Adding bcftools_isec taking a path with several vcfs and its tests

.github/workflows/bcftools_isec.yml

@@ -0,0 +1,44 @@
+name: bcftools_isec
+on:
+    push:
+        paths:
+            - software/bcftools/bgzip/**
+            - software/bcftools/tabix/**
+            - software/bcftools/isec/**
+            - .github/workflows/bcftools_isec.yml
+            - tests/software/bcftools/**
+    pull_request:
+        paths:
+            - software/bcftools/bgzip/**
+            - software/bcftools/tabix/**
+            - software/bcftools/isec/**
+            - .github/workflows/bcftools_tabix.yml
+            - tests/software/bcftools/**
+
+jobs:
+    ci_test:
+        runs-on: ubuntu-latest
+        strategy:
+            matrix:
+                nxf_version: [20.11.0-edge]
+        env:
+            NXF_ANSI_LOG: false
+        steps:
+            - uses: actions/checkout@v2
+
+            - name: Install Nextflow
+              env:
+                  NXF_VER: ${{ matrix.nxf_version }}
+              run: |
+                  wget -qO- get.nextflow.io | bash
+                  sudo mv nextflow /usr/local/bin/
+
+            - name: Set up Python
+              uses: actions/setup-python@v2
+              with:
+                  python-version: "3.x"
+            - name: Install dependencies
+              run: python -m pip install --upgrade pip pytest-workflow
+
+            # Test the module
+            - run: pytest --tag bcftools_isec --symlink --wt 2

software/bcftools/isec/main.nf

@@ -4,7 +4,7 @@ include { initOptions; saveFiles; getSoftwareName } from './functions'
 params.options = [:]
 def options    = initOptions(params.options)
 
-process BCFTOOLS_STATS {
+process BCFTOOLS_ISEC {
     tag "$meta.id"
     publishDir "${params.outdir}",
         mode: params.publish_dir_mode,
@@ -18,17 +18,20 @@ process BCFTOOLS_STATS {
     }
 
     input:
-    tuple val(meta), path(vcf)
+    tuple val(meta), path('vcfs/*')
 
     output:
-    tuple val(meta), path("*.txt"), emit: stats
+    tuple val(meta), path("${prefix}"), emit: results
     path  "*.version.txt"             , emit: version
 
     script:
     def software = getSoftwareName(task.process)
-    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    prefix       = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
     """
-    bcftools stats $options.args $vcf > ${prefix}.bcftools_stats.txt
+    bcftools isec  \\
+        $options.args \\
+        -p $prefix \\
+        */*.vcf.gz
     echo \$(bcftools --version 2>&1) | sed 's/^.*bcftools //; s/ .*\$//' > ${software}.version.txt
     """
 }

software/bcftools/isec/meta.yml

@@ -41,9 +41,10 @@ input:
           Groovy Map containing sample information
           e.g. [ id:'test', single_end:false ]
     - vcf:
-        type: file
-        description: VCF input file
-        pattern: "*.{vcf}"
+        type: files
+        description: |
+          List containing 2 or more vcf files and their respective index (tbi files)
+          e.g. [ 'file1.vcf', 'file1.vcf.tbi', 'file2.vcf', 'file2.vcf.tbi' ]
 output:
     - meta:
         type: map

tests/software/bcftools/main.nf

@@ -8,6 +8,11 @@ include { BCFTOOLS_STATS } from '../../../software/bcftools/stats/main.nf' addPa
 include { BCFTOOLS_BGZIP } from '../../../software/bcftools/bgzip/main.nf' addParams( options: [:] )
 include { BCFTOOLS_TABIX } from '../../../software/bcftools/tabix/main.nf' addParams( options: [:] )
 include { BCFTOOLS_CONSENSUS } from '../../../software/bcftools/consensus/main.nf' addParams( options: [:] )
+include { BCFTOOLS_ISEC } from '../../../software/bcftools/isec/main.nf' addParams( options: ['args': '--nfiles +2 --output-type z'] )
+include { BCFTOOLS_BGZIP as BCFTOOLS_BGZIP2 } from '../../../software/bcftools/bgzip/main.nf' addParams( options: [:] )
+include { BCFTOOLS_TABIX as BCFTOOLS_TABIX2 } from '../../../software/bcftools/tabix/main.nf' addParams( options: [:] )
+include { BCFTOOLS_BGZIP as BCFTOOLS_BGZIP3 } from '../../../software/bcftools/bgzip/main.nf' addParams( options: [:] )
+include { BCFTOOLS_TABIX as BCFTOOLS_TABIX3 } from '../../../software/bcftools/tabix/main.nf' addParams( options: [:] )
 
 workflow test_bcftools_filter {
 
@@ -62,4 +67,31 @@ workflow test_bcftools_consensus {
                                     .join( fasta, by: [0] ) )
 }
 
+workflow test_bcftools_isec {
 
+    def input = []
+    input1 = [ [ id:'test1' ], // meta map
+            file("${launchDir}/tests/data/vcf/test.vcf", checkIfExists: true) ]
+
+    input2 = [ [ id:'test2' ], // meta map
+            file("${launchDir}/tests/data/vcf/test.vcf", checkIfExists: true) ]
+
+    input3 = [ [ id:'test3' ], // meta map
+            file("${launchDir}/tests/data/vcf/test.vcf", checkIfExists: true) ]
+
+    BCFTOOLS_BGZIP  ( input1 )
+    BCFTOOLS_TABIX  ( BCFTOOLS_BGZIP.out.vcf )
+    BCFTOOLS_BGZIP2 ( input2 )
+    BCFTOOLS_TABIX2 ( BCFTOOLS_BGZIP2.out.vcf )
+    BCFTOOLS_BGZIP3 ( input3 )
+    BCFTOOLS_TABIX3 ( BCFTOOLS_BGZIP3.out.vcf )
+    BCFTOOLS_ISEC   ( BCFTOOLS_BGZIP.out.vcf
+                        .mix( BCFTOOLS_TABIX.out.tbi )
+                        .mix( BCFTOOLS_BGZIP2.out.vcf )
+                        .mix( BCFTOOLS_TABIX2.out.tbi )
+                        .mix( BCFTOOLS_BGZIP3.out.vcf )
+                        .mix( BCFTOOLS_TABIX3.out.tbi)
+                        .map { [ it[1] ]}
+                        .collect()
+                        .map { [ [id: 'test'], it ] } )
+}

tests/software/bcftools/test.yml

@@ -46,3 +46,36 @@
       md5sum: 06d52177f819730dd409157914534e8d
     - path: output/bcftools/test.fa
       md5sum: c9e7ac4537756a0b33bcf17117f9a065
+
+- name: Run bcftools isec test workflow
+  command: nextflow run ./tests/software/bcftools/ -profile docker -entry test_bcftools_isec -c tests/config/nextflow.config
+  tags:
+    - bcftools
+    - bcftools_isec
+  files:
+    - path: output/bcftools/test1.vcf.gz
+      md5sum: eb75ae1f08a1884f8edc59ed423471a2
+    - path: output/bcftools/test1.vcf.gz.tbi
+      md5sum: 06d52177f819730dd409157914534e8d
+    - path: output/bcftools/test2.vcf.gz
+      md5sum: eb75ae1f08a1884f8edc59ed423471a2
+    - path: output/bcftools/test2.vcf.gz.tbi
+      md5sum: 06d52177f819730dd409157914534e8d
+    - path: output/bcftools/test3.vcf.gz
+      md5sum: eb75ae1f08a1884f8edc59ed423471a2
+    - path: output/bcftools/test/0000.vcf.gz
+      md5sum: 20bd741594f456c48e1928f07f0be342
+    - path: output/bcftools/test/0000.vcf.gz.tbi
+      md5sum: d4357a62c60df6abcb5cc806b4681dff
+    - path: output/bcftools/test/0001.vcf.gz
+      md5sum: 20bd741594f456c48e1928f07f0be342
+    - path: output/bcftools/test/0001.vcf.gz.tbi
+      md5sum: d4357a62c60df6abcb5cc806b4681dff
+    - path: output/bcftools/test/0002.vcf.gz
+      md5sum: 20bd741594f456c48e1928f07f0be342
+    - path: output/bcftools/test/0002.vcf.gz.tbi
+      md5sum: d4357a62c60df6abcb5cc806b4681dff
+    - path: md5 output/bcftools/test/README.txt
+      md5sum: 9a3a041e63a18e0ad41abab96e2c5f73
+    - path: md5 output/bcftools/test/sites.txt
+      md5sum: 01bb949ed7825ecf692bf0640e363647