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Actually use SnpEFF reports in MultiQC #563

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Apr 11, 2018
Merged

Actually use SnpEFF reports in MultiQC #563

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2ddb8e2
use reports in annotate
maxulysse Apr 11, 2018
8f3b0bc
save reports to a specific directory
maxulysse Apr 11, 2018
8b21c11
actually use SnpEff reports in MultiQC
maxulysse Apr 11, 2018
1c8c9e3
reorder tests in time sensitive manner
maxulysse Apr 11, 2018
cd552e8
add --keep option to test.sh to keep logs
maxulysse Apr 11, 2018
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10 changes: 5 additions & 5 deletions .travis.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -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
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3 changes: 2 additions & 1 deletion annotate.nf
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Expand Up @@ -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
Expand Down Expand Up @@ -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"
]
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4 changes: 3 additions & 1 deletion runMultiQC.nf
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Expand Up @@ -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
"""
}

Expand All @@ -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()

Expand Down Expand Up @@ -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"
Expand Down
9 changes: 7 additions & 2 deletions scripts/test.sh
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Expand Up @@ -2,6 +2,7 @@
set -xeuo pipefail

BUILD=false
KEEP=false
GENOME=smallGRCh37
PROFILE=singularity
SAMPLE=data/tsv/tiny.tsv
Expand Down Expand Up @@ -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
Expand All @@ -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
Expand Down Expand Up @@ -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

Expand Down