Adding Manta module, associated pipeline & config changes

pipeline/call-gSV.nf

@@ -34,6 +34,7 @@ Current Configuration:
 
 - tools:
     delly: ${params.delly_version}
+    manta: ${params.manta_version}
     bcftools: ${params.bcftools_version}
     vcftools: ${params.vcftools_version}
     rtgtools: ${params.rtgtools_version}
@@ -48,6 +49,7 @@ Starting workflow...
 
 include { run_validate } from './modules/validation'
 include { call_gSV_Delly; call_gCNV_Delly } from './modules/delly'
+include { call_gSV_Manta } from './modules/manta'
 include { convert_BCF2VCF_BCFtools as convert_gSV_BCF2VCF_BCFtools; convert_BCF2VCF_BCFtools as convert_gCNV_BCF2VCF_BCFtools } from './modules/bcftools'
 include { run_vcfstats_RTGTools } from './modules/rtgtools'
 include { run_vcf_validator_VCFtools } from './modules/vcftools'
@@ -94,6 +96,7 @@ validation_channel = Channel
 
 workflow {
     run_validate(validation_channel)
+    call_gSV_Manta(input_bam_ch, params.reference_fasta, reference_fasta_index)
     call_gSV_Delly(input_bam_ch, params.reference_fasta, reference_fasta_index, params.exclusion_file)
     call_gCNV_Delly(input_bam_ch, call_gSV_Delly.out.bcf_sv_file, params.reference_fasta, reference_fasta_index, params.mappability_map)
     convert_gSV_BCF2VCF_BCFtools(call_gSV_Delly.out.bcf_sv_file, call_gSV_Delly.out.bam_sample_name, 'SV')
@@ -102,5 +105,6 @@ workflow {
         run_vcfstats_RTGTools(convert_gSV_BCF2VCF_BCFtools.out.vcf_file, call_gSV_Delly.out.bam_sample_name)
         run_vcf_validator_VCFtools(convert_gSV_BCF2VCF_BCFtools.out.vcf_file, call_gSV_Delly.out.bam_sample_name)
     }
-    run_sha512sum(call_gSV_Delly.out.bcf_sv_file.mix(convert_gSV_BCF2VCF_BCFtools.out.vcf_file,call_gCNV_Delly.out.bcf_cnv_file,convert_gCNV_BCF2VCF_BCFtools.out.vcf_file))
+    run_sha512sum(call_gSV_Delly.out.bcf_sv_file.mix(convert_gSV_BCF2VCF_BCFtools.out.vcf_file, call_gCNV_Delly.out.bcf_cnv_file, convert_gCNV_BCF2VCF_BCFtools.out.vcf_file,
+                call_gSV_Manta.out.vcf_small_indel_sv_file, call_gSV_Manta.out.vcf_diploid_sv_file, call_gSV_Manta.out.vcf_candidate_sv_file))
 }

pipeline/config/execute.config

@@ -4,7 +4,11 @@ process {
         memory = 1.GB
     }
     withName: call_gSV_Delly {
-        cpus = 63
-        memory = 940.GB
+        cpus = 31
+        memory = 470.GB
+    }
+    withName: call_gSV_Manta {
+        cpus = 31
+        memory = 470.GB
     }
 }

pipeline/config/lowmem.config

@@ -5,6 +5,10 @@ process {
     }
     withName: call_gSV_Delly {
         cpus = 1
-        memory = 3.GB
+        memory = 2.GB
+    }
+    withName: call_gSV_Manta {
+        cpus = 1
+        memory = 2.GB
     }
 }

pipeline/config/methods.config

@@ -95,6 +95,7 @@ methods.setup()
 params {
     // Pipeline tool versions
     delly_version = '0.8.7'
+    manta_version = '1.6.0'
     bcftools_version = '1.12'
     vcftools_version = '0.1.16'
     rtgtools_version = '3.12'

pipeline/config/midmem.config

@@ -4,7 +4,11 @@ process {
         memory = 1.GB
     }
     withName: call_gSV_Delly {
-        cpus = 71
-        memory = 130.GB
+        cpus = 35
+        memory = 65.GB
+    }
+    withName: call_gSV_Manta {
+        cpus = 35
+        memory = 65.GB
     }
 }

pipeline/modules/manta.nf

@@ -0,0 +1,54 @@
+#!/usr/bin/env nextflow
+
+def docker_image_manta = "blcdsdockerregistry/manta:${params.manta_version}"
+
+log.info """\
+------------------------------------
+             M A N T A
+------------------------------------
+Docker Images:
+- docker_image_manta:   ${docker_image_manta}
+"""
+
+process call_gSV_Manta {
+    container docker_image_manta
+
+    publishDir params.output_dir,
+        pattern: "MantaWorkflow/results",
+        mode: "copy",
+        saveAs: { "manta-${params.manta_version}/${file(it).getName()}" }
+
+    publishDir params.output_log_dir,
+        pattern: ".command.*",
+        mode: "copy",
+        saveAs: { "call_gSV_Manta/${bam_sample_name}.log${file(it).getName()}" }
+
+    input:
+    tuple val(patient), val(bam_sample_name), path(input_bam), path(input_bam_bai)
+    path(reference_fasta)
+    path(reference_fasta_fai)
+
+
+    output:
+    path("MantaWorkflow/results/variants/candidateSmallIndels.vcf.gz"), emit: vcf_small_indel_sv_file
+    path("MantaWorkflow/results/variants/candidateSmallIndels.vcf.gz.tbi")
+    path("MantaWorkflow/results/variants/diploidSV.vcf.gz"), emit: vcf_diploid_sv_file
+    path("MantaWorkflow/results/variants/diploidSV.vcf.gz.tbi")
+    path("MantaWorkflow/results/variants/candidateSV.vcf.gz"), emit: vcf_candidate_sv_file
+    path("MantaWorkflow/results/variants/candidateSV.vcf.gz.tbi")
+    //path "MANTA-${params.manta_version}_SV_${params.dataset_id}_${bam_sample_name}.vcf.gz", emit: vcf_sv_file
+    //path "MANTA-${params.manta_version}_SV_${params.dataset_id}_${bam_sample_name}.vcf.gz.tbi"
+    path "MantaWorkflow/results"
+    path ".command.*"
+    val bam_sample_name, emit: bam_sample_name
+
+    """
+    set -euo pipefail
+    configManta.py \
+        --normalBam $input_bam \
+        --referenceFasta $reference_fasta \
+        --runDir MantaWorkflow
+
+    MantaWorkflow/runWorkflow.py
+    """
+}

pipeline/modules/sha512.nf

@@ -23,6 +23,11 @@ process run_sha512sum {
         mode: "copy",
         saveAs: { "delly-${params.delly_version}/${file(it).getName()}" }
 
+    publishDir params.output_dir,
+        pattern: "*.vcf.gz*.sha512",
+        mode: "copy",
+        saveAs: { "manta-${params.manta_version}/results/variants/${file(it).getName()}" }
+
     publishDir params.output_log_dir,
         pattern: ".command.*",
         mode: "copy",