New module: plink2/extract (#1228)

* add plink2_extract

* fix test yml path

* Update modules/plink2/extract/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/plink2/extract/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* compress output

* add DOI

* make outputs less ambiguous

* update test for compressed output

* brain is dumb

* Update modules/plink2/extract/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

modules/plink2/extract/main.nf

@@ -0,0 +1,37 @@
+process PLINK2_EXTRACT {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::plink2=2.00a2.3" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/plink2:2.00a2.3--h712d239_1' :
+        'quay.io/biocontainers/plink2:2.00a2.3--h712d239_1' }"
+
+    input:
+    tuple val(meta), path(pgen), path(psam), path(pvar), path(variants)
+
+    output:
+    tuple val(meta), path("*.pgen")    , emit: extract_pgen
+    tuple val(meta), path("*.psam")    , emit: extract_psam
+    tuple val(meta), path("*.pvar.zst"), emit: extract_pvar
+    path "versions.yml"                , emit: versions
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    if( "$pgen" == "${prefix}.pgen" ) error "Input and output names are the same, use \"task.ext.prefix\" in modules.config to disambiguate!"
+    """
+    plink2 \\
+        --pfile ${pgen.baseName} \\
+        $args \\
+        --threads $task.cpus \\
+        --extract $variants \\
+        --make-pgen vzs \\
+        --out ${prefix}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        plink2: \$(plink2 --version 2>&1 | sed 's/^PLINK v//; s/ 64.*\$//' )
+    END_VERSIONS
+    """
+}

modules/plink2/extract/meta.yml

@@ -0,0 +1,64 @@
+name: plink2_extract
+description: Subset plink pfiles with a text file of variant identifiers
+keywords:
+  - plink2
+  - extract
+tools:
+  - plink2:
+      description: |
+          Whole genome association analysis toolset, designed to perform a range
+          of basic, large-scale analyses in a computationally efficient manner
+      homepage: http://www.cog-genomics.org/plink/2.0/
+      documentation: http://www.cog-genomics.org/plink/2.0/general_usage
+      tool_dev_url: None
+      doi: "10.1186/s13742-015-0047-8"
+      licence: ['GPL v3']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - pgen:
+      type: file
+      description: PLINK 2 binary genotype table
+      pattern: "*.{pgen}"
+  - psam:
+      type: file
+      description: PLINK 2 sample information file
+      pattern: "*.{psam}"
+  - pvar:
+      type: file
+      description: PLINK 2 variant information file
+      pattern: "*.{pvar}"
+  - variants:
+      type: file
+      description: A text file containing variant identifiers to keep (one per line)
+      pattern: "*.{keep}"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - extract_pgen:
+      type: file
+      description: PLINK 2 binary genotype table, containing extracted variants
+      pattern: "*.{pgen}"
+  - extract_psam:
+      type: file
+      description: PLINK 2 sample information file associated with the extracted data
+      pattern: "*.{psam}"
+  - extract_pvar:
+      type: file
+      description: PLINK 2 variant information file, containing extracted variants
+      pattern: "*.{pvar.zst}"
+
+authors:
+  - "@nebfield"

tests/config/pytest_modules.yml

@@ -1149,6 +1149,10 @@ plink/vcf:
   - modules/plink/vcf/**
   - tests/modules/plink/vcf/**
 
+plink2/extract:
+  - modules/plink2/extract/**
+  - tests/modules/plink2/extract/**
+
 plink2/vcf:
   - modules/plink2/vcf/**
   - tests/modules/plink2/vcf/**

tests/modules/plink2/extract/main.nf

@@ -0,0 +1,30 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PLINK2_VCF     } from '../../../../modules/plink2/vcf/main.nf'
+include { PLINK2_EXTRACT } from '../../../../modules/plink2/extract/main.nf'
+
+workflow test_plink2_extract {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['homo_sapiens']['genome']['syntheticvcf_short_vcf_gz'], checkIfExists: true)
+    ]
+    PLINK2_VCF ( input )
+
+    PLINK2_VCF.out.pvar
+        .splitText(file: 'variants.keep', keepHeader: false, by: 10)
+        .last()
+        .set { ch_variants }
+
+    ch_variants.view()
+
+    PLINK2_VCF.out.pgen
+        .concat(PLINK2_VCF.out.psam, PLINK2_VCF.out.pvar.concat(ch_variants))
+        .groupTuple()
+        .map{ meta, paths -> [meta, paths[0], paths[1], paths[2], paths[3]] }
+        .set { ch_extract }
+
+    PLINK2_EXTRACT ( ch_extract )
+}

tests/modules/plink2/extract/nextflow.config

@@ -0,0 +1,12 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+    withName: PLINK2_VCF {
+        ext.args = '--make-pgen --set-missing-var-ids @:#:\\$1:\\$2'
+    }
+
+    withName: PLINK2_EXTRACT {
+        ext.prefix = { "${meta.id}.extract" }
+    }
+}

tests/modules/plink2/extract/test.yml

@@ -0,0 +1,20 @@
+- name: plink2 extract test_plink2_extract
+  command: nextflow run tests/modules/plink2/extract -entry test_plink2_extract -c tests/config/nextflow.config
+  tags:
+    - plink2/extract
+    - plink2
+  files:
+    - path: output/plink2/test.extract.pgen
+      md5sum: 785e729a293ecabb0d39394865316bda
+    - path: output/plink2/test.extract.psam
+      md5sum: e6c714488754cb8448c3dfda08c4c0ea
+    - path: output/plink2/test.extract.pvar.zst
+      md5sum: 076767e6695e681115eabb924a447ee9
+    - path: output/plink2/test.pgen
+      md5sum: fac12ca9041d6950f6b7d60ac2120721
+    - path: output/plink2/test.psam
+      md5sum: e6c714488754cb8448c3dfda08c4c0ea
+    - path: output/plink2/test.pvar
+      md5sum: ff9e44f8e5f4035d8cf2bfe7be6755b3
+    - path: output/plink2/versions.yml
+      md5sum: c477b7c9f6e39b89710fe1a0bceee50d