Bcftools sort new syntax (#1169)

* Added files for bcftools/sort

* Fixed output format and removed md5 checksum

* Change input to avoid identical in/output names

* Created rows for bcftools/sort in pytest_modules.yml

modules/bcftools/sort/main.nf

@@ -0,0 +1,32 @@
+process BCFTOOLS_SORT {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda (params.enable_conda ? "bioconda::bcftools=1.14" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0':
+        'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
+
+    input:
+    tuple val(meta), path(vcf)
+
+    output:
+    tuple val(meta), path("*.gz"), emit: vcf
+    path "versions.yml"           , emit: versions
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    bcftools \\
+        sort \\
+        --output ${prefix}.vcf.gz \\
+        $args \\
+        $vcf
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
+    END_VERSIONS
+    """
+}

modules/bcftools/sort/meta.yml

@@ -0,0 +1,43 @@
+name: bcftools_sort
+description: Sorts VCF files
+keywords:
+  - sorting
+  - VCF
+  - variant calling
+tools:
+  - sort:
+      description: Sort VCF files by coordinates.
+      homepage: http://samtools.github.io/bcftools/bcftools.html
+      documentation: http://www.htslib.org/doc/bcftools.html
+      tool_dev_url: https://github.com/samtools/bcftools
+      doi: "10.1093/bioinformatics/btp352"
+      licence: ['MIT']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - vcf:
+      type: file
+      description: The VCF/BCF file to be sorted
+      pattern: "*.{vcf.gz,vcf,bcf}"
+
+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"
+  - vcf:
+      type: file
+      description: Sorted VCF file
+      pattern: "*.{vcf.gz}"
+
+authors:
+  - "@Gwennid"

tests/config/pytest_modules.yml

@@ -114,6 +114,10 @@ bcftools/reheader:
   - modules/bcftools/reheader/**
   - tests/modules/bcftools/reheader/**
 
+bcftools/sort:
+  - modules/bcftools/sort/**
+  - tests/modules/bcftools/sort/**
+
 bcftools/stats:
   - modules/bcftools/stats/**
   - tests/modules/bcftools/stats/**

tests/modules/bcftools/sort/main.nf

@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BCFTOOLS_SORT } from '../../../../modules/bcftools/sort/main.nf'
+
+workflow test_bcftools_sort {
+
+    input = [
+        [ id:'test' ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true)
+    ]
+
+    BCFTOOLS_SORT ( input )
+}

tests/modules/bcftools/sort/nextflow.config

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

tests/modules/bcftools/sort/test.yml

@@ -0,0 +1,10 @@
+- name: bcftools sort test_bcftools_sort
+  command: nextflow run tests/modules/bcftools/sort -entry test_bcftools_sort -c tests/config/nextflow.config
+  tags:
+    - bcftools
+    - bcftools/sort
+  files:
+    - path: output/bcftools/test.vcf.gz
+      md5sum: fc178eb342a91dc0d1d568601ad8f8e2
+    - path: output/bcftools/versions.yml
+      md5sum: f1bb553befa5108f81135b8fec613b6b