0.48.0}, SALMON_QUANT={salmon=1.10.1}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.1}}" ], "meta": { "nf-test": "0.9.0", @@ -219,7 +219,7 @@ }, "Params: --pseudo_aligner kallisto --skip_qc --skip_alignment - stub": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, KALLISTO_INDEX={kallisto=0.48.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0dev}}", + "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, KALLISTO_INDEX={kallisto=0.48.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.1}}", "genome_transcriptome.fasta", "genome_transcriptome.gtf", "multiqc_report.html", diff --git a/tests/min_mapped_reads.nf.test.snap b/tests/min_mapped_reads.nf.test.snap index c68828368..c82193e9d 100644 --- a/tests/min_mapped_reads.nf.test.snap +++ b/tests/min_mapped_reads.nf.test.snap @@ -447,7 +447,7 @@ }, "Params: --min_mapped_reads 90 - stub": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, FASTQC={fastqc=0.12.1}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, 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PICARD_MARKDUPLICATES={picard=3.1.1}, QUALIMAP_RNASEQ={qualimap=2.3}, RSEQC_BAMSTAT={rseqc=5.0.2}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_INNERDISTANCE={rseqc=5.0.2}, RSEQC_JUNCTIONANNOTATION={rseqc=5.0.2}, RSEQC_JUNCTIONSATURATION={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, STAR_ALIGN={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.1}}" ], "meta": { "nf-test": "0.9.0", diff --git a/tests/remove_ribo_rna.nf.test.snap b/tests/remove_ribo_rna.nf.test.snap index a6e841b08..64a3f6c91 100644 --- a/tests/remove_ribo_rna.nf.test.snap +++ b/tests/remove_ribo_rna.nf.test.snap @@ -498,7 +498,7 @@ }, "Params: --remove_ribo_rna - stub": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, FASTQC={fastqc=0.12.1}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, SORTMERNA_INDEX={sortmerna=4.3.6}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0dev}}", + "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, FASTQC={fastqc=0.12.1}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, SORTMERNA_INDEX={sortmerna=4.3.6}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.1}}", "genome_transcriptome.fasta", "genome_transcriptome.gtf", "RAP1_IAA_30M_REP1_raw.html", @@ -954,7 +954,7 @@ }, "versions": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV_FW={bedtools=2.31.1}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, DESEQ2_QC_PSEUDO={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DESEQ2_QC_STAR_SALMON={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DUPRADAR={bioconductor-dupradar=1.32.0}, FASTQC={fastqc=0.12.1}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, MULTIQC_CUSTOM_BIOTYPE={python=3.9.5}, PICARD_MARKDUPLICATES={picard=3.1.1}, QUALIMAP_RNASEQ={qualimap=2.3}, RSEQC_BAMSTAT={rseqc=5.0.2}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_INNERDISTANCE={rseqc=5.0.2}, RSEQC_JUNCTIONANNOTATION={rseqc=5.0.2}, RSEQC_JUNCTIONSATURATION={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, SORTMERNA={sortmerna=4.3.6}, SORTMERNA_INDEX={sortmerna=4.3.6}, STAR_ALIGN={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0dev}}" + "{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV_FW={bedtools=2.31.1}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, DESEQ2_QC_PSEUDO={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DESEQ2_QC_STAR_SALMON={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DUPRADAR={bioconductor-dupradar=1.32.0}, FASTQC={fastqc=0.12.1}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, MULTIQC_CUSTOM_BIOTYPE={python=3.9.5}, PICARD_MARKDUPLICATES={picard=3.1.1}, QUALIMAP_RNASEQ={qualimap=2.3}, RSEQC_BAMSTAT={rseqc=5.0.2}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_INNERDISTANCE={rseqc=5.0.2}, RSEQC_JUNCTIONANNOTATION={rseqc=5.0.2}, RSEQC_JUNCTIONSATURATION={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, SORTMERNA={sortmerna=4.3.6}, SORTMERNA_INDEX={sortmerna=4.3.6}, STAR_ALIGN={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.1}}" ], "meta": { "nf-test": "0.9.0", diff --git a/tests/salmon.nf.test.snap b/tests/salmon.nf.test.snap index 004c15ad4..6ce551414 100644 --- a/tests/salmon.nf.test.snap +++ b/tests/salmon.nf.test.snap @@ -61,7 +61,7 @@ }, "versions": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, SALMON_QUANT={salmon=1.10.1}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0dev}}" + "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, SALMON_QUANT={salmon=1.10.1}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.1}}" ], "meta": { "nf-test": "0.9.0", @@ -265,7 +265,7 @@ }, "Params: --pseudo_aligner salmon --skip_qc --skip_alignment - stub": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0dev}}", + "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.1}}", "genome_transcriptome.fasta", "genome_transcriptome.gtf", "RAP1_IAA_30M_REP1_raw.html", diff --git a/tests/skip_qc.nf.test.snap b/tests/skip_qc.nf.test.snap index 7a1eaccf3..7fcb8480a 100644 --- a/tests/skip_qc.nf.test.snap +++ b/tests/skip_qc.nf.test.snap @@ -157,7 +157,7 @@ }, "Params: --skip_qc - stub": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0dev}}", + "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.1}}", "genome_transcriptome.fasta", "genome_transcriptome.gtf", "RAP1_IAA_30M_REP1_raw.html", @@ -477,7 +477,7 @@ }, "versions": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV_FW={bedtools=2.31.1}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, PICARD_MARKDUPLICATES={picard=3.1.1}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, 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SAMTOOLS_STATS={samtools=1.2}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, STAR_ALIGN={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.1}}" ], "meta": { "nf-test": "0.9.0", diff --git a/tests/skip_trimming.nf.test.snap b/tests/skip_trimming.nf.test.snap index 0cced5ad5..d40a54446 100644 --- a/tests/skip_trimming.nf.test.snap +++ b/tests/skip_trimming.nf.test.snap @@ -751,7 +751,7 @@ }, "versions": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV_FW={bedtools=2.31.1}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, DESEQ2_QC_PSEUDO={r-base=4.0.3, 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RSEQC_BAMSTAT={rseqc=5.0.2}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_INNERDISTANCE={rseqc=5.0.2}, RSEQC_JUNCTIONANNOTATION={rseqc=5.0.2}, RSEQC_JUNCTIONSATURATION={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, STAR_ALIGN={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.1}}" ], "meta": { "nf-test": "0.9.0", diff --git a/tests/star_rsem.nf.test.snap b/tests/star_rsem.nf.test.snap index a6a804341..db393113e 100644 --- a/tests/star_rsem.nf.test.snap +++ b/tests/star_rsem.nf.test.snap @@ -766,7 +766,7 @@ }, "Params: --aligner star_rsem - stub": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, FASTQC={fastqc=0.12.1}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_RSEM_INDEX={untar=1.34}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0dev}}", + "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, FASTQC={fastqc=0.12.1}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_RSEM_INDEX={untar=1.34}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.1}}", "genome_transcriptome.fasta", "genome_transcriptome.gtf", "RAP1_IAA_30M_REP1_raw.html", @@ -797,7 +797,7 @@ }, "versions": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV_FW={bedtools=2.31.1}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, DESEQ2_QC_PSEUDO={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DESEQ2_QC_RSEM={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DUPRADAR={bioconductor-dupradar=1.32.0}, FASTQC={fastqc=0.12.1}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, MULTIQC_CUSTOM_BIOTYPE={python=3.9.5}, PICARD_MARKDUPLICATES={picard=3.1.1}, QUALIMAP_RNASEQ={qualimap=2.3}, RSEM_CALCULATEEXPRESSION={rsem=1.3.1, star=2.7.10a}, RSEM_MERGE_COUNTS={sed=4.7}, RSEQC_BAMSTAT={rseqc=5.0.2}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_INNERDISTANCE={rseqc=5.0.2}, RSEQC_JUNCTIONANNOTATION={rseqc=5.0.2}, RSEQC_JUNCTIONSATURATION={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_RSEM_INDEX={untar=1.34}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.16.0dev}}" + "{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV_FW={bedtools=2.31.1}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, DESEQ2_QC_PSEUDO={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DESEQ2_QC_RSEM={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DUPRADAR={bioconductor-dupradar=1.32.0}, FASTQC={fastqc=0.12.1}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, MULTIQC_CUSTOM_BIOTYPE={python=3.9.5}, PICARD_MARKDUPLICATES={picard=3.1.1}, QUALIMAP_RNASEQ={qualimap=2.3}, RSEM_CALCULATEEXPRESSION={rsem=1.3.1, star=2.7.10a}, RSEM_MERGE_COUNTS={sed=4.7}, RSEQC_BAMSTAT={rseqc=5.0.2}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_INNERDISTANCE={rseqc=5.0.2}, RSEQC_JUNCTIONANNOTATION={rseqc=5.0.2}, RSEQC_JUNCTIONSATURATION={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_RSEM_INDEX={untar=1.34}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.1}}" ], "meta": { "nf-test": "0.9.0", diff --git a/workflows/rnaseq/assets/multiqc/multiqc_config.yml b/workflows/rnaseq/assets/multiqc/multiqc_config.yml index 49d3939e2..47e347670 100644 --- a/workflows/rnaseq/assets/multiqc/multiqc_config.yml +++ b/workflows/rnaseq/assets/multiqc/multiqc_config.yml @@ -1,5 +1,5 @@ report_comment: > - This report has been generated by the nf-core/rnaseq analysis pipeline. For information about how to interpret these results, please see the documentation. + This report has been generated by the nf-core/rnaseq analysis pipeline. For information about how to interpret these results, please see the documentation. report_section_order: # Important checks and failures sample-status: From ed31c6fdab2809e4a6f1d98120230851abe45980 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Mon, 16 Sep 2024 14:36:26 +0100 Subject: [PATCH 17/17] update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 05bfbd17f..cd24663bd 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,6 +11,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [PR #1380](https://github.com/nf-core/rnaseq/pull/1380) - Fix issues with R modules changing sample names - [PR #1381](https://github.com/nf-core/rnaseq/pull/1381) - Update all modules following massive conda usage update in nf-core modules - [PR #1382](https://github.com/nf-core/rnaseq/pull/1381) - Slight fixes for rnaseq preprocessing +- [P$ #1383](https://github.com/nf-core/rnaseq/pull/1383) - Prerelease 3.15.1 version bumps ## [[3.15.0](https://github.com/nf-core/rnaseq/releases/tag/3.15.0)] - 2024-09-04