From 53136987053e22197dbcde0ba27995f08904bf58 Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Sat, 13 Feb 2021 00:08:57 +0100 Subject: [PATCH] Add bcftools merge module --- .github/filters.yml | 4 ++ software/bcftools/merge/functions.nf | 60 ++++++++++++++++++++++ software/bcftools/merge/main.nf | 37 ++++++++++++++ software/bcftools/merge/meta.yml | 67 +++++++++++++++++++++++++ tests/data/vcf/test_a.merge.vcf.gz | Bin 0 -> 763 bytes tests/data/vcf/test_a.merge.vcf.gz.tbi | Bin 0 -> 141 bytes tests/data/vcf/test_b.merge.vcf.gz | Bin 0 -> 769 bytes tests/data/vcf/test_b.merge.vcf.gz.tbi | Bin 0 -> 141 bytes tests/software/bcftools/merge/main.nf | 18 +++++++ tests/software/bcftools/merge/test.yml | 8 +++ 10 files changed, 194 insertions(+) create mode 100644 software/bcftools/merge/functions.nf create mode 100644 software/bcftools/merge/main.nf create mode 100644 software/bcftools/merge/meta.yml create mode 100644 tests/data/vcf/test_a.merge.vcf.gz create mode 100644 tests/data/vcf/test_a.merge.vcf.gz.tbi create mode 100644 tests/data/vcf/test_b.merge.vcf.gz create mode 100644 tests/data/vcf/test_b.merge.vcf.gz.tbi create mode 100644 tests/software/bcftools/merge/main.nf create mode 100644 tests/software/bcftools/merge/test.yml diff --git a/.github/filters.yml b/.github/filters.yml index f63a162d..a88c933c 100644 --- a/.github/filters.yml +++ b/.github/filters.yml @@ -18,6 +18,10 @@ bcftools_isec: - software/bcftools/isec/** - tests/software/bcftools/isec/** +bcftools_merge: + - software/bcftools/merge/** + - tests/software/bcftools/merge/** + bcftools_stats: - software/bcftools/stats/** - tests/software/bcftools/stats/** diff --git a/software/bcftools/merge/functions.nf b/software/bcftools/merge/functions.nf new file mode 100644 index 00000000..6f3b4b29 --- /dev/null +++ b/software/bcftools/merge/functions.nf @@ -0,0 +1,60 @@ + +/* + * ----------------------------------------------------- + * Utility functions used in nf-core DSL2 module files + * ----------------------------------------------------- + */ + +/* + * Extract name of software tool from process name using $task.process + */ +def getSoftwareName(task_process) { + return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() +} + +/* + * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules + */ +def initOptions(Map args) { + def Map options = [:] + options.args = args.args ?: '' + options.args2 = args.args2 ?: '' + options.publish_by_id = args.publish_by_id ?: false + options.publish_dir = args.publish_dir ?: '' + options.publish_files = args.publish_files + options.suffix = args.suffix ?: '' + return options +} + +/* + * Tidy up and join elements of a list to return a path string + */ +def getPathFromList(path_list) { + def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries + paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", '') } // Trim whitespace and trailing slashes + return paths.join('/') +} + +/* + * Function to save/publish module results + */ +def saveFiles(Map args) { + if (!args.filename.endsWith('.version.txt')) { + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + if (ioptions.publish_by_id) { + path_list.add(args.publish_id) + } + if (ioptions.publish_files instanceof Map) { + for (ext in ioptions.publish_files) { + if (args.filename.endsWith(ext.key)) { + def ext_list = path_list.collect() + ext_list.add(ext.value) + return "${getPathFromList(ext_list)}/$args.filename" + } + } + } else if (ioptions.publish_files == null) { + return "${getPathFromList(path_list)}/$args.filename" + } + } +} diff --git a/software/bcftools/merge/main.nf b/software/bcftools/merge/main.nf new file mode 100644 index 00000000..e345c475 --- /dev/null +++ b/software/bcftools/merge/main.nf @@ -0,0 +1,37 @@ +// Import generic module functions +include { initOptions; saveFiles; getSoftwareName } from './functions' + +params.options = [:] +def options = initOptions(params.options) + +process BCFTOOLS_MERGE { + tag "$meta.id" + publishDir "${params.outdir}", + mode: params.publish_dir_mode, + saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } + + conda (params.enable_conda ? "bioconda::bcftools=1.11=h7c999a4_0" : null) + if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { + container "https://depot.galaxyproject.org/singularity/bcftools:1.11--h7c999a4_0" + } else { + container "quay.io/biocontainers/bcftools:1.11--h7c999a4_0" + } + + input: + tuple val(meta), path(vcfs), path(tbis) + + output: + tuple val(meta), path("*.gz"), emit: vcf + path "*.version.txt" , emit: version + + script: + def software = getSoftwareName(task.process) + prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" + """ + bcftools merge -Oz\\ + --output ${prefix}.vcf.gz \\ + $options.args \\ + *.vcf.gz + echo \$(bcftools --version 2>&1) | sed 's/^.*bcftools //; s/ .*\$//' > ${software}.version.txt + """ +} diff --git a/software/bcftools/merge/meta.yml b/software/bcftools/merge/meta.yml new file mode 100644 index 00000000..dff0523b --- /dev/null +++ b/software/bcftools/merge/meta.yml @@ -0,0 +1,67 @@ +name: bcftools_merge +description: Merge VCF files +keywords: + - variant calling + - merge + - VCF +tools: + - isec: + description: | + Merge VCF files. + homepage: http://samtools.github.io/bcftools/bcftools.html + documentation: http://www.htslib.org/doc/bcftools.html + doi: 10.1093/bioinformatics/btp352 +params: + - outdir: + type: string + description: | + The pipeline's output directory. By default, the module will + output files into `$params.outdir/` + - publish_dir_mode: + type: string + description: | + Value for the Nextflow `publishDir` mode parameter. + Available: symlink, rellink, link, copy, copyNoFollow, move. + - enable_conda: + type: boolean + description: | + Run the module with Conda using the software specified + via the `conda` directive + - singularity_pull_docker_container: + type: boolean + description: | + Instead of directly downloading Singularity images for use with Singularity, + force the workflow to pull and convert Docker containers instead. +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcfs: + type: files + description: | + List containing 2 or more vcf files + e.g. [ 'file1.vcf', 'file2.vcf' ] + - tbis: + type: files + description: | + List containing the tbi index files corresponding to the vcfs input files + e.g. [ 'file1.vcf.tbi', 'file2.vcf.tbi' ] +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: VCF merged output file + pattern: "*.{vcf.gz}" + - version: + type: file + description: File containing software version + pattern: "*.{version.txt}" +authors: + - "@joseespinosa" + - "@drpatelh" diff --git a/tests/data/vcf/test_a.merge.vcf.gz b/tests/data/vcf/test_a.merge.vcf.gz new file mode 100644 index 0000000000000000000000000000000000000000..7ab659d78f2160ed965fd0ef136a501a1d1047b8 GIT binary patch literal 763 zcmVNEnvctRr>;HdFK00xu!og0*h zBfz~3puwkv$1u#Z3^R!78ZH|`inoL<8>(OSsyCC;RYJvpGA@_P#^WyMLM~fF1$11I zH?^yH>@)E+VVp$qm&YAW6aEYfviTx*=?NEWxWbGuO$`-fPYOmfh*N%?ml4YTVY1ZM zcV$@L)&(!b`cH!x5}I={`NllERJ%@1Nilq4yL`K~p4wk>4JR+AlDU?3UDNiD$M;c~~ zWUKVqSy|UwN@&Dm$Fy(Ew$U+BO>O>@+Im-wZoV3(Xg16>bjop7%zw}mWz29BcrWvi~J7>InyKbpbLYZ;e_5FM)i1?VR|p7?)TPpYl9ib zii_77aa`42`nRgRt`E0&Nx8adN>U;UZ$~*yD2xv0%ub8V9ba^LjW1q|GUpHfm%5)u-ak|cPUP6bFEF;7WgG;CGWii%J)+Lj}5 zD_h7#)MrlPL%SOSd~6{Hn6K8);0=|P4v|Td^ZCayY3AZD8n#~jmll8dup}|nexu1E bzD5Ry_x#Hq9b;o)kVmsnnt>T?KZpPT-=Zl6 literal 0 HcmV?d00001 diff --git a/tests/data/vcf/test_b.merge.vcf.gz b/tests/data/vcf/test_b.merge.vcf.gz new file mode 100644 index 0000000000000000000000000000000000000000..751f5a66d4cf4df0039d538b18e2dc58fe1fd97a GIT binary patch literal 769 zcmV+c1OEIUiwFb&00000{{{d;LjnNg0;QB)bD}U5hOg6Kki5ySadTyzi5fa1PDpI!@?1%TprkUv6(_weVH5IT-cE z_P2p&`}cDnjkf8M<~BzD>xS9`CTK`=#PSf9kxgi#zu*Uwv$#Nrj^bbT#v>4oGgxFno%R7~Y`M{`aQB#Ahzs|eM2zgX() zx6-d)>s;jW{KrA`Da(Xh{9vA5@=Yo?oR){EQ@qI~lo=%}=+TXcK14CB{Qc73OEMzP z#4wDXXc9+Rwkk1$p?^OsFwa;&_UyxjOPXXa5bJe={IKG5^2l5kG%xf)#zY(zdW;C? zG+idI_R_pT31y*(Y{R-W+Iq*pHMQ|qYV)KT-+s{z!!q@n+B&1gxNR9X9i^68MRUpm zYOBKRYMPd8xyY#|k4r=lVZE(w^6WPa1lL0Rq)CI8l9)a2XSHaX680#U9(U$VYfZQy z1(&Q+YCA=H8{ZY}eSJ9YCFSZQ2~DUhye$(jW-#1;XMS94&gi0_MVCcu0mkFBQv)^xULIK z>-6ptQ*A8G@47XHfBpcUB8<1&`yT{Whycj6KLtVhg&1QW398+yt}yx@GXyQI)y2p{ z9b}+3GJzVI$hi6g6%Y)lk_P|)ABzYC000000RIL6LPG)o8vp|U0000000000aJOu- literal 0 HcmV?d00001 diff --git a/tests/data/vcf/test_b.merge.vcf.gz.tbi b/tests/data/vcf/test_b.merge.vcf.gz.tbi new file mode 100644 index 0000000000000000000000000000000000000000..eadd6a4d3cbef55b424d2b57c6b8042adb39f394 GIT binary patch literal 141 zcmb2|=3rp}f&Xj_PR>jW1q|GUpHfm%5)u-ak|cPUP6bFEF;7WgG;CGWii%J)x|Snw zD_h7#)MrlPL(Llkd~6{Hn6K7%@P^7thsdPK`TXOUG;{G64O_4NON+mJSdy4(ztLn7 bUn2v(&A<${A4C8E-e)NC literal 0 HcmV?d00001 diff --git a/tests/software/bcftools/merge/main.nf b/tests/software/bcftools/merge/main.nf new file mode 100644 index 00000000..d9fe395d --- /dev/null +++ b/tests/software/bcftools/merge/main.nf @@ -0,0 +1,18 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +//keep --no-verson argument, otherwise md5 will change on each execution +include { BCFTOOLS_MERGE } from '../../../../software/bcftools/merge/main.nf' addParams( options: ['args': '--force-samples --no-version'] ) + +workflow test_bcftools_merge { + + def input = [] + input = [ [ id:'test' ], // meta map + [ file("${launchDir}/tests/data/vcf/test_a.merge.vcf.gz", checkIfExists: true), + file("${launchDir}/tests/data/vcf/test_b.merge.vcf.gz", checkIfExists: true) ], + [ file("${launchDir}/tests/data/vcf/test_a.merge.vcf.gz.tbi", checkIfExists: true), + file("${launchDir}/tests/data/vcf/test_b.merge.vcf.gz.tbi", checkIfExists: true) ]] + + BCFTOOLS_MERGE ( input ) +} diff --git a/tests/software/bcftools/merge/test.yml b/tests/software/bcftools/merge/test.yml new file mode 100644 index 00000000..471ea52b --- /dev/null +++ b/tests/software/bcftools/merge/test.yml @@ -0,0 +1,8 @@ +- name: bcftools merge + command: nextflow run ./tests/software/bcftools/merge -entry test_bcftools_merge -c tests/config/nextflow.config + tags: + - bcftools + - bcftools_merge + files: + - path: output/bcftools/test.vcf.gz + md5sum: 23eee1acfd99581889be3fd2b86b6950