From f2777604a06b93d0604f9777640ec6823e6badbc Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Sat, 3 Feb 2024 14:50:54 +0000 Subject: [PATCH 1/6] Bump centrifuge version to hopefully fix mkfifo errors --- CHANGELOG.md | 6 + modules.json | 4 +- .../centrifuge/centrifuge/environment.yml | 7 + modules/nf-core/centrifuge/centrifuge/main.nf | 39 +++++- .../nf-core/centrifuge/centrifuge/meta.yml | 4 + .../centrifuge/centrifuge/tests/main.nf.test | 106 +++++++++++++++ .../centrifuge/tests/main.nf.test.snap | 125 ++++++++++++++++++ .../centrifuge/centrifuge/tests/tags.yml | 2 + .../centrifuge/kreport/environment.yml | 7 + modules/nf-core/centrifuge/kreport/main.nf | 22 ++- modules/nf-core/centrifuge/kreport/meta.yml | 12 +- .../centrifuge/kreport/tests/main.nf.test | 81 ++++++++++++ .../kreport/tests/main.nf.test.snap | 47 +++++++ .../nf-core/centrifuge/kreport/tests/tags.yml | 2 + 14 files changed, 453 insertions(+), 11 deletions(-) create mode 100644 modules/nf-core/centrifuge/centrifuge/environment.yml create mode 100644 modules/nf-core/centrifuge/centrifuge/tests/main.nf.test create mode 100644 modules/nf-core/centrifuge/centrifuge/tests/main.nf.test.snap create mode 100644 modules/nf-core/centrifuge/centrifuge/tests/tags.yml create mode 100644 modules/nf-core/centrifuge/kreport/environment.yml create mode 100644 modules/nf-core/centrifuge/kreport/tests/main.nf.test create mode 100644 modules/nf-core/centrifuge/kreport/tests/main.nf.test.snap create mode 100644 modules/nf-core/centrifuge/kreport/tests/tags.yml diff --git a/CHANGELOG.md b/CHANGELOG.md index 5a5d6f70..7a13a7c8 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -12,8 +12,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Fixed` +- [#444](https://github.com/nf-core/taxprofiler/pull/440) Centrifuge uses dedicated /tmp directory to hopefully prevent mkfifo clashes (reported by @erinyoung, fix by @jfy133) + ### `Dependencies` +| Tool | Previous version | New version | +| ---------- | ---------------- | ----------- | +| Centrifuge | 1.0.4_beta | 1.0.4.1 | + ### `Deprecated` ## v1.1.4 - Augmented Akita Patch [2024-01-24] diff --git a/modules.json b/modules.json index b680e7d2..44841d23 100644 --- a/modules.json +++ b/modules.json @@ -42,12 +42,12 @@ }, "centrifuge/centrifuge": { "branch": "master", - "git_sha": "7b0b4276fbad744a69c35d3cbf9d55fdfc9491bd", + "git_sha": "32a99bba21c961f8642ddd38fcd4ea2844c10990", "installed_by": ["modules"] }, "centrifuge/kreport": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "32a99bba21c961f8642ddd38fcd4ea2844c10990", "installed_by": ["modules"] }, "custom/dumpsoftwareversions": { diff --git a/modules/nf-core/centrifuge/centrifuge/environment.yml b/modules/nf-core/centrifuge/centrifuge/environment.yml new file mode 100644 index 00000000..0de46a99 --- /dev/null +++ b/modules/nf-core/centrifuge/centrifuge/environment.yml @@ -0,0 +1,7 @@ +name: centrifuge_centrifuge +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::centrifuge-core=1.0.4.1 diff --git a/modules/nf-core/centrifuge/centrifuge/main.nf b/modules/nf-core/centrifuge/centrifuge/main.nf index 6e45ba4e..d02cbeb8 100644 --- a/modules/nf-core/centrifuge/centrifuge/main.nf +++ b/modules/nf-core/centrifuge/centrifuge/main.nf @@ -2,10 +2,10 @@ process CENTRIFUGE_CENTRIFUGE { tag "$meta.id" label 'process_high' - conda "bioconda::centrifuge=1.0.4_beta" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/centrifuge:1.0.4_beta--h9a82719_6' : - 'biocontainers/centrifuge:1.0.4_beta--h9a82719_6' }" + 'https://depot.galaxyproject.org/singularity/centrifuge-core:1.0.4.1--h43eeafb_0' : + 'biocontainers/centrifuge-core:1.0.4.1--h43eeafb_0' }" input: tuple val(meta), path(reads) @@ -40,8 +40,15 @@ process CENTRIFUGE_CENTRIFUGE { """ ## we add "-no-name ._" to ensure silly Mac OSX metafiles files aren't included db_name=`find -L ${db} -name "*.1.cf" -not -name "._*" | sed 's/\\.1.cf\$//'` + + ## make a directory for placing the pipe files in somewhere other than default /tmp + ## otherwise get pipefile name clashes when multiple centrifuge runs on same node + ## use /tmp at the same time + mkdir ./temp + centrifuge \\ -x \$db_name \\ + --temp-directory ./temp \\ -p $task.cpus \\ $paired \\ --report-file ${prefix}.report.txt \\ @@ -55,4 +62,30 @@ process CENTRIFUGE_CENTRIFUGE { centrifuge: \$( centrifuge --version | sed -n 1p | sed 's/^.*centrifuge-class version //') END_VERSIONS """ + + stub: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def paired = meta.single_end ? "-U ${reads}" : "-1 ${reads[0]} -2 ${reads[1]}" + def unaligned = '' + def aligned = '' + if (meta.single_end) { + unaligned = save_unaligned ? "--un-gz ${prefix}.unmapped.fastq.gz" : '' + aligned = save_aligned ? "--al-gz ${prefix}.mapped.fastq.gz" : '' + } else { + unaligned = save_unaligned ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : '' + aligned = save_aligned ? "--al-conc-gz ${prefix}.mapped.fastq.gz" : '' + } + """ + touch ${prefix}.report.txt + touch ${prefix}.results.txt + touch ${prefix}.sam + echo | gzip -n > ${prefix}.unmapped.fastq.gz + echo | gzip -n > ${prefix}.mapped.fastq.gz + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + centrifuge: \$( centrifuge --version | sed -n 1p | sed 's/^.*centrifuge-class version //') + END_VERSIONS + """ } diff --git a/modules/nf-core/centrifuge/centrifuge/meta.yml b/modules/nf-core/centrifuge/centrifuge/meta.yml index b51e2522..a06104e1 100644 --- a/modules/nf-core/centrifuge/centrifuge/meta.yml +++ b/modules/nf-core/centrifuge/centrifuge/meta.yml @@ -69,3 +69,7 @@ authors: - "@sofstam" - "@jfy133" - "@sateeshperi" +maintainers: + - "@sofstam" + - "@jfy133" + - "@sateeshperi" diff --git a/modules/nf-core/centrifuge/centrifuge/tests/main.nf.test b/modules/nf-core/centrifuge/centrifuge/tests/main.nf.test new file mode 100644 index 00000000..d83b522a --- /dev/null +++ b/modules/nf-core/centrifuge/centrifuge/tests/main.nf.test @@ -0,0 +1,106 @@ +nextflow_process { + + name "Test Process CENTRIFUGE_CENTRIFUGE" + script "../main.nf" + process "CENTRIFUGE_CENTRIFUGE" + + tag "modules" + tag "modules_nfcore" + tag "centrifuge" + tag "centrifuge/centrifuge" + tag "untar" + + setup { + run("UNTAR") { + script "../../../untar/main.nf" + process { + """ + input[0] = db = [ [], file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/minigut_cf.tar.gz', checkIfExists: true) ] + """ + } + } + } + + test("sarscov2_fastq_se") { + + when { + process { + """ + input[0] = [ [id: 'test', single_end: true], file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ] + input[1] = UNTAR.out.untar.map{ it[1] } + input[2] = true + input[3] = true + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + file(process.out.report[0][1]).name, + file(process.out.results[0][1]).name, + file(process.out.fastq_mapped[0][1][0]).name, + file(process.out.fastq_unmapped[0][1][0]).name, + ).match() } + ) + } + + } + + test("sarscov2_fastq_pe") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ] + ] + input[1] = UNTAR.out.untar.map{ it[1] } + input[2] = true + input[3] = true + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + file(process.out.report[0][1]).name, + file(process.out.results[0][1]).name, + file(process.out.fastq_mapped[0][1][0]).name, + file(process.out.fastq_unmapped[0][1][0]).name, + ).match() } + ) + } + + } + + test("sarscov2_fastq_se_stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ [id: 'test'], file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ] + input[1] = UNTAR.out.untar.map{ it[1] } + input[2] = true + input[3] = true + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/centrifuge/centrifuge/tests/main.nf.test.snap b/modules/nf-core/centrifuge/centrifuge/tests/main.nf.test.snap new file mode 100644 index 00000000..f8a2ef7b --- /dev/null +++ b/modules/nf-core/centrifuge/centrifuge/tests/main.nf.test.snap @@ -0,0 +1,125 @@ +{ + "sarscov2_fastq_se_stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.report.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test.results.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + [ + { + "id": "test" + }, + "test.sam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + [ + { + "id": "test" + }, + "test.mapped.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "4": [ + [ + { + "id": "test" + }, + "test.unmapped.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "5": [ + "versions.yml:md5,1ce028d9f968eca6df31586fe3b77c84" + ], + "fastq_mapped": [ + [ + { + "id": "test" + }, + "test.mapped.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "fastq_unmapped": [ + [ + { + "id": "test" + }, + "test.unmapped.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "report": [ + [ + { + "id": "test" + }, + "test.report.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "results": [ + [ + { + "id": "test" + }, + "test.results.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "sam": [ + [ + { + "id": "test" + }, + "test.sam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,1ce028d9f968eca6df31586fe3b77c84" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-02T07:47:36.886757827" + }, + "sarscov2_fastq_se": { + "content": [ + "test.report.txt", + "test.results.txt", + "", + "" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-02T08:22:31.470316024" + }, + "sarscov2_fastq_pe": { + "content": [ + "test.report.txt", + "test.results.txt", + "test.mapped.fastq.1.gz", + "test.unmapped.fastq.1.gz" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-02T08:22:48.866073154" + } +} \ No newline at end of file diff --git a/modules/nf-core/centrifuge/centrifuge/tests/tags.yml b/modules/nf-core/centrifuge/centrifuge/tests/tags.yml new file mode 100644 index 00000000..53444cd2 --- /dev/null +++ b/modules/nf-core/centrifuge/centrifuge/tests/tags.yml @@ -0,0 +1,2 @@ +centrifuge/centrifuge: + - "modules/nf-core/centrifuge/centrifuge/**" diff --git a/modules/nf-core/centrifuge/kreport/environment.yml b/modules/nf-core/centrifuge/kreport/environment.yml new file mode 100644 index 00000000..e50aedf2 --- /dev/null +++ b/modules/nf-core/centrifuge/kreport/environment.yml @@ -0,0 +1,7 @@ +name: centrifuge_kreport +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::centrifuge-core=1.0.4.1 diff --git a/modules/nf-core/centrifuge/kreport/main.nf b/modules/nf-core/centrifuge/kreport/main.nf index da746ca2..5d34c02d 100644 --- a/modules/nf-core/centrifuge/kreport/main.nf +++ b/modules/nf-core/centrifuge/kreport/main.nf @@ -2,18 +2,18 @@ process CENTRIFUGE_KREPORT { tag "$meta.id" label 'process_single' - conda "bioconda::centrifuge=1.0.4_beta" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/centrifuge:1.0.4_beta--h9a82719_6': - 'biocontainers/centrifuge:1.0.4_beta--h9a82719_6' }" + 'https://depot.galaxyproject.org/singularity/centrifuge-core:1.0.4.1--h43eeafb_0' : + 'biocontainers/centrifuge-core:1.0.4.1--h43eeafb_0' }" input: tuple val(meta), path(report) path db output: - tuple val(meta), path('*.txt') , emit: kreport - path "versions.yml" , emit: versions + tuple val(meta), path('*.txt'), emit: kreport + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when @@ -30,4 +30,16 @@ process CENTRIFUGE_KREPORT { centrifuge: \$( centrifuge --version | sed -n 1p | sed 's/^.*centrifuge-class version //') END_VERSIONS """ + + stub: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.txt + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + centrifuge: \$( centrifuge --version | sed -n 1p | sed 's/^.*centrifuge-class version //') + END_VERSIONS + """ } diff --git a/modules/nf-core/centrifuge/kreport/meta.yml b/modules/nf-core/centrifuge/kreport/meta.yml index 822a280e..5641152b 100644 --- a/modules/nf-core/centrifuge/kreport/meta.yml +++ b/modules/nf-core/centrifuge/kreport/meta.yml @@ -1,7 +1,12 @@ name: "centrifuge_kreport" description: Creates Kraken-style reports from centrifuge out files keywords: + - classify - metagenomics + - fastq + - db + - report + - kraken tools: - centrifuge: description: Centrifuge is a classifier for metagenomic sequences. @@ -19,7 +24,9 @@ input: type: file description: File containing the centrifuge classification report pattern: "*.{txt}" - + - db: + type: directory + description: Path to directory containing centrifuge database files output: - meta: type: map @@ -39,3 +46,6 @@ output: authors: - "@sofstam" - "@jfy133" +maintainers: + - "@sofstam" + - "@jfy133" diff --git a/modules/nf-core/centrifuge/kreport/tests/main.nf.test b/modules/nf-core/centrifuge/kreport/tests/main.nf.test new file mode 100644 index 00000000..6347bd7c --- /dev/null +++ b/modules/nf-core/centrifuge/kreport/tests/main.nf.test @@ -0,0 +1,81 @@ +// nf-core modules test centrifuge/kreport +nextflow_process { + + name "Test Process CENTRIFUGE_KREPORT" + script "../main.nf" + process "CENTRIFUGE_KREPORT" + + tag "modules" + tag "modules_nfcore" + tag "centrifuge" + tag "centrifuge/centrifuge" + tag "centrifuge/kreport" + tag "untar" + + setup { + run("UNTAR") { + script "../../../untar/main.nf" + process { + """ + input[0] = db = [ [], file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/minigut_cf.tar.gz', checkIfExists: true) ] + """ + } + } + run("CENTRIFUGE_CENTRIFUGE") { + script "../../../centrifuge/centrifuge/main.nf" + process { + """ + input[0] = [ [id: 'test', single_end: true], file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ] + input[1] = UNTAR.out.untar.map{ it[1] } + input[2] = true + input[3] = true + """ + } + } + } + + test("sarscov2_fastq_se") { + + when { + process { + """ + input[0] = CENTRIFUGE_CENTRIFUGE.out.results + input[1] = UNTAR.out.untar.map{it[1]} + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + file(process.out.kreport[0][1]).name, + ).match() } + ) + } + + } + + test("sarscov2 - bam - stub") { + + options "-stub" + + when { + process { + """ + input[0] = CENTRIFUGE_CENTRIFUGE.out.results + input[1] = UNTAR.out.untar.map{it[1]} + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/centrifuge/kreport/tests/main.nf.test.snap b/modules/nf-core/centrifuge/kreport/tests/main.nf.test.snap new file mode 100644 index 00000000..4e0aaa79 --- /dev/null +++ b/modules/nf-core/centrifuge/kreport/tests/main.nf.test.snap @@ -0,0 +1,47 @@ +{ + "sarscov2 - bam - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,43c766a19f2edf7e05d1a2a0b1816b13" + ], + "kreport": [ + [ + { + "id": "test", + "single_end": true + }, + "test.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,43c766a19f2edf7e05d1a2a0b1816b13" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-02T06:18:36.794405448" + }, + "sarscov2_fastq_se": { + "content": [ + "test.txt" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-02T06:28:20.461891873" + } +} \ No newline at end of file diff --git a/modules/nf-core/centrifuge/kreport/tests/tags.yml b/modules/nf-core/centrifuge/kreport/tests/tags.yml new file mode 100644 index 00000000..a3823d76 --- /dev/null +++ b/modules/nf-core/centrifuge/kreport/tests/tags.yml @@ -0,0 +1,2 @@ +centrifuge/kreport: + - "modules/nf-core/centrifuge/kreport/**" From 6b255deeea47cd08d6f4f4d0c96ec5c1cd00d571 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Sat, 3 Feb 2024 14:52:27 +0000 Subject: [PATCH 2/6] Update CHANGELOG --- CHANGELOG.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 7a13a7c8..2373cc5e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,10 +9,11 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#439](https://github.com/nf-core/taxprofiler/pull/439) Read deduplication with fastp (added by @maxibor) - [#440](https://github.com/nf-core/taxprofiler/pull/440) Include pre-built kaiju databases in tutorial.md (added by @Joon-Klaps) +- [#424](https://github.com/nf-core/taxprofiler/pull/424) Updated to nf-core pipeline template v2.12 (added by @sofstam) ### `Fixed` -- [#444](https://github.com/nf-core/taxprofiler/pull/440) Centrifuge uses dedicated /tmp directory to hopefully prevent mkfifo clashes (reported by @erinyoung, fix by @jfy133) +- [#444](https://github.com/nf-core/taxprofiler/pull/440) Centrifuge uses dedicated /tmp directory to hopefully prevent mkfifo clashes (❤️ to @erinyoung for reporting, fix by @jfy133) ### `Dependencies` From ba5c7c179b69df68f474dfa6bbe45528a50c4649 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Sat, 3 Feb 2024 14:52:36 +0000 Subject: [PATCH 3/6] More Changelog updates --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 2373cc5e..cba789df 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -8,7 +8,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Added` - [#439](https://github.com/nf-core/taxprofiler/pull/439) Read deduplication with fastp (added by @maxibor) -- [#440](https://github.com/nf-core/taxprofiler/pull/440) Include pre-built kaiju databases in tutorial.md (added by @Joon-Klaps) +- [#440](https://github.com/nf-core/taxprofiler/pull/440) Include mention of pre-built kaiju databases in tutorial.md (added by @Joon-Klaps) - [#424](https://github.com/nf-core/taxprofiler/pull/424) Updated to nf-core pipeline template v2.12 (added by @sofstam) ### `Fixed` From de2a4fa54dfbc8aed23aff785a1fec234392c33a Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Sat, 3 Feb 2024 16:00:05 +0100 Subject: [PATCH 4/6] Apply suggestions from code review --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index cba789df..b63941be 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -13,7 +13,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Fixed` -- [#444](https://github.com/nf-core/taxprofiler/pull/440) Centrifuge uses dedicated /tmp directory to hopefully prevent mkfifo clashes (❤️ to @erinyoung for reporting, fix by @jfy133) +- [#444](https://github.com/nf-core/taxprofiler/pull/440) Centrifuge now uses dedicated tmp directory to hopefully prevent mkfifo clashes (❤️ to @erinyoung for reporting, fix by @jfy133) ### `Dependencies` From 003bad19db1e18d4aa8884b156c0b42ad9943fff Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Mon, 5 Feb 2024 10:23:53 +0100 Subject: [PATCH 5/6] Update CHANGELOG.md Co-authored-by: Lili Andersson-Li <64467552+LilyAnderssonLee@users.noreply.github.com> --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index b63941be..707b5cfb 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -13,7 +13,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Fixed` -- [#444](https://github.com/nf-core/taxprofiler/pull/440) Centrifuge now uses dedicated tmp directory to hopefully prevent mkfifo clashes (❤️ to @erinyoung for reporting, fix by @jfy133) +- [#444](https://github.com/nf-core/taxprofiler/pull/444) Centrifuge now uses dedicated tmp directory to hopefully prevent mkfifo clashes (❤️ to @erinyoung for reporting, fix by @jfy133) ### `Dependencies` From f9aee61105eadc32b8b4ce81a776143857d9e0cd Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Mon, 5 Feb 2024 16:01:42 +0000 Subject: [PATCH 6/6] Kreport friendly container --- modules.json | 4 ++-- modules/nf-core/centrifuge/centrifuge/environment.yml | 2 +- modules/nf-core/centrifuge/centrifuge/main.nf | 4 ++-- modules/nf-core/centrifuge/kreport/environment.yml | 2 +- modules/nf-core/centrifuge/kreport/main.nf | 4 ++-- 5 files changed, 8 insertions(+), 8 deletions(-) diff --git a/modules.json b/modules.json index 44841d23..7e0ccda3 100644 --- a/modules.json +++ b/modules.json @@ -42,12 +42,12 @@ }, "centrifuge/centrifuge": { "branch": "master", - "git_sha": "32a99bba21c961f8642ddd38fcd4ea2844c10990", + "git_sha": "9a07a1293d9b818d1e06d0f7b58152f74d462012", "installed_by": ["modules"] }, "centrifuge/kreport": { "branch": "master", - "git_sha": "32a99bba21c961f8642ddd38fcd4ea2844c10990", + "git_sha": "9a07a1293d9b818d1e06d0f7b58152f74d462012", "installed_by": ["modules"] }, "custom/dumpsoftwareversions": { diff --git a/modules/nf-core/centrifuge/centrifuge/environment.yml b/modules/nf-core/centrifuge/centrifuge/environment.yml index 0de46a99..cf34dc0e 100644 --- a/modules/nf-core/centrifuge/centrifuge/environment.yml +++ b/modules/nf-core/centrifuge/centrifuge/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::centrifuge-core=1.0.4.1 + - bioconda::centrifuge=1.0.4.1 diff --git a/modules/nf-core/centrifuge/centrifuge/main.nf b/modules/nf-core/centrifuge/centrifuge/main.nf index d02cbeb8..d9a5653d 100644 --- a/modules/nf-core/centrifuge/centrifuge/main.nf +++ b/modules/nf-core/centrifuge/centrifuge/main.nf @@ -4,8 +4,8 @@ process CENTRIFUGE_CENTRIFUGE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/centrifuge-core:1.0.4.1--h43eeafb_0' : - 'biocontainers/centrifuge-core:1.0.4.1--h43eeafb_0' }" + 'https://depot.galaxyproject.org/singularity/centrifuge:1.0.4.1--hdcf5f25_1' : + 'biocontainers/centrifuge:1.0.4.1--hdcf5f25_1' }" input: tuple val(meta), path(reads) diff --git a/modules/nf-core/centrifuge/kreport/environment.yml b/modules/nf-core/centrifuge/kreport/environment.yml index e50aedf2..5c8fb451 100644 --- a/modules/nf-core/centrifuge/kreport/environment.yml +++ b/modules/nf-core/centrifuge/kreport/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::centrifuge-core=1.0.4.1 + - bioconda::centrifuge=1.0.4.1 diff --git a/modules/nf-core/centrifuge/kreport/main.nf b/modules/nf-core/centrifuge/kreport/main.nf index 5d34c02d..25eb7167 100644 --- a/modules/nf-core/centrifuge/kreport/main.nf +++ b/modules/nf-core/centrifuge/kreport/main.nf @@ -4,8 +4,8 @@ process CENTRIFUGE_KREPORT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/centrifuge-core:1.0.4.1--h43eeafb_0' : - 'biocontainers/centrifuge-core:1.0.4.1--h43eeafb_0' }" + 'https://depot.galaxyproject.org/singularity/centrifuge:1.0.4.1--hdcf5f25_1' : + 'biocontainers/centrifuge:1.0.4.1--hdcf5f25_1' }" input: tuple val(meta), path(report)