Merge pull request #571 from MaxUlysse/QCTools

Only one container for all QC tools

buildContainers.nf

@@ -178,21 +178,18 @@ def grabRevision() {
 def defineContainersList(){
   // Return list of authorized containers
   return [
-    'fastqc',
     'freebayes',
     'gatk',
     'igvtools',
-    'multiqc',
     'mutect1',
     'picard',
-    'qualimap',
+    'qctools',
     'r-base',
     'runallelecount',
     'sarek',
     'snpeff',
     'snpeffgrch37',
     'snpeffgrch38',
-    'vcftools',
     'vepgrch37',
     'vepgrch38'
     ]
@@ -211,9 +208,9 @@ def helpMessage() {
   log.info "    --containers: Choose which containers to build"
   log.info "       Default: all"
   log.info "       Possible values:"
-  log.info "         all, fastqc, freebayes, gatk, igvtools, multiqc, mutect1"
-  log.info "         picard, qualimap, r-base, runallelecount, sarek, snpeff"
-  log.info "         snpeffgrch37, snpeffgrch38, vcftools, vepgrch37, vepgrch38"
+  log.info "         all, freebayes, gatk, igvtools, mutect1, picard, qctools"
+  log.info "         r-base, runallelecount, sarek, snpeff"
+  log.info "         snpeffgrch37, snpeffgrch38, vepgrch37, vepgrch38"
   log.info "    --docker: Build containers using Docker"
   log.info "    --help"
   log.info "       you're reading it"

configuration/containers.config

@@ -22,15 +22,15 @@ process {
   $RecalibrateBam.container           = "${params.repository}/gatk:${params.tag}"
   $RunAlleleCount.container           = "${params.repository}/runallelecount:${params.tag}"
   $RunAscat.container                 = "${params.repository}/r-base:${params.tag}"
-  $RunBamQC.container                 = "${params.repository}/qualimap:${params.tag}"
+  $RunBamQC.container                 = "${params.repository}/qctools:${params.tag}"
   $RunBcftoolsStats.container         = "${params.repository}/sarek:${params.tag}"
   $RunConvertAlleleCounts.container   = "${params.repository}/r-base:${params.tag}"
-  $RunFastQC.container                = "${params.repository}/fastqc:${params.tag}"
+  $RunFastQC.container                = "${params.repository}/qctools:${params.tag}"
   $RunFreeBayes.container             = "${params.repository}/freebayes:${params.tag}"
   $RunGenotypeGVCFs.container         = "${params.repository}/gatk:${params.tag}"
   $RunHaplotypecaller.container       = "${params.repository}/gatk:${params.tag}"
   $RunManta.container                 = "${params.repository}/sarek:${params.tag}"
-  $RunMultiQC.container               = "${params.repository}/multiqc:${params.tag}"
+  $RunMultiQC.container               = "${params.repository}/qctools:${params.tag}"
   $RunMutect1.container               = "${params.repository}/mutect1:${params.tag}"
   $RunMutect2.container               = "${params.repository}/gatk:${params.tag}"
   $RunSamtoolsStats.container         = "${params.repository}/sarek:${params.tag}"
@@ -39,6 +39,6 @@ process {
   $RunSnpeff.container = {params.genome == 'GRCh38' ? "${params.repository}/snpeffgrch38:${params.tag}" : "${params.repository}/snpeffgrch37:${params.tag}"}
   $RunStrelka.container               = "${params.repository}/sarek:${params.tag}"
   $RunStrelkaBP.container             = "${params.repository}/sarek:${params.tag}"
-  $RunVcftools.container              = "${params.repository}/vcftools:${params.tag}"
+  $RunVcftools.container              = "${params.repository}/qctools:${params.tag}"
   $RunVEP.container = {params.genome == 'GRCh38' ? "${params.repository}/vepgrch38:${params.tag}" : "${params.repository}/vepgrch37:${params.tag}"}
 }

configuration/singularity-path.config

@@ -19,7 +19,7 @@ process {
   $BuildVCFIndex.container            = "${params.containerPath}/igvtools-${params.tag}.img"
   $ConcatVCF.container                = "${params.containerPath}/sarek-${params.tag}.img"
   $CreateRecalibrationTable.container = "${params.containerPath}/gatk-${params.tag}.img"
-  $GenerateMultiQCconfig.container    = "${params.containerPath}/multiqc-${params.tag}.img"
+  $GenerateMultiQCconfig.container    = "${params.containerPath}/qctools-${params.tag}.img"
   $IndelRealigner.container           = "${params.containerPath}/gatk-${params.tag}.img"
   $MapReads.container                 = "${params.containerPath}/sarek-${params.tag}.img"
   $MarkDuplicates.container           = "${params.containerPath}/picard-${params.tag}.img"
@@ -28,15 +28,15 @@ process {
   $RecalibrateBam.container           = "${params.containerPath}/gatk-${params.tag}.img"
   $RunAlleleCount.container           = "${params.containerPath}/runallelecount-${params.tag}.img"
   $RunAscat.container                 = "${params.containerPath}/r-base-${params.tag}.img"
-  $RunBamQC.container                 = "${params.containerPath}/qualimap-${params.tag}.img"
+  $RunBamQC.container                 = "${params.containerPath}/qctools-${params.tag}.img"
   $RunBcftoolsStats.container         = "${params.containerPath}/sarek-${params.tag}.img"
   $RunConvertAlleleCounts.container   = "${params.containerPath}/r-base-${params.tag}.img"
-  $RunFastQC.container                = "${params.containerPath}/fastqc-${params.tag}.img"
+  $RunFastQC.container                = "${params.containerPath}/qctools-${params.tag}.img"
   $RunFreeBayes.container             = "${params.containerPath}/freebayes-${params.tag}.img"
   $RunGenotypeGVCFs.container         = "${params.containerPath}/gatk-${params.tag}.img"
   $RunHaplotypecaller.container       = "${params.containerPath}/gatk-${params.tag}.img"
   $RunManta.container                 = "${params.containerPath}/sarek-${params.tag}.img"
-  $RunMultiQC.container               = "${params.containerPath}/multiqc-${params.tag}.img"
+  $RunMultiQC.container               = "${params.containerPath}/qctools-${params.tag}.img"
   $RunMutect1.container               = "${params.containerPath}/mutect1-${params.tag}.img"
   $RunMutect2.container               = "${params.containerPath}/gatk-${params.tag}.img"
   $RunSamtoolsStats.container         = "${params.containerPath}/sarek-${params.tag}.img"
@@ -45,6 +45,6 @@ process {
   $RunSnpeff.container                = {params.genome == 'GRCh38' ? "${params.containerPath}/snpeffgrch38-${params.tag}.img" : "${params.containerPath}/snpeffgrch37-${params.tag}.img"}
   $RunStrelka.container               = "${params.containerPath}/sarek-${params.tag}.img"
   $RunStrelkaBP.container             = "${params.containerPath}/sarek-${params.tag}.img"
-  $RunVcftools.container              = "${params.containerPath}/vcftools-${params.tag}.img"
+  $RunVcftools.container              = "${params.containerPath}/qctools-${params.tag}.img"
   $RunVEP.container                   = {params.genome == 'GRCh38' ? "${params.containerPath}/vepgrch38-${params.tag}.img" : "${params.containerPath}/vepgrch37-${params.tag}.img"}
 }

containers/vcftools/Dockerfile → containers/qctools/Dockerfile

@@ -2,7 +2,7 @@ FROM nfcore/base:latest
 
 LABEL \
   author="Maxime Garcia" \
-  description="vcftools image used in Sarek 2.0" \
+  description="Image with QC tools used in Sarek" \
   maintainer="maxime.garcia@scilifelab.se"
 
 COPY environment.yml /
@@ -12,4 +12,4 @@ RUN \
   conda clean -a
 
   # Export PATH
-ENV PATH /opt/conda/envs/sarek-vcftools-2.0/bin:$PATH
+ENV PATH /opt/conda/envs/sarek-qctools-2.0/bin:$PATH

containers/vcftools/environment.yml → containers/qctools/environment.yml

@@ -1,9 +1,13 @@
 # You can use this file to create a conda environment:
 #   conda env create -f environment.yml
-name: sarek-vcftools-2.0
+name: sarek-qctools-2.0
 channels:
-  - defaults
-  - conda-forge
   - bioconda
+  - conda-forge
+  - defaults
 dependencies:
-- vcftools=0.1.15
+  - conda-forge::openjdk=8.0.144
+  - fastqc=0.11.7
+  - multiqc=1.5
+  - qualimap=2.2.2a
+  - vcftools=0.1.15

doc/CONTAINERS.md

@@ -3,26 +3,18 @@
 Subsets of all containers can be dowloaded:
 
 For processing + germline variant calling + Reports:
- - [fastqc](#fastqc-)
  - [gatk](#gatk-)
- - [multiqc](#multiqc-)
  - [picard](#picard-)
- - [qualimap](#qualimap-)
  - [sarek](#sarek-)
- - [vcftools](#vcftools-)
 
 For processing + somatic variant calling + Reports:
- - [fastqc](#fastqc-)
  - [freebayes](#freebayes-)
  - [gatk](#gatk-)
- - [multiqc](#multiqc-)
  - [mutect1](#mutect1-)
  - [picard](#picard-)
- - [qualimap](#qualimap-)
  - [r-base](#r-base-)
  - [runallelecount](#runallelecount-)
  - [sarek](#sarek-)
- - [vcftools](#vcftools-)
 
 For annotation for GRCh37, you will need:
  - [snpeffgrch37](#snpeffgrch37-)
@@ -34,11 +26,6 @@ For annotation for GRCh38, you will need:
 
 A container named after the process is made for each process. If a container can be reused, it will be named after the tool used.
 
-## fastqc [![fastqc-docker status][fastqc-docker-badge]][fastqc-docker-link]
-
-- Based on `openjdk:8`
-- Contain **[FastQC][fastqc-link]** 0.11.5
-
 ## freebayes [![freebayes-docker status][freebayes-docker-badge]][freebayes-docker-link]
 
 - Based on `debian:8.6`
@@ -54,11 +41,6 @@ A container named after the process is made for each process. If a container can
 - Based on `openjdk:8-slim`
 - Contain **[IGVTools][igvtools-link]** 2.3.98
 
-## multiqc [![multiqc-docker status][multiqc-docker-badge]][multiqc-docker-link]
-
-- Based on `ewels/multiqc:v1.4`
-- Contain **[MultiQC][multiqc-link]** 143
-
 ## mutect1 [![mutect1-docker status][mutect1-docker-badge]][mutect1-docker-link]
 
 - Based on `openjdk:7-slim`
@@ -69,10 +51,13 @@ A container named after the process is made for each process. If a container can
 - Based on `openjdk:8-slim`
 - Contain **[Picard][picard-link]** 2.0.1
 
-## qualimap [![qualimap-docker status][qualimap-docker-badge]][qualimap-docker-link]
+## qctools [![qctools-docker status][qctools-docker-badge]][qctools-docker-link]
 
-- Based on `openjdk:8`
+- Based on `nfcore/base:latest`
+- Contain **[FastQC][fastqc-link]** 0.11.7
+- Contain **[MultiQC][multiqc-link]** 1.5
 - Contain **[qualimap][qualimap-link]** 2.2.1
+- Contain **[vcftools][vcftools-link]** 0.1.15
 
 ## runallelecount [![runallelecount-docker status][runallelecount-docker-badge]][runallelecount-docker-link]
 
@@ -106,12 +91,6 @@ A container named after the process is made for each process. If a container can
 - Contain **[snpEff][snpeff-link]** 4.3i
 - Contain GRCh38.86
 
-## vcftools [![vcftools-docker status][vcftools-docker-badge]][vcftools-docker-link]
-
-- Based on `nfcore/base:latest`
-- Contain **[vcftools][vcftools-link]** 0.1.15
-
-
 ## vepgrch37 [![vepgrch37-docker status][vepgrch37-docker-badge]][vepgrch37-docker-link]
 
 - Based on `willmclaren/ensembl-vep:release_90.6`
@@ -157,8 +136,8 @@ A container named after the process is made for each process. If a container can
 [picard-docker-badge]: https://img.shields.io/docker/automated/maxulysse/picard.svg
 [picard-docker-link]: https://hub.docker.com/r/maxulysse/picard
 [picard-link]: https://github.com/broadinstitute/picard
-[qualimap-docker-badge]: https://img.shields.io/docker/automated/maxulysse/qualimap.svg
-[qualimap-docker-link]: https://hub.docker.com/r/maxulysse/qualimap
+[qctools-docker-badge]: https://img.shields.io/docker/automated/maxulysse/qctools.svg
+[qctools-docker-link]: https://hub.docker.com/r/maxulysse/qctools
 [qualimap-link]: http://qualimap.bioinfo.cipf.es
 [rcolorbrewer-link]: https://CRAN.R-project.org/package=RColorBrewer
 [runallelecount-docker-badge]: https://img.shields.io/docker/automated/maxulysse/runallelecount.svg

scripts/do_all.sh

@@ -57,8 +57,8 @@ function toLower() {
 
 if [[ $TOOL = docker ]] && [[ GRCh37,GRCh38 =~ $GENOME ]]
 then
-    nextflow run buildContainers.nf -profile ${PROFILE} --verbose --docker ${PUSH} --repository ${REPOSITORY} --tag ${TAG} --containers fastqc,freebayes,gatk,igvtools,multiqc,mutect1,picard,qualimap,r-base,runallelecount,sarek,snpeff,vcftools
+    nextflow run buildContainers.nf -profile ${PROFILE} --verbose --docker ${PUSH} --repository ${REPOSITORY} --tag ${TAG} --containers freebayes,gatk,igvtools,mutect1,picard,qctools,r-base,runallelecount,sarek,snpeff
     nextflow run buildContainers.nf -profile ${PROFILE} --verbose --docker ${PUSH} --repository ${REPOSITORY} --tag ${TAG} --containers snpeff$(toLower ${GENOME}),vep$(toLower ${GENOME})
 else
-    nextflow run buildContainers.nf -profile ${PROFILE} --verbose --singularity --repository ${REPOSITORY} --tag ${TAG} --containerPath containers/ --containers fastqc,freebayes,gatk,igvtools,multiqc,mutect1,picard,qualimap,r-base,runallelecount,sarek,snpeff$(toLower ${GENOME}),vcftools,vep$(toLower ${GENOME})
+    nextflow run buildContainers.nf -profile ${PROFILE} --verbose --singularity --repository ${REPOSITORY} --tag ${TAG} --containerPath containers/ --containers freebayes,gatk,igvtools,mutect1,picard,qctools,r-base,runallelecount,sarek,snpeff$(toLower ${GENOME}),vep$(toLower ${GENOME})
 fi

scripts/test.sh

@@ -138,6 +138,6 @@ fi
 
 if [[ ALL,BUILDCONTAINERS =~ $TEST ]] && [[ $PROFILE == docker ]]
 then
-  nf_test buildContainers.nf --docker --containers fastqc,gatk,igvtools,multiqc,mutect1,picard,qualimap,runallelecount,r-base,snpeff,sarek
+  nf_test buildContainers.nf --docker --containers gatk,igvtools,mutect1,picard,qctools,runallelecount,r-base,snpeff,sarek
   clean_repo
 fi