Add subworkflows

.github/workflows/ci.yml

@@ -38,7 +38,7 @@ jobs:
           - 'gatk4_spark'
           #- 'save_bam_mapped'
           - 'skip_markduplicates'
-          # - 'targeted'
+          - 'targeted'
           - 'tumor_normal_pair'
           - 'variant_calling'
     steps:

modules/local/gatk4/intervallisttobed.nf

@@ -0,0 +1,38 @@
+process GATK4_INTERVALLISTTOBED {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0':
+        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(interval)
+
+    output:
+    tuple val(meta), path("*.bed"), emit: bed
+    path "versions.yml"           , emit: versions
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    def avail_mem = 3
+    if (!task.memory) {
+        log.info '[GATK IntervalListToBed] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
+    } else {
+        avail_mem = task.memory.giga
+    }
+    """
+    gatk --java-options "-Xmx${avail_mem}g" IntervalListToBed \\
+        --INPUT ${interval} \\
+        --OUTPUT ${meta.id}.bed \\
+        $args
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
+    END_VERSIONS
+    """
+}

subworkflows/local/germline_variant_calling.nf

@@ -214,7 +214,7 @@ workflow GERMLINE_VARIANT_CALLING {
         if(joint_germline){
             run_haplotypecaller = false
             run_vqsr            = true //parameter?
-            //some feedback from gavin
+            some feedback from gavin
             // GATK_JOINT_GERMLINE_VARIANT_CALLING(
             //     haplotypecaller_vcf_gz_tbi,
             //     run_haplotypecaller,

subworkflows/local/prepare_genome.nf

@@ -9,6 +9,7 @@ include { BWA_INDEX as BWAMEM1_INDEX                          } from '../../modu
 include { BWAMEM2_INDEX                                       } from '../../modules/nf-core/modules/bwamem2/index/main'
 include { CREATE_INTERVALS_BED                                } from '../../modules/local/create_intervals_bed/main'
 include { GATK4_CREATESEQUENCEDICTIONARY                      } from '../../modules/nf-core/modules/gatk4/createsequencedictionary/main'
+include { GATK4_INTERVALLISTTOBED                             } from '../../modules/local/gatk4/intervallisttobed'
 include { MSISENSORPRO_SCAN                                   } from '../../modules/nf-core/modules/msisensorpro/scan/main'
 include { SAMTOOLS_FAIDX                                      } from '../../modules/nf-core/modules/samtools/faidx/main'
 include { TABIX_BGZIPTABIX as TABIX_BGZIPTABIX_INTERVAL_SPLIT } from '../../modules/nf-core/modules/tabix/bgziptabix/main'
@@ -119,12 +120,18 @@ workflow PREPARE_GENOME {
         }else{
 
             tabix_in_combined = Channel.fromPath(file(params.intervals)).map{it -> [[id:it.baseName], it] }
+            if(!params.intervals.endsWith(".bed")){
+                GATK4_INTERVALLISTTOBED(tabix_in_combined)
+                tabix_in_combined = GATK4_INTERVALLISTTOBED.out.bed
+                ch_versions = ch_versions.mix(GATK4_INTERVALLISTTOBED.out.versions)
+            }
             ch_intervals = CREATE_INTERVALS_BED(file(params.intervals))
 
         }
     }
 
     if (!('annotate' in step) && !('controlfreec' in step)){
+
         TABIX_BGZIPTABIX_INTERVAL_ALL(tabix_in_combined)
         ch_intervals_combined_bed_gz_tbi = TABIX_BGZIPTABIX_INTERVAL_ALL.out.gz_tbi.map{ meta, bed, tbi -> [bed, tbi] }
         ch_versions = ch_versions.mix(TABIX_BGZIPTABIX_INTERVAL_ALL.out.versions)