Added new module snpsift/split (#1031)

* added new module snpsift/split

* added options.args

* added .vcf.gz to input

* removed test and updated to new NF DSL2 syntax

* Updated to new NF DSL2 syntax

* added option to join vcf files

Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>

modules/snpsift/split/main.nf

@@ -0,0 +1,48 @@
+process SNPSIFT_SPLIT {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::snpsift=4.3.1t" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/snpsift:4.3.1t--hdfd78af_3' :
+        'quay.io/biocontainers/snpsift:4.3.1t--hdfd78af_3' }"
+
+    input:
+    tuple val(meta), path(vcf)
+
+    output:
+    tuple val(meta), path("*.vcf"), emit: out_vcfs
+    path "versions.yml"           , emit: versions
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    if (meta.split) {
+        """
+        SnpSift \\
+            split \\
+            $args \\
+            $vcf
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            snpsift: \$( echo \$(SnpSift split -h 2>&1) | sed 's/^.*version //' | sed 's/(.*//' | sed 's/t//g' )
+        END_VERSIONS
+        """
+    } else {
+        """
+        SnpSift \\
+            split \\
+            -j \\
+            $args \\
+            $vcf \\
+            > ${prefix}.joined.vcf
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            snpsift: \$( echo \$(SnpSift split -h 2>&1) | sed 's/^.*version //' | sed 's/(.*//' | sed 's/t//g' )
+        END_VERSIONS
+        """
+    }
+
+}

modules/snpsift/split/meta.yml

@@ -0,0 +1,44 @@
+name: snpsift_split
+description: Splits/Joins VCF(s) file into chromosomes
+keywords:
+  - split
+  - join
+  - vcf
+tools:
+  - snpsift:
+      description: SnpSift is a toolbox that allows you to filter and manipulate annotated files
+      homepage: https://pcingola.github.io/SnpEff/ss_introduction/
+      documentation: https://pcingola.github.io/SnpEff/ss_introduction/
+      tool_dev_url: https://github.com/pcingola/SnpEff
+      doi: "10.3389/fgene.2012.00035"
+      licence: ['MIT']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - vcf:
+      type: file (split) or list of files (join)
+      description: VCF file(s)
+      pattern: "*.{vcf,vcf.gz}"
+
+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"
+  - out_vcfs:
+      type: file
+      description: Split/Joined VCF file(s)
+      pattern: "*.vcf"
+
+authors:
+  - "@SusiJo"
+  - "@jonasscheid"

tests/config/pytest_modules.yml

@@ -1337,6 +1337,10 @@ snpeff:
   - modules/snpeff/**
   - tests/modules/snpeff/**
 
+snpsift/split:
+  - modules/snpsift/split/**
+  - tests/modules/snpsift/split/**
+
 snpsites:
   - modules/snpsites/**
   - tests/modules/snpsites/**

tests/config/test_data.config

@@ -250,6 +250,8 @@ params {
 
                 cutandrun_bedgraph_test_1                     = "${test_data_dir}/genomics/homo_sapiens/illumina/bedgraph/cutandtag_h3k27me3_test_1.bedGraph"
                 cutandrun_bedgraph_test_2                     = "${test_data_dir}/genomics/homo_sapiens/illumina/bedgraph/cutandtag_igg_test_1.bedGraph"
+
+                test_rnaseq_vcf                               =  "${test_data_dir}/genomics/homo_sapiens/illumina/vcf/test.rnaseq.vcf"
             }
             'pacbio' {
                 primers                                       = "${test_data_dir}/genomics/homo_sapiens/pacbio/fasta/primers.fasta"

tests/modules/snpsift/split/main.nf

@@ -0,0 +1,32 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SNPSIFT_SPLIT } from '../../../../modules/snpsift/split/main.nf'
+
+workflow test_snpsift_split_base {
+
+    input = [ [ id:'test', split:true], // meta map
+            file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_vcf'], checkIfExists: true) ]
+
+    SNPSIFT_SPLIT ( input )
+}
+
+workflow test_snpsift_split_gz {
+
+    input = [ [ id:'test', split:true ], // meta map
+            file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true) ]
+
+    SNPSIFT_SPLIT ( input )
+}
+
+workflow test_snpsift_join {
+
+    input = [   [ id:'test', split:false ], // meta map
+                [   file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true),
+                    file(params.test_data['sarscov2']['illumina']['test2_vcf'], checkIfExists: true) ]
+            ]
+
+    SNPSIFT_SPLIT ( input )
+
+}

tests/modules/snpsift/split/nextflow.config

@@ -0,0 +1,5 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}

tests/modules/snpsift/split/test.yml

@@ -0,0 +1,32 @@
+- name: snpsift split test_snpsift_split_base
+  command: nextflow run tests/modules/snpsift/split -entry test_snpsift_split_base -c tests/config/nextflow.config
+  tags:
+    - snpsift/split
+    - snpsift
+  files:
+    - path: output/snpsift/test.rnaseq.chr22.vcf
+      md5sum: 1bb8724dcbe6fa3101a814c0be51d1ea
+    - path: output/snpsift/versions.yml
+      md5sum: 2b9f6b788db6c4fcbf258db763d8fab7
+
+- name: snpsift split test_snpsift_split_gz
+  command: nextflow run tests/modules/snpsift/split -entry test_snpsift_split_gz -c tests/config/nextflow.config
+  tags:
+    - snpsift/split
+    - snpsift
+  files:
+    - path: output/snpsift/test.MT192765.1.vcf
+      md5sum: 9d491cfa84067450342ba8e66c75e5b8
+    - path: output/snpsift/versions.yml
+      md5sum: 6bd63376670d6c1445caea2f31a3f579
+
+- name: snpsift split test_snpsift_join
+  command: nextflow run tests/modules/snpsift/split -entry test_snpsift_join -c tests/config/nextflow.config
+  tags:
+    - snpsift/split
+    - snpsift
+  files:
+    - path: output/snpsift/test.joined.vcf
+      md5sum: c400c7458524d889e0967b06ed72534f
+    - path: output/snpsift/versions.yml
+      md5sum: be54682a73d3b91a17eacc0e533448f5