add gatk4/gatherbqsr (#1130)

* nf-core modules create

* add module files

* indent

* remove templte code

* manually revert pytest changes from tools

* manually revert pytest changes from tools

* add include statement back in

Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>

modules/gatk4/gatherbqsrreports/main.nf

@@ -0,0 +1,41 @@
+process GATK4_GATHERBQSRREPORTS {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_1':
+        'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_1' }"
+
+    input:
+    tuple val(meta), path(recal_table)
+
+    output:
+    tuple val(meta), path("*.table"), emit: table
+    path "versions.yml"             , emit: versions
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def input = recal_table.collect{"-I ${it}"}.join(' ')
+
+    def avail_mem = 3
+    if (!task.memory) {
+        log.info '[GATK GatherBQSRReports] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
+    } else {
+        avail_mem = task.memory.giga
+    }
+    """
+    gatk --java-options "-Xmx${avail_mem}g" \\
+        GatherBQSRReports \
+        ${input} \
+        --tmp-dir . \
+        $args \
+        --output ${prefix}.table
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
+    END_VERSIONS
+    """
+}

modules/gatk4/gatherbqsrreports/meta.yml

@@ -0,0 +1,43 @@
+name: gatk4_gatherbqsrreports
+description: write your description here
+keywords:
+  - gatk4
+  - gatk4_gatherbqsrreports
+  - base_recalibration
+tools:
+  - gatk4:
+      description: Genome Analysis Toolkit (GATK4)
+      homepage: https://gatk.broadinstitute.org/hc/en-us
+      documentation: https://gatk.broadinstitute.org/hc/en-us
+      tool_dev_url: https://github.com/broadinstitute/gatk
+      doi: "10.1158/1538-7445.AM2017-3590"
+      licence: ['BSD-3-clause']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - recal_table:
+      type: file
+      description: File(s) containing BQSR table(s)
+      pattern: "*.table"
+
+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"
+  - recal_table:
+      type: file
+      description: File containing joined BQSR table
+      pattern: "*.table"
+
+authors:
+  - "@FriederikeHanssen"

tests/config/pytest_modules.yml

@@ -314,26 +314,26 @@ cnvkit/batch:
   - modules/cnvkit/batch/**
   - tests/modules/cnvkit/batch/**
 
-cooler/digest:
-  - modules/cooler/digest/**
-  - tests/modules/cooler/digest/**
-
 cooler/cload:
   - modules/cooler/cload/**
   - tests/modules/cooler/cload/**
 
+cooler/digest:
+  - modules/cooler/digest/**
+  - tests/modules/cooler/digest/**
+
 cooler/dump:
   - modules/cooler/dump/**
   - tests/modules/cooler/dump/**
 
-cooler/zoomify:
-  - modules/cooler/zoomify/**
-  - tests/software/cooler/zoomify/**
-
 cooler/merge:
   - modules/cooler/merge/**
   - tests/modules/cooler/merge/**
 
+cooler/zoomify:
+  - modules/cooler/zoomify/**
+  - tests/software/cooler/zoomify/**
+
 csvtk/concat:
   - modules/csvtk/concat/**
   - tests/modules/csvtk/concat/**
@@ -538,6 +538,10 @@ gatk4/filtermutectcalls: #&gatk4_filtermutectcalls
   - modules/gatk4/filtermutectcalls/**
   - tests/modules/gatk4/filtermutectcalls/**
 
+gatk4/gatherbqsrreports:
+  - modules/gatk4/gatherbqsrreports/**
+  - tests/modules/gatk4/gatherbqsrreports/**
+
 gatk4/genomicsdbimport: #&gatk4_genomicsdbimport
   - modules/gatk4/genomicsdbimport/**
   - tests/modules/gatk4/genomicsdbimport/**
@@ -1035,6 +1039,10 @@ pbccs:
   - modules/pbccs/**
   - tests/modules/pbccs/**
 
+peddy:
+  - modules/peddy/**
+  - tests/modules/peddy/**
+
 phyloflash:
   - modules/phyloflash/**
   - tests/modules/phyloflash/**
@@ -1043,10 +1051,6 @@ picard/collecthsmetrics:
   - modules/picard/collecthsmetrics/**
   - tests/modules/picard/collecthsmetrics/**
 
-peddy:
-  - modules/peddy/**
-  - tests/modules/peddy/**
-
 picard/collectmultiplemetrics:
   - modules/picard/collectmultiplemetrics/**
   - tests/modules/picard/collectmultiplemetrics/**

tests/modules/gatk4/gatherbqsrreports/main.nf

@@ -0,0 +1,27 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GATK4_GATHERBQSRREPORTS } from '../../../../modules/gatk4/gatherbqsrreports/main.nf'
+
+workflow test_gatk4_gatherbqsrreports {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_baserecalibrator_table'], checkIfExists: true)
+    ]
+
+    GATK4_GATHERBQSRREPORTS ( input )
+}
+
+workflow test_gatk4_gatherbqsrreports_multiple {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [file(params.test_data['homo_sapiens']['illumina']['test_baserecalibrator_table'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test2_baserecalibrator_table'], checkIfExists: true)
+        ]
+    ]
+
+    GATK4_GATHERBQSRREPORTS ( input )
+}

tests/modules/gatk4/gatherbqsrreports/nextflow.config

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

tests/modules/gatk4/gatherbqsrreports/test.yml

@@ -0,0 +1,21 @@
+- name: gatk4 gatherbqsrreports test_gatk4_gatherbqsrreports
+  command: nextflow run tests/modules/gatk4/gatherbqsrreports -entry test_gatk4_gatherbqsrreports -c tests/config/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/gatherbqsrreports
+  files:
+    - path: output/gatk4/test.table
+      md5sum: 9603b69fdc3b5090de2e0dd78bfcc4bf
+    - path: output/gatk4/versions.yml
+      md5sum: 50238fd0f3b6f4efb2b5335b6324f905
+
+- name: gatk4 gatherbqsrreports test_gatk4_gatherbqsrreports_multiple
+  command: nextflow run tests/modules/gatk4/gatherbqsrreports -entry test_gatk4_gatherbqsrreports_multiple -c tests/config/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/gatherbqsrreports
+  files:
+    - path: output/gatk4/test.table
+      md5sum: 0c1257eececf95db8ca378272d0f21f9
+    - path: output/gatk4/versions.yml
+      md5sum: c6ce163062dd3609848fc5bc10660427