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Merge pull request #486 from SciLifeLab/dev
merge dev into master for bug fixes and for v 1.2.3
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,12 +1,13 @@ | ||
| data/chr17_testdata | ||
| Annotation | ||
| Annotation/ | ||
| data/chr17_testdata/ | ||
| Preprocessing/ | ||
| Reports/ | ||
| References/ | ||
| Reports/ | ||
| VariantCalling/ | ||
| work/ | ||
| .*swp | ||
| .nextflow* | ||
| *.img | ||
| *.tar.gz | ||
| timeline.html* | ||
| trace.txt* | ||
| *.tar.gz |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,44 @@ | ||
| /* | ||
| vim: syntax=groovy | ||
| -*- mode: groovy;-*- | ||
| * ------------------------------------------------- | ||
| * Nextflow config file for CAW project | ||
| * ------------------------------------------------- | ||
| * Images for every process | ||
| * All images will be pulled automatically | ||
| * ------------------------------------------------- | ||
| */ | ||
|
|
||
| process { | ||
| $BuildBWAindexes.container = "${params.repository}/caw:${params.tag}" | ||
| $BuildPicardIndex.container = "${params.repository}/picard:${params.tag}" | ||
| $BuildSAMToolsIndex.container = "${params.repository}/caw:${params.tag}" | ||
| $BuildVCFIndex.container = "${params.repository}/igvtools:${params.tag}" | ||
| $ConcatVCF.container = "${params.repository}/caw:${params.tag}" | ||
| $CreateRecalibrationTable.container = "${params.repository}/gatk:${params.tag}" | ||
| $IndelRealigner.container = "${params.repository}/gatk:${params.tag}" | ||
| $MapReads.container = "${params.repository}/caw:${params.tag}" | ||
| $MarkDuplicates.container = "${params.repository}/picard:${params.tag}" | ||
| $MergeBams.container = "${params.repository}/caw:${params.tag}" | ||
| $RealignerTargetCreator.container = "${params.repository}/gatk:${params.tag}" | ||
| $RecalibrateBam.container = "${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}" | ||
| $RunBcftoolsStats.container = "${params.repository}/caw:${params.tag}" | ||
| $RunConvertAlleleCounts.container = "${params.repository}/r-base:${params.tag}" | ||
| $RunFastQC.container = "${params.repository}/fastqc:${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}/caw:${params.tag}" | ||
| $RunMultiQC.container = "${params.repository}/multiqc:${params.tag}" | ||
| $RunMutect1.container = "${params.repository}/mutect1:${params.tag}" | ||
| $RunMutect2.container = "${params.repository}/gatk:${params.tag}" | ||
| $RunSamtoolsStats.container = "${params.repository}/caw:${params.tag}" | ||
| $RunSingleManta.container = "${params.repository}/caw:${params.tag}" | ||
| $RunSingleStrelka.container = "${params.repository}/caw:${params.tag}" | ||
| $RunSnpeff.container = {params.genome == "GRCh38" ? "${params.repository}/snpeffgrch38:${params.tag}" : "${params.repository}/snpeffgrch37:${params.tag}"} | ||
| $RunStrelka.container = "${params.repository}/caw:${params.tag}" | ||
| $RunVEP.container = {params.genome == "GRCh38" ? "${params.repository}/vepgrch38:${params.tag}" : "${params.repository}/vepgrch37:${params.tag}"} | ||
| } |
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