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Merge pull request nf-core#571 from MaxUlysse/QCTools
Only one container for all QC tools
2 parents 6d325ae + 24f91de commit 5c21bf5

11 files changed

Lines changed: 33 additions & 108 deletions

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‎buildContainers.nf‎

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

‎configuration/containers.config‎

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

‎configuration/singularity-path.config‎

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@@ -19,7 +19,7 @@ process {
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$BuildVCFIndex.container = "${params.containerPath}/igvtools-${params.tag}.img"
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$ConcatVCF.container = "${params.containerPath}/sarek-${params.tag}.img"
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$CreateRecalibrationTable.container = "${params.containerPath}/gatk-${params.tag}.img"
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$GenerateMultiQCconfig.container = "${params.containerPath}/multiqc-${params.tag}.img"
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$GenerateMultiQCconfig.container = "${params.containerPath}/qctools-${params.tag}.img"
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$IndelRealigner.container = "${params.containerPath}/gatk-${params.tag}.img"
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$MapReads.container = "${params.containerPath}/sarek-${params.tag}.img"
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$MarkDuplicates.container = "${params.containerPath}/picard-${params.tag}.img"
@@ -28,15 +28,15 @@ process {
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$RecalibrateBam.container = "${params.containerPath}/gatk-${params.tag}.img"
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$RunAlleleCount.container = "${params.containerPath}/runallelecount-${params.tag}.img"
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$RunAscat.container = "${params.containerPath}/r-base-${params.tag}.img"
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$RunBamQC.container = "${params.containerPath}/qualimap-${params.tag}.img"
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$RunBamQC.container = "${params.containerPath}/qctools-${params.tag}.img"
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$RunBcftoolsStats.container = "${params.containerPath}/sarek-${params.tag}.img"
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$RunConvertAlleleCounts.container = "${params.containerPath}/r-base-${params.tag}.img"
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$RunFastQC.container = "${params.containerPath}/fastqc-${params.tag}.img"
34+
$RunFastQC.container = "${params.containerPath}/qctools-${params.tag}.img"
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$RunFreeBayes.container = "${params.containerPath}/freebayes-${params.tag}.img"
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$RunGenotypeGVCFs.container = "${params.containerPath}/gatk-${params.tag}.img"
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$RunHaplotypecaller.container = "${params.containerPath}/gatk-${params.tag}.img"
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$RunManta.container = "${params.containerPath}/sarek-${params.tag}.img"
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$RunMultiQC.container = "${params.containerPath}/multiqc-${params.tag}.img"
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$RunMultiQC.container = "${params.containerPath}/qctools-${params.tag}.img"
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$RunMutect1.container = "${params.containerPath}/mutect1-${params.tag}.img"
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$RunMutect2.container = "${params.containerPath}/gatk-${params.tag}.img"
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$RunSamtoolsStats.container = "${params.containerPath}/sarek-${params.tag}.img"
@@ -45,6 +45,6 @@ process {
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$RunSnpeff.container = {params.genome == 'GRCh38' ? "${params.containerPath}/snpeffgrch38-${params.tag}.img" : "${params.containerPath}/snpeffgrch37-${params.tag}.img"}
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$RunStrelka.container = "${params.containerPath}/sarek-${params.tag}.img"
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$RunStrelkaBP.container = "${params.containerPath}/sarek-${params.tag}.img"
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$RunVcftools.container = "${params.containerPath}/vcftools-${params.tag}.img"
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$RunVcftools.container = "${params.containerPath}/qctools-${params.tag}.img"
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$RunVEP.container = {params.genome == 'GRCh38' ? "${params.containerPath}/vepgrch38-${params.tag}.img" : "${params.containerPath}/vepgrch37-${params.tag}.img"}
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}

‎containers/fastqc/Dockerfile‎

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This file was deleted.

‎containers/multiqc/Dockerfile‎

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This file was deleted.

containers/vcftools/Dockerfile renamed to containers/qctools/Dockerfile

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@@ -2,7 +2,7 @@ FROM nfcore/base:latest
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33
LABEL \
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author="Maxime Garcia" \
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description="vcftools image used in Sarek 2.0" \
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description="Image with QC tools used in Sarek" \
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maintainer="maxime.garcia@scilifelab.se"
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COPY environment.yml /
@@ -12,4 +12,4 @@ RUN \
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conda clean -a
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# Export PATH
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ENV PATH /opt/conda/envs/sarek-vcftools-2.0/bin:$PATH
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ENV PATH /opt/conda/envs/sarek-qctools-2.0/bin:$PATH

containers/vcftools/environment.yml renamed to containers/qctools/environment.yml

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@@ -1,9 +1,13 @@
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# You can use this file to create a conda environment:
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# conda env create -f environment.yml
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name: sarek-vcftools-2.0
3+
name: sarek-qctools-2.0
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channels:
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- defaults
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- conda-forge
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- bioconda
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- conda-forge
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- defaults
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dependencies:
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- vcftools=0.1.15
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- conda-forge::openjdk=8.0.144
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- fastqc=0.11.7
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- multiqc=1.5
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- qualimap=2.2.2a
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- vcftools=0.1.15

‎containers/qualimap/Dockerfile‎

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This file was deleted.

‎doc/CONTAINERS.md‎

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@@ -3,26 +3,18 @@
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Subsets of all containers can be dowloaded:
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55
For processing + germline variant calling + Reports:
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- [fastqc](#fastqc-)
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- [gatk](#gatk-)
8-
- [multiqc](#multiqc-)
97
- [picard](#picard-)
10-
- [qualimap](#qualimap-)
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- [sarek](#sarek-)
12-
- [vcftools](#vcftools-)
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For processing + somatic variant calling + Reports:
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- [fastqc](#fastqc-)
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- [freebayes](#freebayes-)
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- [gatk](#gatk-)
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- [multiqc](#multiqc-)
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- [mutect1](#mutect1-)
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- [picard](#picard-)
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- [qualimap](#qualimap-)
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- [r-base](#r-base-)
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- [runallelecount](#runallelecount-)
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- [sarek](#sarek-)
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- [vcftools](#vcftools-)
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For annotation for GRCh37, you will need:
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- [snpeffgrch37](#snpeffgrch37-)
@@ -34,11 +26,6 @@ For annotation for GRCh38, you will need:
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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.
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37-
## fastqc [![fastqc-docker status][fastqc-docker-badge]][fastqc-docker-link]
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39-
- Based on `openjdk:8`
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- Contain **[FastQC][fastqc-link]** 0.11.5
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## freebayes [![freebayes-docker status][freebayes-docker-badge]][freebayes-docker-link]
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- Based on `debian:8.6`
@@ -54,11 +41,6 @@ A container named after the process is made for each process. If a container can
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- Based on `openjdk:8-slim`
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- Contain **[IGVTools][igvtools-link]** 2.3.98
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## multiqc [![multiqc-docker status][multiqc-docker-badge]][multiqc-docker-link]
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- Based on `ewels/multiqc:v1.4`
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- Contain **[MultiQC][multiqc-link]** 143
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## mutect1 [![mutect1-docker status][mutect1-docker-badge]][mutect1-docker-link]
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- Based on `openjdk:7-slim`
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- Based on `openjdk:8-slim`
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- Contain **[Picard][picard-link]** 2.0.1
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72-
## qualimap [![qualimap-docker status][qualimap-docker-badge]][qualimap-docker-link]
54+
## qctools [![qctools-docker status][qctools-docker-badge]][qctools-docker-link]
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74-
- Based on `openjdk:8`
56+
- Based on `nfcore/base:latest`
57+
- Contain **[FastQC][fastqc-link]** 0.11.7
58+
- Contain **[MultiQC][multiqc-link]** 1.5
7559
- Contain **[qualimap][qualimap-link]** 2.2.1
60+
- Contain **[vcftools][vcftools-link]** 0.1.15
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## runallelecount [![runallelecount-docker status][runallelecount-docker-badge]][runallelecount-docker-link]
7863

@@ -106,12 +91,6 @@ A container named after the process is made for each process. If a container can
10691
- Contain **[snpEff][snpeff-link]** 4.3i
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- Contain GRCh38.86
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## vcftools [![vcftools-docker status][vcftools-docker-badge]][vcftools-docker-link]
110-
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- Based on `nfcore/base:latest`
112-
- Contain **[vcftools][vcftools-link]** 0.1.15
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114-
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## vepgrch37 [![vepgrch37-docker status][vepgrch37-docker-badge]][vepgrch37-docker-link]
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- 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
157136
[picard-docker-badge]: https://img.shields.io/docker/automated/maxulysse/picard.svg
158137
[picard-docker-link]: https://hub.docker.com/r/maxulysse/picard
159138
[picard-link]: https://github.com/broadinstitute/picard
160-
[qualimap-docker-badge]: https://img.shields.io/docker/automated/maxulysse/qualimap.svg
161-
[qualimap-docker-link]: https://hub.docker.com/r/maxulysse/qualimap
139+
[qctools-docker-badge]: https://img.shields.io/docker/automated/maxulysse/qctools.svg
140+
[qctools-docker-link]: https://hub.docker.com/r/maxulysse/qctools
162141
[qualimap-link]: http://qualimap.bioinfo.cipf.es
163142
[rcolorbrewer-link]: https://CRAN.R-project.org/package=RColorBrewer
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[runallelecount-docker-badge]: https://img.shields.io/docker/automated/maxulysse/runallelecount.svg

‎scripts/do_all.sh‎

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@@ -57,8 +57,8 @@ function toLower() {
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if [[ $TOOL = docker ]] && [[ GRCh37,GRCh38 =~ $GENOME ]]
5959
then
60-
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
60+
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
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nextflow run buildContainers.nf -profile ${PROFILE} --verbose --docker ${PUSH} --repository ${REPOSITORY} --tag ${TAG} --containers snpeff$(toLower ${GENOME}),vep$(toLower ${GENOME})
6262
else
63-
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})
63+
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})
6464
fi

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