From f038a6712ff9e5ad5c1b9a64c98007b60d728a9a Mon Sep 17 00:00:00 2001
From: Abhinav Sharma <abhi18av@gmail.com>
Date: Wed, 7 Jul 2021 10:21:18 +0200
Subject: [PATCH] Integrate stubs into the germline caller subworkflow

---
 modules/local/deepvariant/main.nf              | 18 ++++++++----------
 subworkflows/local/germline_variant_calling.nf | 13 +++++++++++++
 workflows/sarek.nf                             |  2 +-
 3 files changed, 22 insertions(+), 11 deletions(-)

diff --git a/modules/local/deepvariant/main.nf b/modules/local/deepvariant/main.nf
index 08d70e16af..f810295bf8 100644
--- a/modules/local/deepvariant/main.nf
+++ b/modules/local/deepvariant/main.nf
@@ -34,12 +34,13 @@ process DEEPVARIANT {
     //               MUST be provided as an input via a Groovy Map called "meta".
     //               This information may not be required in some instances e.g. indexing reference genome files:
     //               https://github.com/nf-core/modules/blob/master/software/bwa/index/main.nf
-    tuple val(meta), path(fasta), path(fai)
     tuple val(meta), path(bam), path(bai)
+    path fasta
+    path fai
 
     output:
-    // TODO nf-core: Named file extensions MUST be emitted for ALL output channels
-    tuple val(meta), path("*.vcf*"), emit: vcf
+    tuple val(meta), path("*.vcf*"),  emit: vcf
+    tuple val(meta), path("*.g.vcf*"), emit: gvcf
     path "*.version.txt"          , emit: version
 
     script:
@@ -76,24 +77,21 @@ process DEEPVARIANT {
     echo \$(/opt/deepvariant/bin/run_deepvariant --version)  > ${software}.version.txt
     """
 
-
 }
 
 
 workflow test {
 
-    fasta_ch = Channel.of([[id: "GRCh38_no_alt_analysis_set"],
-                          "${launchDir}/data/GRCh38_no_alt_analysis_set.fasta",
-                          "${launchDir}/data/GRCh38_no_alt_analysis_set.fasta.fai"]
-    )
-
     bam_ch = Channel.of([[id: "HG003.novaseq.pcr-free.35x.dedup.grch38_no_alt.chr20"],
                         "${launchDir}/data/HG003.novaseq.pcr-free.35x.dedup.grch38_no_alt.chr20.bam",
                         "${launchDir}/data/HG003.novaseq.pcr-free.35x.dedup.grch38_no_alt.chr20.bam.bai"]
     )
 
+    fasta_ch = Channel.of("${launchDir}/data/GRCh38_no_alt_analysis_set.fasta")
+
+    fai_ch = Channel.of("${launchDir}/data/GRCh38_no_alt_analysis_set.fasta.fai")
 
-    DEEPVARIANT(fasta_ch, bam_ch)
+    DEEPVARIANT(bam_ch, fasta_ch, fai_ch )
 
 
 }
diff --git a/subworkflows/local/germline_variant_calling.nf b/subworkflows/local/germline_variant_calling.nf
index c0151add27..3bae4eaf6b 100644
--- a/subworkflows/local/germline_variant_calling.nf
+++ b/subworkflows/local/germline_variant_calling.nf
@@ -5,12 +5,14 @@
 */
 
 params.haplotypecaller_options        = [:]
+params.deepvariant_options            = [:]
 params.genotypegvcf_options           = [:]
 params.concat_gvcf_options            = [:]
 params.concat_haplotypecaller_options = [:]
 params.strelka_options                = [:]
 
 include { GATK4_HAPLOTYPECALLER as HAPLOTYPECALLER } from '../../modules/nf-core/software/gatk4/haplotypecaller/main' addParams(options: params.haplotypecaller_options)
+include { DEEPVARIANT }                              from '../../modules/local/deepvariant/main'                      addParams(options: params.deepvariant_options)
 include { GATK4_GENOTYPEGVCF as GENOTYPEGVCF }       from '../../modules/nf-core/software/gatk4/genotypegvcf/main'    addParams(options: params.genotypegvcf_options)
 include { CONCAT_VCF as CONCAT_GVCF }                from '../../modules/local/concat_vcf/main'                       addParams(options: params.concat_gvcf_options)
 include { CONCAT_VCF as CONCAT_HAPLOTYPECALLER }     from '../../modules/local/concat_vcf/main'                       addParams(options: params.concat_haplotypecaller_options)
@@ -94,6 +96,17 @@ workflow GERMLINE_VARIANT_CALLING {
         haplotypecaller_vcf = CONCAT_HAPLOTYPECALLER.out.vcf
     }
 
+    if ('deepvariant' in params.tools.toLowerCase()) {
+
+        DEEPVARIANT(
+            bam,
+            fasta,
+            fai)
+
+        deepvariant_vcf = DEEPVARIANT.out.vcf
+        deepvariant_gvcf = DEEPVARIANT.out.gvcf
+    }
+
     if ('strelka' in params.tools.toLowerCase()) {
         STRELKA(
             bam,
diff --git a/workflows/sarek.nf b/workflows/sarek.nf
index ecbb37e277..cba96b44ed 100644
--- a/workflows/sarek.nf
+++ b/workflows/sarek.nf
@@ -259,7 +259,7 @@ workflow SAREK {
     msisensorpro_scan = BUILD_INDICES.out.msisensorpro_scan
     target_bed_gz_tbi = BUILD_INDICES.out.target_bed_gz_tbi
 
-    // PREPREOCESSING
+    // PREPROCESSING
 
     bam_mapped          = Channel.empty()
     bam_mapped_qc       = Channel.empty()