Merge pull request #563 from MaxUlysse/snpEff

Actually use SnpEFF reports in MultiQC

Author: Szilveszter Juhos

.travis.yml

@@ -11,15 +11,15 @@ services:
 
 env:
   - NXF_VER=0.27.0 SGT_VER=2.4.2 PROFILE=singularity TEST=TOOLS TOOL_INSTALL=all
-  - NXF_VER=0.27.0 PROFILE=docker TEST=TOOLS TOOL_INSTALL=nextflow
-  - NXF_VER=0.27.0 SGT_VER=2.4.2 PROFILE=singularity TEST=STEP TOOL_INSTALL=all
   - NXF_VER=0.27.0 SGT_VER=2.4.2 PROFILE=singularity TEST=MANTA TOOL_INSTALL=all
+  - NXF_VER=0.27.0 PROFILE=docker TEST=MANTA TOOL_INSTALL=nextflow
+  - NXF_VER=0.27.0 PROFILE=docker TEST=TOOLS TOOL_INSTALL=nextflow
+  - NXF_VER=0.27.0 PROFILE=docker TEST=ANNOTATEVEP TOOL_INSTALL=nextflow
   - NXF_VER=0.27.0 SGT_VER=2.4.2 PROFILE=singularity TEST=ANNOTATESNPEFF TOOL_INSTALL=all
+  - NXF_VER=0.27.0 SGT_VER=2.4.2 PROFILE=singularity TEST=STEP TOOL_INSTALL=all
   - NXF_VER=0.27.0 SGT_VER=2.4.2 PROFILE=singularity TEST=GERMLINE TOOL_INSTALL=all
-  - NXF_VER=0.27.0 PROFILE=docker TEST=ANNOTATEVEP TOOL_INSTALL=nextflow
-  - NXF_VER=0.27.0 PROFILE=docker TEST=ANNOTATESNPEFF TOOL_INSTALL=nextflow
   - NXF_VER=0.27.0 SGT_VER=2.4.2 PROFILE=singularity TEST=DIR TOOL_INSTALL=all
-  - NXF_VER=0.27.0 PROFILE=docker TEST=MANTA TOOL_INSTALL=nextflow
+  - NXF_VER=0.27.0 PROFILE=docker TEST=ANNOTATESNPEFF TOOL_INSTALL=nextflow
   - NXF_VER=0.27.0 PROFILE=docker TEST=STEP TOOL_INSTALL=nextflow
   - NXF_VER=0.27.0 PROFILE=docker TEST=GERMLINE TOOL_INSTALL=nextflow
   - NXF_VER=0.27.0 PROFILE=docker TEST=DIR TOOL_INSTALL=nextflow

annotate.nf

@@ -131,7 +131,7 @@ if (params.verbose) bcfReport = bcfReport.view {
 process RunSnpeff {
   tag {vcf}
 
-  publishDir directoryMap.snpeff, mode: 'link'
+  publishDir params.outDir , saveAs: { it == "${vcf.baseName}.snpEff.csv" ? "${directoryMap.snpeffReports}/${it}" : "${directoryMap.snpeff}/${it}" }, mode: 'link'
 
   input:
     set variantCaller, file(vcf) from vcfForSnpeff
@@ -228,6 +228,7 @@ def defineDirectoryMap() {
     'strelka'          : "${params.outDir}/VariantCalling/Strelka",
     'strelkabp'        : "${params.outDir}/VariantCalling/StrelkaBP",
     'bcftoolsStats'    : "${params.outDir}/Reports/BCFToolsStats",
+    'snpeffReports'    : "${params.outDir}/Reports/SnpEff",
     'snpeff'           : "${params.outDir}/Annotation/SnpEff",
     'vep'              : "${params.outDir}/Annotation/VEP"
   ]

runMultiQC.nf

@@ -88,8 +88,8 @@ process GenerateMultiQCconfig {
   echo "- 'picard'" >> multiqc_config.yaml
   echo "- 'samtools'" >> multiqc_config.yaml
   echo "- 'qualimap'" >> multiqc_config.yaml
+  echo "- 'bcftools'" >> multiqc_config.yaml
   echo "- 'snpeff'" >> multiqc_config.yaml
-  echo "- 'vep'" >> multiqc_config.yaml
   """
 }
 
@@ -105,6 +105,7 @@ reportsForMultiQC = Channel.empty()
     Channel.fromPath("${directoryMap.fastQC}/*/*"),
     Channel.fromPath("${directoryMap.markDuplicatesQC}/*"),
     Channel.fromPath("${directoryMap.samtoolsStats}/*"),
+    Channel.fromPath("${directoryMap.snpeffReports}/*"),
     multiQCconfig
   ).collect()
 
@@ -147,6 +148,7 @@ def defineDirectoryMap() {
     'bamQC'            : "${params.outDir}/Reports/bamQC",
     'bcftoolsStats'    : "${params.outDir}/Reports/BCFToolsStats",
     'fastQC'           : "${params.outDir}/Reports/FastQC",
+    'snpeffReports'    : "${params.outDir}/Reports/SnpEff",
     'markDuplicatesQC' : "${params.outDir}/Reports/MarkDuplicates",
     'multiQC'          : "${params.outDir}/Reports/MultiQC",
     'samtoolsStats'    : "${params.outDir}/Reports/SamToolsStats"

scripts/test.sh

@@ -2,6 +2,7 @@
 set -xeuo pipefail
 
 BUILD=false
+KEEP=false
 GENOME=smallGRCh37
 PROFILE=singularity
 SAMPLE=data/tsv/tiny.tsv
@@ -32,6 +33,10 @@ do
     shift # past argument
     shift # past value
     ;;
+    -k|--keep)
+    KEEP=true
+    shift # past value
+    ;;
     -b|--build)
     BUILD=true
     shift # past value
@@ -52,7 +57,7 @@ function run_wrapper() {
 }
 
 function clean_repo() {
-  if [[ $TRAVIS == false ]]
+  if [[ $TRAVIS == false ]] && [[ $KEEP == true ]]
   then
     rm -rf work .nextflow* Preprocessing Reports Annotation VariantCalling Results
   fi
@@ -127,7 +132,7 @@ then
     rm -rf work/singularity/picard-latest.img
   fi
   run_wrapper --annotate --tools ${ANNOTATOR} --annotateVCF data/tiny/vcf/Strelka_1234N_variants.vcf.gz --noReports
-  run_wrapper --annotate --tools ${ANNOTATOR} --annotateVCF data/tiny/vcf/Strelka_1234N_variants.vcf.gz,data/tiny/vcf/Strelka_9876T_variants.vcf.gz --noReports
+  run_wrapper --annotate --tools ${ANNOTATOR} --annotateVCF data/tiny/vcf/Strelka_1234N_variants.vcf.gz,data/tiny/vcf/Strelka_9876T_variants.vcf.gz
   clean_repo
 fi