From c920039bc52737974d29186fdc1e5484397e914b Mon Sep 17 00:00:00 2001 From: darcy220606 Date: Fri, 15 Mar 2024 12:39:56 +0100 Subject: [PATCH 1/7] changesamplesheet to reduced --- conf/test.config | 4 ++-- conf/test_bgc.config | 2 +- conf/test_nothing.config | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/conf/test.config b/conf/test.config index 724fd58f..74f69b6c 100644 --- a/conf/test.config +++ b/conf/test.config @@ -20,8 +20,8 @@ params { max_time = '6.h' // Input data - input = 'https://raw.githubusercontent.com/nf-core/test-datasets/funcscan/samplesheet.csv' - amp_hmmsearch_models = 'https://raw.githubusercontent.com/nf-core/test-datasets/funcscan/hmms/mybacteriocin.hmm' + input = 'https://raw.githubusercontent.com/nf-core/test-datasets/funcscan/samplesheet_reduced.csv' + amp_hmmsearch_models = 'https://raw.githubusercontent.com/nf-core/test-datasets/funcscan/hmms/mybacteriocin.hmm' annotation_tool = 'prodigal' diff --git a/conf/test_bgc.config b/conf/test_bgc.config index 07623670..17df755d 100644 --- a/conf/test_bgc.config +++ b/conf/test_bgc.config @@ -20,7 +20,7 @@ params { max_time = '6.h' // Input data - input = 'https://raw.githubusercontent.com/nf-core/test-datasets/funcscan/samplesheet.csv' + input = 'https://raw.githubusercontent.com/nf-core/test-datasets/funcscan/samplesheet_reduced.csv' bgc_hmmsearch_models = 'https://raw.githubusercontent.com/antismash/antismash/fd61de057e082fbf071732ac64b8b2e8883de32f/antismash/detection/hmm_detection/data/ToyB.hmm' annotation_tool = 'prodigal' diff --git a/conf/test_nothing.config b/conf/test_nothing.config index f5df5b3b..5f850139 100644 --- a/conf/test_nothing.config +++ b/conf/test_nothing.config @@ -22,7 +22,7 @@ params { max_time = '6.h' // Input data - input = 'https://raw.githubusercontent.com/nf-core/test-datasets/funcscan/samplesheet.csv' + input = 'https://raw.githubusercontent.com/nf-core/test-datasets/funcscan/samplesheet_reduced.csv' amp_hmmsearch_models = 'https://raw.githubusercontent.com/nf-core/test-datasets/funcscan/hmms/mybacteriocin.hmm' annotation_tool = 'prodigal' From 8d8409821d42adc2d59936dea039001549b3d39a Mon Sep 17 00:00:00 2001 From: darcy220606 Date: Fri, 15 Mar 2024 12:58:51 +0100 Subject: [PATCH 2/7] update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index b8147b46..fd375893 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -13,6 +13,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#338](https://github.com/nf-core/funcscan/pull/338) Set `--meta` parameter to default for Bakta, with singlemode optional. (by @jasmezz) ### `Fixed` +- [#348](https://github.com/nf-core/funcscan/pull/348) Updated config files samplesheet to 'samplesheet_reduced.csv' to reduce resource consumption. (by @darcy220606) ### `Dependencies` From e390ffe791598ad0fba600f0619aa72b95f6266f Mon Sep 17 00:00:00 2001 From: darcy220606 Date: Fri, 15 Mar 2024 13:03:20 +0100 Subject: [PATCH 3/7] apply prettier --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index fd375893..beaf6a76 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -13,6 +13,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#338](https://github.com/nf-core/funcscan/pull/338) Set `--meta` parameter to default for Bakta, with singlemode optional. (by @jasmezz) ### `Fixed` + - [#348](https://github.com/nf-core/funcscan/pull/348) Updated config files samplesheet to 'samplesheet_reduced.csv' to reduce resource consumption. (by @darcy220606) ### `Dependencies` From 9bd8d68baa7ab14685962596ec73f758f9678efb Mon Sep 17 00:00:00 2001 From: darcy220606 Date: Tue, 19 Mar 2024 09:36:58 +0100 Subject: [PATCH 4/7] update prodigal --- .gitignore | 1 - modules.json | 4 +- modules/nf-core/prodigal/main.nf | 22 +- modules/nf-core/prodigal/tests/main.nf.test | 101 +++++++++ .../nf-core/prodigal/tests/main.nf.test.snap | 196 ++++++++++++++++ modules/nf-core/prodigal/tests/tags.yml | 2 + modules/nf-core/pyrodigal/environment.yml | 3 +- modules/nf-core/pyrodigal/main.nf | 21 +- modules/nf-core/pyrodigal/meta.yml | 10 +- modules/nf-core/pyrodigal/tests/main.nf.test | 105 +++++++++ .../nf-core/pyrodigal/tests/main.nf.test.snap | 210 ++++++++++++++++++ modules/nf-core/pyrodigal/tests/tags.yml | 2 + 12 files changed, 659 insertions(+), 18 deletions(-) create mode 100644 modules/nf-core/prodigal/tests/main.nf.test create mode 100644 modules/nf-core/prodigal/tests/main.nf.test.snap create mode 100644 modules/nf-core/prodigal/tests/tags.yml create mode 100644 modules/nf-core/pyrodigal/tests/main.nf.test create mode 100644 modules/nf-core/pyrodigal/tests/main.nf.test.snap create mode 100644 modules/nf-core/pyrodigal/tests/tags.yml diff --git a/.gitignore b/.gitignore index ced46a87..5124c9ac 100644 --- a/.gitignore +++ b/.gitignore @@ -6,4 +6,3 @@ results/ testing/ testing* *.pyc -tests/ diff --git a/modules.json b/modules.json index e9daa87d..70e18e4c 100644 --- a/modules.json +++ b/modules.json @@ -143,7 +143,7 @@ }, "prodigal": { "branch": "master", - "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "git_sha": "2a196d6bfea8b6b5f49fc1885e39fae5f50bc2a0", "installed_by": ["modules"] }, "prokka": { @@ -153,7 +153,7 @@ }, "pyrodigal": { "branch": "master", - "git_sha": "0e70547d116de782ec3825f1a449a56abb894482", + "git_sha": "94c4df7840d1ee5ec4d817310ff60b02e6459353", "installed_by": ["modules"] }, "rgi/main": { diff --git a/modules/nf-core/prodigal/main.nf b/modules/nf-core/prodigal/main.nf index b7df4787..49ced167 100644 --- a/modules/nf-core/prodigal/main.nf +++ b/modules/nf-core/prodigal/main.nf @@ -33,7 +33,10 @@ process PRODIGAL { -a "${prefix}.faa" \\ -s "${prefix}_all.txt" - pigz -nm ${prefix}* + pigz -nm ${prefix}.fna + pigz -nm ${prefix}.${output_format} + pigz -nm ${prefix}.faa + pigz -nm ${prefix}_all.txt cat <<-END_VERSIONS > versions.yml "${task.process}": @@ -41,4 +44,21 @@ process PRODIGAL { pigz: \$(pigz -V 2>&1 | sed 's/pigz //g') END_VERSIONS """ + + stub: + def args = task.ext.args ?: '' + prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.fna.gz + touch ${prefix}.${output_format}.gz + touch ${prefix}.faa.gz + touch ${prefix}_all.txt.gz + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + prodigal: \$(prodigal -v 2>&1 | sed -n 's/Prodigal V\\(.*\\):.*/\\1/p') + pigz: \$(pigz -V 2>&1 | sed 's/pigz //g') + END_VERSIONS + """ + } diff --git a/modules/nf-core/prodigal/tests/main.nf.test b/modules/nf-core/prodigal/tests/main.nf.test new file mode 100644 index 00000000..5bcb67d5 --- /dev/null +++ b/modules/nf-core/prodigal/tests/main.nf.test @@ -0,0 +1,101 @@ +nextflow_process { + + name "Test Process PRODIGAL" + script "../main.nf" + process "PRODIGAL" + + tag "modules" + tag "modules_nfcore" + tag "prodigal" + + test("prodigal - sarscov2 - gff") { + when { + process { + """ + input[0] = [ + [id:'test', single_end:false ], // meta map + file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + ] + input[1] = 'gff' + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("prodigal - sarscov2 - gbk") { + when { + process { + """ + input[0] = [ + [id:'test', single_end:false ], // meta map + file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + ] + input[1] = 'gbk' + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("prodigal - sarscov2 - gff - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [id:'test', single_end:false ], // meta map + file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + ] + input[1] = 'gff' + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.out).match() } + ) + } + } + + test("prodigal - sarscov2 - gbk - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [id:'test', single_end:false ], // meta map + file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + ] + input[1] = 'gbk' + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.out).match() } + ) + } + } + +} \ No newline at end of file diff --git a/modules/nf-core/prodigal/tests/main.nf.test.snap b/modules/nf-core/prodigal/tests/main.nf.test.snap new file mode 100644 index 00000000..f29802b4 --- /dev/null +++ b/modules/nf-core/prodigal/tests/main.nf.test.snap @@ -0,0 +1,196 @@ +{ + "prodigal - sarscov2 - gbk - stub": { + "content": null, + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-18T13:58:09.852618454" + }, + "prodigal - sarscov2 - gff": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.gff.gz:md5,612c2724c2891c63350f171f74165757" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.fna.gz:md5,1bc8a05bcb72a3c324f5e4ffaa716d3b" + ] + ], + "2": [ + [ + { + "id": "test", + "single_end": false + }, + "test.faa.gz:md5,7168b854103f3586ccfdb71a44c389f7" + ] + ], + "3": [ + [ + { + "id": "test", + "single_end": false + }, + "test_all.txt.gz:md5,e6d6c50f0c39e5169f84ae3c90837fa9" + ] + ], + "4": [ + "versions.yml:md5,9541e53a6927e9856036bb97bfb30307" + ], + "all_gene_annotations": [ + [ + { + "id": "test", + "single_end": false + }, + "test_all.txt.gz:md5,e6d6c50f0c39e5169f84ae3c90837fa9" + ] + ], + "amino_acid_fasta": [ + [ + { + "id": "test", + "single_end": false + }, + "test.faa.gz:md5,7168b854103f3586ccfdb71a44c389f7" + ] + ], + "gene_annotations": [ + [ + { + "id": "test", + "single_end": false + }, + "test.gff.gz:md5,612c2724c2891c63350f171f74165757" + ] + ], + "nucleotide_fasta": [ + [ + { + "id": "test", + "single_end": false + }, + "test.fna.gz:md5,1bc8a05bcb72a3c324f5e4ffaa716d3b" + ] + ], + "versions": [ + "versions.yml:md5,9541e53a6927e9856036bb97bfb30307" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-18T13:57:49.57989696" + }, + "prodigal - sarscov2 - gff - stub": { + "content": null, + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-18T13:58:03.210222528" + }, + "prodigal - sarscov2 - gbk": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.gbk.gz:md5,188b3a0e3f78740ded7f3ec4d876cb4b" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.fna.gz:md5,1bc8a05bcb72a3c324f5e4ffaa716d3b" + ] + ], + "2": [ + [ + { + "id": "test", + "single_end": false + }, + "test.faa.gz:md5,7168b854103f3586ccfdb71a44c389f7" + ] + ], + "3": [ + [ + { + "id": "test", + "single_end": false + }, + "test_all.txt.gz:md5,e6d6c50f0c39e5169f84ae3c90837fa9" + ] + ], + "4": [ + "versions.yml:md5,9541e53a6927e9856036bb97bfb30307" + ], + "all_gene_annotations": [ + [ + { + "id": "test", + "single_end": false + }, + "test_all.txt.gz:md5,e6d6c50f0c39e5169f84ae3c90837fa9" + ] + ], + "amino_acid_fasta": [ + [ + { + "id": "test", + "single_end": false + }, + "test.faa.gz:md5,7168b854103f3586ccfdb71a44c389f7" + ] + ], + "gene_annotations": [ + [ + { + "id": "test", + "single_end": false + }, + "test.gbk.gz:md5,188b3a0e3f78740ded7f3ec4d876cb4b" + ] + ], + "nucleotide_fasta": [ + [ + { + "id": "test", + "single_end": false + }, + "test.fna.gz:md5,1bc8a05bcb72a3c324f5e4ffaa716d3b" + ] + ], + "versions": [ + "versions.yml:md5,9541e53a6927e9856036bb97bfb30307" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-18T13:57:56.606374214" + } +} \ No newline at end of file diff --git a/modules/nf-core/prodigal/tests/tags.yml b/modules/nf-core/prodigal/tests/tags.yml new file mode 100644 index 00000000..fc0cb020 --- /dev/null +++ b/modules/nf-core/prodigal/tests/tags.yml @@ -0,0 +1,2 @@ +prodigal: + - "modules/nf-core/prodigal/**" diff --git a/modules/nf-core/pyrodigal/environment.yml b/modules/nf-core/pyrodigal/environment.yml index a0dad862..3e538e8c 100644 --- a/modules/nf-core/pyrodigal/environment.yml +++ b/modules/nf-core/pyrodigal/environment.yml @@ -6,4 +6,5 @@ channels: - bioconda - defaults dependencies: - - bioconda::pyrodigal=2.1.0 + - bioconda::pyrodigal=3.3.0 + - conda-forge::pigz=2.8 diff --git a/modules/nf-core/pyrodigal/main.nf b/modules/nf-core/pyrodigal/main.nf index 9b898574..7cb97594 100644 --- a/modules/nf-core/pyrodigal/main.nf +++ b/modules/nf-core/pyrodigal/main.nf @@ -4,18 +4,19 @@ process PYRODIGAL { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-2fe9a8ce513c91df34b43a6610df94c3a2eb3bd0:697b3838b186fac6a9ceec198b09d4032162a079-0': - 'biocontainers/mulled-v2-2fe9a8ce513c91df34b43a6610df94c3a2eb3bd0:697b3838b186fac6a9ceec198b09d4032162a079-0' }" + 'https://depot.galaxyproject.org/singularity/mulled-v2-2fe9a8ce513c91df34b43a6610df94c3a2eb3bd0:47e7d40834619419f202394563267d74cef857be-0': + 'biocontainers/mulled-v2-2fe9a8ce513c91df34b43a6610df94c3a2eb3bd0:47e7d40834619419f202394563267d74cef857be-0' }" input: tuple val(meta), path(fasta) + val(output_format) output: - tuple val(meta), path("*.gff.gz") , emit: gff - tuple val(meta), path("*.fna.gz") , emit: fna - tuple val(meta), path("*.faa.gz") , emit: faa - tuple val(meta), path("*.score.gz") , emit: score - path "versions.yml" , emit: versions + tuple val(meta), path("*.${output_format}.gz") , emit: annotations + tuple val(meta), path("*.fna.gz") , emit: fna + tuple val(meta), path("*.faa.gz") , emit: faa + tuple val(meta), path("*.score.gz") , emit: score + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when @@ -29,7 +30,8 @@ process PYRODIGAL { pyrodigal \\ $args \\ -i pigz_fasta.fna \\ - -o ${prefix}.gff \\ + -f $output_format \\ + -o "${prefix}.${output_format}" \\ -d ${prefix}.fna \\ -a ${prefix}.faa \\ -s ${prefix}.score @@ -41,12 +43,11 @@ process PYRODIGAL { pyrodigal: \$(echo \$(pyrodigal --version 2>&1 | sed 's/pyrodigal v//')) END_VERSIONS """ - stub: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" """ - touch ${prefix}.gff.gz + touch ${prefix}.${output_format}.gz touch ${prefix}.fna.gz touch ${prefix}.faa.gz touch ${prefix}.score.gz diff --git a/modules/nf-core/pyrodigal/meta.yml b/modules/nf-core/pyrodigal/meta.yml index 024d04ff..0967606f 100644 --- a/modules/nf-core/pyrodigal/meta.yml +++ b/modules/nf-core/pyrodigal/meta.yml @@ -23,6 +23,10 @@ input: type: file description: FASTA file pattern: "*.{fasta.gz,fa.gz,fna.gz}" + - output_format: + type: string + description: Output format + pattern: "{gbk,gff}" output: - meta: type: map @@ -33,10 +37,10 @@ output: type: file description: File containing software versions pattern: "versions.yml" - - gff: + - annotations: type: file - description: gene annotations in gff format - pattern: "*.{gff.gz}" + description: Gene annotations. The file format is specified via input channel "output_format". + pattern: "*.{gbk,gff}.gz" - faa: type: file description: protein translations file diff --git a/modules/nf-core/pyrodigal/tests/main.nf.test b/modules/nf-core/pyrodigal/tests/main.nf.test new file mode 100644 index 00000000..95ea3b2b --- /dev/null +++ b/modules/nf-core/pyrodigal/tests/main.nf.test @@ -0,0 +1,105 @@ +nextflow_process { + + name "Test Process PYRODIGAL" + script "../main.nf" + process "PYRODIGAL" + + tag "modules" + tag "modules_nfcore" + tag "pyrodigal" + + test("pyrodigal - sarscov2 - gff") { + when { + process { + """ + input[0] = [ + [id:'test', single_end:false ], // meta map + file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + ] + input[1] = 'gff' + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("pyrodigal - sarscov2 - gbk") { + when { + process { + """ + input[0] = [ + [id:'test', single_end:false ], // meta map + file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + ] + input[1] = 'gbk' + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("pyrodigal - sarscov2 - gff - stub") { + options "-stub" + when { + process { + """ + input[0] = [ + [id:'test', single_end:false ], // meta map + file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + ] + input[1] = 'gff' + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.gff.collect { file(it[1]).getName() } + + process.out.fna.collect { file(it[1]).getName() } + + process.out.faa.collect { file(it[1]).getName() } + + process.out.score.collect { file(it[1]).getName() } + + process.out.versions).match() } + ) + } + } + + test("pyrodigal - sarscov2 - gbk - stub") { + options "-stub" + when { + process { + """ + input[0] = [ + [id:'test', single_end:false ], // meta map + file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + ] + input[1] = 'gbk' + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.gff.collect { file(it[1]).getName() } + + process.out.fna.collect { file(it[1]).getName() } + + process.out.faa.collect { file(it[1]).getName() } + + process.out.score.collect { file(it[1]).getName() } + + process.out.versions).match() } + ) + } + } + +} \ No newline at end of file diff --git a/modules/nf-core/pyrodigal/tests/main.nf.test.snap b/modules/nf-core/pyrodigal/tests/main.nf.test.snap new file mode 100644 index 00000000..82f4c48d --- /dev/null +++ b/modules/nf-core/pyrodigal/tests/main.nf.test.snap @@ -0,0 +1,210 @@ +{ + "pyrodigal - sarscov2 - gff - stub": { + "content": [ + [ + "test.fna.gz", + "test.faa.gz", + "test.score.gz", + "versions.yml:md5,4aab54554829148e01cc0dc7bf6cb5d3" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-18T15:42:12.012112014" + }, + "pyrodigal - sarscov2 - gbk": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.gbk.gz:md5,2dcc29d50022d1d74ea1133a60c5bd51" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.fna.gz:md5,1bc8a05bcb72a3c324f5e4ffaa716d3b" + ] + ], + "2": [ + [ + { + "id": "test", + "single_end": false + }, + "test.faa.gz:md5,7168b854103f3586ccfdb71a44c389f7" + ] + ], + "3": [ + [ + { + "id": "test", + "single_end": false + }, + "test.score.gz:md5,c0703a9e662ae0b21c7bbb082ef3fb5f" + ] + ], + "4": [ + "versions.yml:md5,4aab54554829148e01cc0dc7bf6cb5d3" + ], + "annotations": [ + [ + { + "id": "test", + "single_end": false + }, + "test.gbk.gz:md5,2dcc29d50022d1d74ea1133a60c5bd51" + ] + ], + "faa": [ + [ + { + "id": "test", + "single_end": false + }, + "test.faa.gz:md5,7168b854103f3586ccfdb71a44c389f7" + ] + ], + "fna": [ + [ + { + "id": "test", + "single_end": false + }, + "test.fna.gz:md5,1bc8a05bcb72a3c324f5e4ffaa716d3b" + ] + ], + "score": [ + [ + { + "id": "test", + "single_end": false + }, + "test.score.gz:md5,c0703a9e662ae0b21c7bbb082ef3fb5f" + ] + ], + "versions": [ + "versions.yml:md5,4aab54554829148e01cc0dc7bf6cb5d3" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-18T15:42:04.374845155" + }, + "pyrodigal - sarscov2 - gff": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.gff.gz:md5,8fcd2d93131cf9fb0c82b81db059ad27" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.fna.gz:md5,1bc8a05bcb72a3c324f5e4ffaa716d3b" + ] + ], + "2": [ + [ + { + "id": "test", + "single_end": false + }, + "test.faa.gz:md5,7168b854103f3586ccfdb71a44c389f7" + ] + ], + "3": [ + [ + { + "id": "test", + "single_end": false + }, + "test.score.gz:md5,c0703a9e662ae0b21c7bbb082ef3fb5f" + ] + ], + "4": [ + "versions.yml:md5,4aab54554829148e01cc0dc7bf6cb5d3" + ], + "annotations": [ + [ + { + "id": "test", + "single_end": false + }, + "test.gff.gz:md5,8fcd2d93131cf9fb0c82b81db059ad27" + ] + ], + "faa": [ + [ + { + "id": "test", + "single_end": false + }, + "test.faa.gz:md5,7168b854103f3586ccfdb71a44c389f7" + ] + ], + "fna": [ + [ + { + "id": "test", + "single_end": false + }, + "test.fna.gz:md5,1bc8a05bcb72a3c324f5e4ffaa716d3b" + ] + ], + "score": [ + [ + { + "id": "test", + "single_end": false + }, + "test.score.gz:md5,c0703a9e662ae0b21c7bbb082ef3fb5f" + ] + ], + "versions": [ + "versions.yml:md5,4aab54554829148e01cc0dc7bf6cb5d3" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-18T15:41:55.822235843" + }, + "pyrodigal - sarscov2 - gbk - stub": { + "content": [ + [ + "test.fna.gz", + "test.faa.gz", + "test.score.gz", + "versions.yml:md5,4aab54554829148e01cc0dc7bf6cb5d3" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-18T15:42:19.81157751" + } +} \ No newline at end of file diff --git a/modules/nf-core/pyrodigal/tests/tags.yml b/modules/nf-core/pyrodigal/tests/tags.yml new file mode 100644 index 00000000..8851ca8b --- /dev/null +++ b/modules/nf-core/pyrodigal/tests/tags.yml @@ -0,0 +1,2 @@ +pyrodigal: + - "modules/nf-core/pyrodigal/**" From 1efed835f47a0756077ac4a270b9407a2bf1d2a9 Mon Sep 17 00:00:00 2001 From: darcy220606 Date: Tue, 19 Mar 2024 09:59:53 +0100 Subject: [PATCH 5/7] update the changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index beaf6a76..5c179240 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -15,6 +15,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Fixed` - [#348](https://github.com/nf-core/funcscan/pull/348) Updated config files samplesheet to 'samplesheet_reduced.csv' to reduce resource consumption. (by @darcy220606) +- [#348](https://github.com/nf-core/funcscan/pull/348) Updated prodigal module to fix pigz issue. (by @darcy220606) ### `Dependencies` From 7872d65fefb8d850a966988a9a572512ac3f9a90 Mon Sep 17 00:00:00 2001 From: Anan Ibrahim <81744003+Darcy220606@users.noreply.github.com> Date: Tue, 19 Mar 2024 10:52:49 +0100 Subject: [PATCH 6/7] Update conf/test.config Co-authored-by: Jasmin Frangenberg <73216762+jasmezz@users.noreply.github.com> --- conf/test.config | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/conf/test.config b/conf/test.config index 74f69b6c..79fd38be 100644 --- a/conf/test.config +++ b/conf/test.config @@ -20,8 +20,8 @@ params { max_time = '6.h' // Input data - input = 'https://raw.githubusercontent.com/nf-core/test-datasets/funcscan/samplesheet_reduced.csv' - amp_hmmsearch_models = 'https://raw.githubusercontent.com/nf-core/test-datasets/funcscan/hmms/mybacteriocin.hmm' + input = 'https://raw.githubusercontent.com/nf-core/test-datasets/funcscan/samplesheet_reduced.csv' + amp_hmmsearch_models = 'https://raw.githubusercontent.com/nf-core/test-datasets/funcscan/hmms/mybacteriocin.hmm' annotation_tool = 'prodigal' From 10dcce57bc0efaf92a06dd6452dc8ccdd264dc33 Mon Sep 17 00:00:00 2001 From: Anan Ibrahim <81744003+Darcy220606@users.noreply.github.com> Date: Tue, 19 Mar 2024 10:53:46 +0100 Subject: [PATCH 7/7] Update CHANGELOG.md Co-authored-by: Jasmin Frangenberg <73216762+jasmezz@users.noreply.github.com> --- CHANGELOG.md | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 5c179240..61a453a6 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -14,8 +14,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Fixed` -- [#348](https://github.com/nf-core/funcscan/pull/348) Updated config files samplesheet to 'samplesheet_reduced.csv' to reduce resource consumption. (by @darcy220606) -- [#348](https://github.com/nf-core/funcscan/pull/348) Updated prodigal module to fix pigz issue. (by @darcy220606) +- [#348](https://github.com/nf-core/funcscan/pull/348) Updated samplesheet for pipeline tests to 'samplesheet_reduced.csv' with smaller datasets to reduce resource consumption. Updated prodigal module to fix pigz issue. (by @darcy220606) ### `Dependencies`