update manta to enable jointcalling (#1218)

* update manta to enable jointcalling

* fix lint errors

* fix error

* update comment

* remove comment

* suggestions from code review

* add stub

modules/manta/germline/main.nf

@@ -8,11 +8,11 @@ process MANTA_GERMLINE {
         'quay.io/biocontainers/manta:1.6.0--h9ee0642_1' }"
 
     input:
-    tuple val(meta), path(input), path(input_index)
+    tuple val(meta), path(input), path(index)
     path fasta
-    path fai
-    path target_bed
-    path target_bed_tbi
+    path fasta_fai
+    tuple path(target_bed), path(target_bed_tbi)
+
 
     output:
     tuple val(meta), path("*candidate_small_indels.vcf.gz")    , emit: candidate_small_indels_vcf
@@ -29,13 +29,14 @@ process MANTA_GERMLINE {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def options_manta = target_bed ? "--exome --callRegions $target_bed" : ""
+    def options_manta = target_bed ? "--callRegions $target_bed" : ""
     """
     configManta.py \
-        --bam $input \
+        --bam ${input.join(' --bam ')} \
         --reference $fasta \
+        --runDir manta \
         $options_manta \
-        --runDir manta
+        $args
 
     python manta/runWorkflow.py -m local -j $task.cpus
 
@@ -57,4 +58,20 @@ process MANTA_GERMLINE {
         manta: \$( configManta.py --version )
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.candidate_small_indels.vcf.gz
+    touch ${prefix}.candidate_small_indels.vcf.gz.tbi
+    touch ${prefix}.candidate_sv.vcf.gz
+    touch ${prefix}.candidate_sv.vcf.gz.tbi
+    touch ${prefix}.diploid_sv.vcf.gz
+    touch ${prefix}.diploid_sv.vcf.gz.tbi
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        manta: \$( configManta.py --version )
+    END_VERSIONS
+    """
 }

modules/manta/germline/meta.yml

@@ -25,17 +25,17 @@ input:
         e.g. [ id:'test', single_end:false ]
   - input:
       type: file
-      description: BAM/CRAM/SAM file
+      description: BAM/CRAM/SAM file. For joint calling use a list of files.
       pattern: "*.{bam,cram,sam}"
-  - input_index:
+  - index:
       type: file
-      description: BAM/CRAM/SAM index file
+      description: BAM/CRAM/SAM index file. For joint calling use a list of files.
       pattern: "*.{bai,crai,sai}"
   - fasta:
       type: file
       description: Genome reference FASTA file
       pattern: "*.{fa,fasta}"
-  - fai:
+  - fasta_fai:
       type: file
       description: Genome reference FASTA index file
       pattern: "*.{fa.fai,fasta.fai}"
@@ -85,3 +85,4 @@ output:
 
 authors:
   - "@maxulysse"
+  - "@ramprasadn"

tests/modules/manta/germline/main.nf

@@ -7,29 +7,46 @@ include { MANTA_GERMLINE } from '../../../../modules/manta/germline/main.nf'
 workflow test_manta_germline {
     input = [
         [ id:'test'], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true)
+        [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true)],
+        [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true)]
     ]
-
     fasta   = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
     fai     = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-    bed     = []
-    bed_tbi = []
+    bed     = [[],[]]
 
-    MANTA_GERMLINE ( input, fasta, fai, bed, bed_tbi )
+    MANTA_GERMLINE ( input, fasta, fai, bed )
 }
 
 workflow test_manta_germline_target_bed {
     input = [
         [ id:'test'], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true)
+        [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true)],
+        [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true)]
     ]
-
     fasta   = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
     fai     = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-    bed     = file(params.test_data['homo_sapiens']['genome']['genome_bed_gz'], checkIfExists: true)
-    bed_tbi = file(params.test_data['homo_sapiens']['genome']['genome_bed_gz_tbi'], checkIfExists: true)
+    bed     = [
+        file(params.test_data['homo_sapiens']['genome']['genome_bed_gz'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['genome']['genome_bed_gz_tbi'], checkIfExists: true),
+    ]
 
-    MANTA_GERMLINE ( input, fasta, fai, bed, bed_tbi )
+    MANTA_GERMLINE ( input, fasta, fai, bed )
+}
+
+workflow test_manta_germline_target_bed_jointcalling {
+    input = [
+        [ id:'test'], // meta map
+        [file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_cram'], checkIfExists: true)],
+        [file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_cram_crai'], checkIfExists: true),]
+    ]
+    fasta   = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    fai     = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+    bed     = [
+        file(params.test_data['homo_sapiens']['genome']['genome_bed_gz'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['genome']['genome_bed_gz_tbi'], checkIfExists: true),
+    ]
+
+    MANTA_GERMLINE ( input, fasta, fai, bed )
 }

tests/modules/manta/germline/nextflow.config

@@ -2,4 +2,8 @@ process {
 
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
 
+    withName: MANTA_GERMLINE {
+         ext.args = '--exome '
+    }
+
 }

tests/modules/manta/germline/test.yml

@@ -22,3 +22,15 @@
     - path: output/manta/test.candidate_sv.vcf.gz.tbi
     - path: output/manta/test.diploid_sv.vcf.gz
     - path: output/manta/test.diploid_sv.vcf.gz.tbi
+- name: manta germline target bed jointcalling
+  command: nextflow run ./tests/modules/manta/germline -entry test_manta_germline_target_bed_jointcalling -c ./tests/config/nextflow.config -c ./tests/modules/manta/germline/nextflow.config
+  tags:
+    - manta
+    - manta/germline
+  files:
+    - path: output/manta/test.candidate_small_indels.vcf.gz
+    - path: output/manta/test.candidate_small_indels.vcf.gz.tbi
+    - path: output/manta/test.candidate_sv.vcf.gz
+    - path: output/manta/test.candidate_sv.vcf.gz.tbi
+    - path: output/manta/test.diploid_sv.vcf.gz
+    - path: output/manta/test.diploid_sv.vcf.gz.tbi