From 5fccf3e0e066ba0923d17bd280e69b35e72d06a1 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 7 Jan 2025 15:42:05 +0100 Subject: [PATCH 1/2] update CHANGELOG --- CHANGELOG.md | 17 ++ README.md | 2 +- assets/schema_input.json | 2 +- assets/test/default_extended.yml | 5 + modules.json | 5 + .../nf-core/tabix/bgziptabix/environment.yml | 7 + modules/nf-core/tabix/bgziptabix/main.nf | 48 ++++ modules/nf-core/tabix/bgziptabix/meta.yml | 65 ++++++ .../tabix/bgziptabix/tests/main.nf.test | 123 +++++++++++ .../tabix/bgziptabix/tests/main.nf.test.snap | 206 ++++++++++++++++++ .../tabix/bgziptabix/tests/tabix_csi.config | 5 + .../tabix/bgziptabix/tests/tabix_tbi.config | 5 + .../nf-core/tabix/bgziptabix/tests/tags.yml | 2 + subworkflows/local/asset_to_channel/main.nf | 3 +- subworkflows/local/index_vcf/main.nf | 17 +- tests/tabix.nf.test.snap | 20 +- 16 files changed, 519 insertions(+), 13 deletions(-) create mode 100644 modules/nf-core/tabix/bgziptabix/environment.yml create mode 100644 modules/nf-core/tabix/bgziptabix/main.nf create mode 100644 modules/nf-core/tabix/bgziptabix/meta.yml create mode 100644 modules/nf-core/tabix/bgziptabix/tests/main.nf.test create mode 100644 modules/nf-core/tabix/bgziptabix/tests/main.nf.test.snap create mode 100644 modules/nf-core/tabix/bgziptabix/tests/tabix_csi.config create mode 100644 modules/nf-core/tabix/bgziptabix/tests/tabix_tbi.config create mode 100644 modules/nf-core/tabix/bgziptabix/tests/tags.yml diff --git a/CHANGELOG.md b/CHANGELOG.md index 3db72b41..d1a6ef91 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,22 @@ 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). +## dev + +### Added + +- [71](https://github.com/nf-core/references/pull/71) - Compress vcf files when they are not already compressed + +### Changed + +### Fixed + +### Dependencies + +### Subworkflows + +### Deprecated + ## [0.1](https://github.com/nf-core/references/releases/tag/0.1) - Tar Tarasque Initial pre-release of nf-core/references, created with the [nf-core](https://nf-co.re/) template. @@ -60,6 +76,7 @@ Tar is a dark grey color ( #383838), and the Tarasque is a legendary dragon from - [64](https://github.com/nf-core/references/pull/64) - Improve documentation - [68](https://github.com/nf-core/references/pull/68) - Minor refactoring - [69](https://github.com/nf-core/references/pull/69) - Better comments +- [70](https://github.com/nf-core/references/pull/70) - Prepare release 0.1 ### Fixed diff --git a/README.md b/README.md index cb5af672..92156e97 100644 --- a/README.md +++ b/README.md @@ -47,7 +47,7 @@ With an additional annotation file describing the genes (either GFF3 or GTF), it - STAR index - Transcript fasta (with RSEM) -With a vcf file, it will tabix index it. +With a vcf file, it will compress it, if it was not already compressed, and tabix index it. ## Assets diff --git a/assets/schema_input.json b/assets/schema_input.json index be1c72c2..51010acc 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -191,7 +191,7 @@ "vcf": { "meta": ["vcf"], "type": "string", - "pattern": "^\\S+\\.vcf\\.gz$", + "pattern": "^\\S+\\.vcf(\\.gz)?$", "errorMessage": "VCF file, cannot contain spaces" }, "vcf_tbi": { diff --git a/assets/test/default_extended.yml b/assets/test/default_extended.yml index 9bab46af..1c3b96d0 100644 --- a/assets/test/default_extended.yml +++ b/assets/test/default_extended.yml @@ -25,3 +25,8 @@ source_vcf: "GATK_BUNDLE" species: "Homo_sapiens" vcf: "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz" +- genome: "GRCh38_MT" + source: "nf-core/references" + source_vcf: "genmod_compound" + species: "Homo_sapiens" + vcf: "https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/modules/data/genomics/homo_sapiens/genome/vcf/genmod_compound.vcf" diff --git a/modules.json b/modules.json index 5eec101b..1bda0e85 100644 --- a/modules.json +++ b/modules.json @@ -117,6 +117,11 @@ "installed_by": ["modules"], "patch": "modules/nf-core/star/genomegenerate/star-genomegenerate.diff" }, + "tabix/bgziptabix": { + "branch": "master", + "git_sha": "f448e846bdadd80fc8be31fbbc78d9f5b5131a45", + "installed_by": ["modules"] + }, "tabix/tabix": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", diff --git a/modules/nf-core/tabix/bgziptabix/environment.yml b/modules/nf-core/tabix/bgziptabix/environment.yml new file mode 100644 index 00000000..017c259d --- /dev/null +++ b/modules/nf-core/tabix/bgziptabix/environment.yml @@ -0,0 +1,7 @@ +channels: + - conda-forge + - bioconda + +dependencies: + - bioconda::htslib=1.20 + - bioconda::tabix=1.11 diff --git a/modules/nf-core/tabix/bgziptabix/main.nf b/modules/nf-core/tabix/bgziptabix/main.nf new file mode 100644 index 00000000..22f37a77 --- /dev/null +++ b/modules/nf-core/tabix/bgziptabix/main.nf @@ -0,0 +1,48 @@ +process TABIX_BGZIPTABIX { + tag "$meta.id" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/htslib:1.20--h5efdd21_2' : + 'biocontainers/htslib:1.20--h5efdd21_2' }" + + input: + tuple val(meta), path(input) + + output: + tuple val(meta), path("*.gz"), path("*.tbi"), optional: true, emit: gz_tbi + tuple val(meta), path("*.gz"), path("*.csi"), optional: true, emit: gz_csi + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def args2 = task.ext.args2 ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + bgzip --threads ${task.cpus} -c $args $input > ${prefix}.${input.getExtension()}.gz + tabix --threads ${task.cpus} $args2 ${prefix}.${input.getExtension()}.gz + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//') + END_VERSIONS + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + def args2 = task.ext.args2 ?: '' + def index = args2.contains("-C ") || args2.contains("--csi") ? "csi" : "tbi" + """ + echo "" | gzip > ${prefix}.${input.getExtension()}.gz + touch ${prefix}.${input.getExtension()}.gz.${index} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//') + END_VERSIONS + """ +} diff --git a/modules/nf-core/tabix/bgziptabix/meta.yml b/modules/nf-core/tabix/bgziptabix/meta.yml new file mode 100644 index 00000000..806fbc12 --- /dev/null +++ b/modules/nf-core/tabix/bgziptabix/meta.yml @@ -0,0 +1,65 @@ +name: tabix_bgziptabix +description: bgzip a sorted tab-delimited genome file and then create tabix index +keywords: + - bgzip + - compress + - index + - tabix + - vcf +tools: + - tabix: + description: Generic indexer for TAB-delimited genome position files. + homepage: https://www.htslib.org/doc/tabix.html + documentation: https://www.htslib.org/doc/tabix.1.html + doi: 10.1093/bioinformatics/btq671 + licence: ["MIT"] + identifier: biotools:tabix +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: Sorted tab-delimited genome file +output: + - gz_tbi: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.gz": + type: file + description: bgzipped tab-delimited genome file + pattern: "*.gz" + - "*.tbi": + type: file + description: tabix index file + pattern: "*.tbi" + - gz_csi: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.gz": + type: file + description: bgzipped tab-delimited genome file + pattern: "*.gz" + - "*.csi": + type: file + description: csi index file + pattern: "*.csi" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@maxulysse" + - "@DLBPointon" +maintainers: + - "@maxulysse" + - "@DLBPointon" diff --git a/modules/nf-core/tabix/bgziptabix/tests/main.nf.test b/modules/nf-core/tabix/bgziptabix/tests/main.nf.test new file mode 100644 index 00000000..4d4130dc --- /dev/null +++ b/modules/nf-core/tabix/bgziptabix/tests/main.nf.test @@ -0,0 +1,123 @@ +nextflow_process { + + name "Test Process TABIX_BGZIPTABIX" + script "modules/nf-core/tabix/bgziptabix/main.nf" + process "TABIX_BGZIPTABIX" + + tag "modules" + tag "modules_nfcore" + tag "tabix" + tag "tabix/bgziptabix" + + test("sarscov2_bed_tbi") { + config "./tabix_tbi.config" + + when { + process { + """ + input[0] = [ + [ id:'tbi_test' ], + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert snapshot( + file(process.out.gz_tbi[0][1]).name + ).match("tbi_test") + } + ) + } + } + + test("sarscov2_bed_csi") { + config "./tabix_csi.config" + + when { + process { + """ + input[0] = [ + [ id:'csi_test' ], + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert snapshot( + file(process.out.gz_csi[0][1]).name + ).match("csi_test") + } + ) + } + + } + + test("sarscov2_bed_csi_stub") { + config "./tabix_csi.config" + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert snapshot( + file(process.out.gz_csi[0][1]).name + ).match("csi_stub") + } + ) + } + + } + + test("sarscov2_bed_tbi_stub") { + config "./tabix_tbi.config" + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert snapshot( + file(process.out.gz_tbi[0][1]).name + ).match("tbi_stub") + } + ) + } + + } + +} diff --git a/modules/nf-core/tabix/bgziptabix/tests/main.nf.test.snap b/modules/nf-core/tabix/bgziptabix/tests/main.nf.test.snap new file mode 100644 index 00000000..fb87799b --- /dev/null +++ b/modules/nf-core/tabix/bgziptabix/tests/main.nf.test.snap @@ -0,0 +1,206 @@ +{ + "sarscov2_bed_tbi": { + "content": [ + { + "0": [ + [ + { + "id": "tbi_test" + }, + "tbi_test.bed.gz:md5,fe4053cf4de3aebbdfc3be2efb125a74", + "tbi_test.bed.gz.tbi:md5,ca06caf88b1e3c67d5fcba0a1460b52c" + ] + ], + "1": [ + + ], + "2": [ + "versions.yml:md5,736e7c3b16a3ac525253e5b5f5d8fdfa" + ], + "gz_csi": [ + + ], + "gz_tbi": [ + [ + { + "id": "tbi_test" + }, + "tbi_test.bed.gz:md5,fe4053cf4de3aebbdfc3be2efb125a74", + "tbi_test.bed.gz.tbi:md5,ca06caf88b1e3c67d5fcba0a1460b52c" + ] + ], + "versions": [ + "versions.yml:md5,736e7c3b16a3ac525253e5b5f5d8fdfa" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-19T11:29:16.053817543" + }, + "sarscov2_bed_csi": { + "content": [ + { + "0": [ + + ], + "1": [ + [ + { + "id": "csi_test" + }, + "csi_test.bed.gz:md5,fe4053cf4de3aebbdfc3be2efb125a74", + "csi_test.bed.gz.csi:md5,c9c0377de58fdc89672bb3005a0d69f5" + ] + ], + "2": [ + "versions.yml:md5,736e7c3b16a3ac525253e5b5f5d8fdfa" + ], + "gz_csi": [ + [ + { + "id": "csi_test" + }, + "csi_test.bed.gz:md5,fe4053cf4de3aebbdfc3be2efb125a74", + "csi_test.bed.gz.csi:md5,c9c0377de58fdc89672bb3005a0d69f5" + ] + ], + "gz_tbi": [ + + ], + "versions": [ + "versions.yml:md5,736e7c3b16a3ac525253e5b5f5d8fdfa" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-19T11:29:27.667745444" + }, + "csi_test": { + "content": [ + "csi_test.bed.gz" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-02-19T14:51:00.548801" + }, + "sarscov2_bed_tbi_stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + + ], + "2": [ + "versions.yml:md5,736e7c3b16a3ac525253e5b5f5d8fdfa" + ], + "gz_csi": [ + + ], + "gz_tbi": [ + [ + { + "id": "test" + }, + "test.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,736e7c3b16a3ac525253e5b5f5d8fdfa" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-25T14:45:18.533169949" + }, + "csi_stub": { + "content": [ + "test.bed.gz" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-02-19T14:51:09.218454" + }, + "tbi_stub": { + "content": [ + "test.bed.gz" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-25T14:45:18.550930179" + }, + "tbi_test": { + "content": [ + "tbi_test.bed.gz" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-02-19T14:50:51.579654" + }, + "sarscov2_bed_csi_stub": { + "content": [ + { + "0": [ + + ], + "1": [ + [ + { + "id": "test" + }, + "test.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,736e7c3b16a3ac525253e5b5f5d8fdfa" + ], + "gz_csi": [ + [ + { + "id": "test" + }, + "test.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "gz_tbi": [ + + ], + "versions": [ + "versions.yml:md5,736e7c3b16a3ac525253e5b5f5d8fdfa" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-25T14:44:19.786135972" + } +} \ No newline at end of file diff --git a/modules/nf-core/tabix/bgziptabix/tests/tabix_csi.config b/modules/nf-core/tabix/bgziptabix/tests/tabix_csi.config new file mode 100644 index 00000000..fb41a314 --- /dev/null +++ b/modules/nf-core/tabix/bgziptabix/tests/tabix_csi.config @@ -0,0 +1,5 @@ +process { + withName: TABIX_BGZIPTABIX { + ext.args2 = '-p vcf --csi' + } +} diff --git a/modules/nf-core/tabix/bgziptabix/tests/tabix_tbi.config b/modules/nf-core/tabix/bgziptabix/tests/tabix_tbi.config new file mode 100644 index 00000000..c1915dc4 --- /dev/null +++ b/modules/nf-core/tabix/bgziptabix/tests/tabix_tbi.config @@ -0,0 +1,5 @@ +process { + withName: TABIX_BGZIPTABIX { + ext.args2 = '-p vcf' + } +} \ No newline at end of file diff --git a/modules/nf-core/tabix/bgziptabix/tests/tags.yml b/modules/nf-core/tabix/bgziptabix/tests/tags.yml new file mode 100644 index 00000000..5052b4d7 --- /dev/null +++ b/modules/nf-core/tabix/bgziptabix/tests/tags.yml @@ -0,0 +1,2 @@ +tabix/bgziptabix: + - "modules/nf-core/tabix/bgziptabix/**" diff --git a/subworkflows/local/asset_to_channel/main.nf b/subworkflows/local/asset_to_channel/main.nf index 339bd4ec..7dce3096 100644 --- a/subworkflows/local/asset_to_channel/main.nf +++ b/subworkflows/local/asset_to_channel/main.nf @@ -143,7 +143,8 @@ workflow ASSET_TO_CHANNEL { vcf_branch = asset.branch { meta, _fasta -> file: meta.vcf // If we already have the vcf_tbi, then we don't need to index the vcf - def meta_extra = [run_tabix: meta.vcf_tbi ? false : true] + def meta_extra = [run_tabix: meta.vcf_tbi || meta.vcf.endsWith('.vcf') ? false : true] + meta_extra += [compress_vcf: meta.vcf.endsWith('.vcf') ?: false] // return a file, because we can catch globs this way, but it create issues with publishing return [reduce(meta) + meta_extra, file(meta.vcf)] other: true diff --git a/subworkflows/local/index_vcf/main.nf b/subworkflows/local/index_vcf/main.nf index cbabffc3..926c78b9 100644 --- a/subworkflows/local/index_vcf/main.nf +++ b/subworkflows/local/index_vcf/main.nf @@ -1,4 +1,5 @@ -include { TABIX_TABIX } from '../../../modules/nf-core/tabix/tabix' +include { TABIX_BGZIPTABIX } from '../../../modules/nf-core/tabix/bgziptabix' +include { TABIX_TABIX } from '../../../modules/nf-core/tabix/tabix' workflow INDEX_VCF { take: @@ -6,21 +7,29 @@ workflow INDEX_VCF { run_tabix // boolean: true/false main: + vcf_gz = Channel.empty() vcf_tbi = Channel.empty() versions = Channel.empty() - if (run_tabix) { // Do not run TABIX_TABIX if the condition is false vcf_tabix = vcf.map { meta, vcf_ -> meta.run_tabix ? [meta, vcf_] : null } + // Do not run TABIX_BGZIPTABIX if the condition is false + vcf_bgziptabix = vcf.map { meta, vcf_ -> meta.compress_vcf ? [meta, vcf_] : null } + + TABIX_BGZIPTABIX(vcf_bgziptabix) TABIX_TABIX(vcf_tabix) - vcf_tbi = TABIX_TABIX.out.tbi + vcf_gz = TABIX_BGZIPTABIX.out.gz_tbi.map { meta, vcf_gz_, _vcf_tbi -> [meta, vcf_gz_] } + vcf_tbi = TABIX_TABIX.out.tbi.mix(TABIX_BGZIPTABIX.out.gz_tbi.map { meta, _vcf_gz, vcf_tbi_ -> [meta, vcf_tbi_] }) + + versions = versions.mix(TABIX_BGZIPTABIX.out.versions) versions = versions.mix(TABIX_TABIX.out.versions) } emit: - vcf_tbi // channel: [meta, *.vcf.tbi] + vcf_gz // channel: [meta, *.vcf.gz] + vcf_tbi // channel: [meta, *.vcf.gz.tbi] versions // channel: [versions.yml] } diff --git a/tests/tabix.nf.test.snap b/tests/tabix.nf.test.snap index f65f95b9..3f64971a 100644 --- a/tests/tabix.nf.test.snap +++ b/tests/tabix.nf.test.snap @@ -26,14 +26,17 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.2" + "nextflow": "24.10.3" }, - "timestamp": "2024-12-10T12:44:36.213381921" + "timestamp": "2025-01-07T15:37:06.912762838" }, "Run with profile test with tabix | --input assets/test/default_extended.yml": { "content": [ - 4, + 5, { + "TABIX_BGZIPTABIX": { + "tabix": 1.2 + }, "TABIX_TABIX": { "tabix": 1.2 }, @@ -45,6 +48,10 @@ "Homo_sapiens", "Homo_sapiens/nf-core", "Homo_sapiens/nf-core/references", + "Homo_sapiens/nf-core/references/GRCh38_MT", + "Homo_sapiens/nf-core/references/GRCh38_MT/Annotation", + "Homo_sapiens/nf-core/references/GRCh38_MT/Annotation/genmod_compound", + "Homo_sapiens/nf-core/references/GRCh38_MT/Annotation/genmod_compound/GRCh38_MT.vcf.gz.tbi", "Homo_sapiens/nf-core/references/GRCh38_chr21", "Homo_sapiens/nf-core/references/GRCh38_chr21/Annotation", "Homo_sapiens/nf-core/references/GRCh38_chr21/Annotation/GATK_BUNDLE", @@ -64,6 +71,7 @@ "pipeline_info/nf_core_references_software_mqc_versions.yml" ], [ + "GRCh38_MT.vcf.gz.tbi:md5,2473d74262eddbb8ab7bceaa74f23c50", "dbsnp_146.hg38.vcf.gz.tbi:md5,628232d0c870f2dbf73c3e81aff7b4b4", "gnomAD.r2.1.1.vcf.gz.tbi:md5,d95bc4bd1eee441d13ed99f0f3d501f8", "mills_and_1000G.indels.vcf.gz.tbi:md5,1bb7ab8f22eb798efd796439d3b29b7a", @@ -72,8 +80,8 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.2" + "nextflow": "24.10.3" }, - "timestamp": "2024-12-02T11:21:55.801035083" + "timestamp": "2025-01-07T15:33:47.912344456" } -} +} \ No newline at end of file From cc96c889058e2453cbdd1807f2aa955aaf4d1d3d Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 7 Jan 2025 15:44:29 +0100 Subject: [PATCH 2/2] fix PR number --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index d1a6ef91..c808d607 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,7 +7,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Added -- [71](https://github.com/nf-core/references/pull/71) - Compress vcf files when they are not already compressed +- [72](https://github.com/nf-core/references/pull/72) - Compress vcf files when they are not already compressed ### Changed