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Commit c562e33

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author
Szilveszter Juhos
authored
Merge branch 'master' into installNextflowDoc
2 parents 92cfb1b + 4517f57 commit c562e33

5 files changed

Lines changed: 341 additions & 154 deletions

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‎CHANGELOG.md‎

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Original file line numberDiff line numberDiff line change
@@ -55,6 +55,9 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
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- [#604](https://github.com/SciLifeLab/Sarek/pull/604) - Synching `GRCh38` `wgs_calling_regions` bedfiles
5656
- [#607](https://github.com/SciLifeLab/Sarek/pull/607) - Update to GATK4
5757
- [#607](https://github.com/SciLifeLab/Sarek/pull/607) - One container approach
58+
- [#608](https://github.com/SciLifeLab/Sarek/pull/608) - Update Nextflow required version
59+
- [#616](https://github.com/SciLifeLab/Sarek/pull/616) - Update CHANGELOG
60+
- [#617](https://github.com/SciLifeLab/Sarek/pull/617) - Replace depreciated $name syntax with withName
5861

5962
### `Fixed`
6063
- [#560](https://github.com/SciLifeLab/Sarek/pull/560) - Display message for `repository` and `containerPath`

‎configuration/containers.config‎

Lines changed: 135 additions & 45 deletions
Original file line numberDiff line numberDiff line change
@@ -8,49 +8,139 @@
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*/
99

1010
process {
11-
$BuildBWAindexes.container = "${params.repository}/sarek:${params.tag}"
12-
$BuildReferenceIndex.container = "${params.repository}/sarek:${params.tag}"
13-
$BuildSAMToolsIndex.container = "${params.repository}/sarek:${params.tag}"
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$BuildVCFIndex.container = "${params.repository}/sarek:${params.tag}"
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$CompressVCF.container = "${params.repository}/sarek:${params.tag}"
16-
$ConcatVCF.container = "${params.repository}/sarek:${params.tag}"
17-
$CreateRecalibrationTable.container = "${params.repository}/sarek:${params.tag}"
18-
$GetVersionAll.container = "${params.repository}/sarek:${params.tag}"
19-
$GetVersionAlleleCount.container = "${params.repository}/runallelecount:${params.tag}"
20-
$GetVersionASCAT.container = "${params.repository}/r-base:${params.tag}"
21-
$GetVersionBamQC.container = "${params.repository}/sarek:${params.tag}"
22-
$GetVersionBCFtools.container = "${params.repository}/sarek:${params.tag}"
23-
$GetVersionBWAsamtools.container = "${params.repository}/sarek:${params.tag}"
24-
$GetVersionFastQC.container = "${params.repository}/sarek:${params.tag}"
25-
$GetVersionFreeBayes.container = "${params.repository}/sarek:${params.tag}"
26-
$GetVersionGATK.container = "${params.repository}/sarek:${params.tag}"
27-
$GetVersionManta.container = "${params.repository}/sarek:${params.tag}"
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$GetVersionSnpeff.container = {params.genome == 'GRCh38' ? "${params.repository}/snpeffgrch38:${params.tag}" : "${params.repository}/snpeffgrch37:${params.tag}"}
29-
$GetVersionStrelka.container = "${params.repository}/sarek:${params.tag}"
30-
$GetVersionVCFtools.container = "${params.repository}/sarek:${params.tag}"
31-
$GetVersionVEP.container = {params.genome == 'GRCh38' ? "${params.repository}/vepgrch38:${params.tag}" : "${params.repository}/vepgrch37:${params.tag}"}
32-
$MapReads.container = "${params.repository}/sarek:${params.tag}"
33-
$MarkDuplicates.container = "${params.repository}/sarek:${params.tag}"
34-
$MergeBams.container = "${params.repository}/sarek:${params.tag}"
35-
$RecalibrateBam.container = "${params.repository}/sarek:${params.tag}"
36-
$RunAlleleCount.container = "${params.repository}/runallelecount:${params.tag}"
37-
$RunAscat.container = "${params.repository}/r-base:${params.tag}"
38-
$RunBamQC.container = "${params.repository}/sarek:${params.tag}"
39-
$RunBcftoolsStats.container = "${params.repository}/sarek:${params.tag}"
40-
$RunConvertAlleleCounts.container = "${params.repository}/r-base:${params.tag}"
41-
$RunFastQC.container = "${params.repository}/sarek:${params.tag}"
42-
$RunFreeBayes.container = "${params.repository}/sarek:${params.tag}"
43-
$RunGenotypeGVCFs.container = "${params.repository}/sarek:${params.tag}"
44-
$RunHaplotypecaller.container = "${params.repository}/sarek:${params.tag}"
45-
$RunManta.container = "${params.repository}/sarek:${params.tag}"
46-
$RunMultiQC.container = "${params.repository}/sarek:${params.tag}"
47-
$RunMutect2.container = "${params.repository}/sarek:${params.tag}"
48-
$RunSamtoolsStats.container = "${params.repository}/sarek:${params.tag}"
49-
$RunSingleManta.container = "${params.repository}/sarek:${params.tag}"
50-
$RunSingleStrelka.container = "${params.repository}/sarek:${params.tag}"
51-
$RunSnpeff.container = {params.genome == 'GRCh38' ? "${params.repository}/snpeffgrch38:${params.tag}" : "${params.repository}/snpeffgrch37:${params.tag}"}
52-
$RunStrelka.container = "${params.repository}/sarek:${params.tag}"
53-
$RunStrelkaBP.container = "${params.repository}/sarek:${params.tag}"
54-
$RunVcftools.container = "${params.repository}/sarek:${params.tag}"
55-
$RunVEP.container = {params.genome == 'GRCh38' ? "${params.repository}/vepgrch38:${params.tag}" : "${params.repository}/vepgrch37:${params.tag}"}
11+
withName:BuildBWAindexes {
12+
container = "${params.repository}/sarek:${params.tag}"
13+
}
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withName:BuildReferenceIndex {
15+
container = "${params.repository}/sarek:${params.tag}"
16+
}
17+
withName:BuildSAMToolsIndex {
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container = "${params.repository}/sarek:${params.tag}"
19+
}
20+
withName:BuildVCFIndex {
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container = "${params.repository}/sarek:${params.tag}"
22+
}
23+
withName:CompressVCF {
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container = "${params.repository}/sarek:${params.tag}"
25+
}
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withName:ConcatVCF {
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container = "${params.repository}/sarek:${params.tag}"
28+
}
29+
withName:CreateRecalibrationTable {
30+
container = "${params.repository}/sarek:${params.tag}"
31+
}
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withName:GetVersionAll {
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container = "${params.repository}/sarek:${params.tag}"
34+
}
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withName:GetVersionAlleleCount {
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container = "${params.repository}/runallelecount:${params.tag}"
37+
}
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withName:GetVersionASCAT {
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container = "${params.repository}/r-base:${params.tag}"
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}
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withName:GetVersionBamQC {
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container = "${params.repository}/sarek:${params.tag}"
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}
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withName:GetVersionBCFtools {
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container = "${params.repository}/sarek:${params.tag}"
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}
47+
withName:GetVersionBWAsamtools {
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container = "${params.repository}/sarek:${params.tag}"
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}
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withName:GetVersionFastQC {
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container = "${params.repository}/sarek:${params.tag}"
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}
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withName:GetVersionFreeBayes {
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container = "${params.repository}/sarek:${params.tag}"
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}
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withName:GetVersionGATK {
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container = "${params.repository}/sarek:${params.tag}"
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}
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withName:GetVersionManta {
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container = "${params.repository}/sarek:${params.tag}"
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}
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withName:GetVersionSnpeff {
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container = {params.genome == 'GRCh38' ? "${params.repository}/snpeffgrch38:${params.tag}" : "${params.repository}/snpeffgrch37:${params.tag}"}
64+
}
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withName:GetVersionStrelka {
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container = "${params.repository}/sarek:${params.tag}"
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}
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withName:GetVersionVCFtools {
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container = "${params.repository}/sarek:${params.tag}"
70+
}
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withName:GetVersionVEP {
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container = {params.genome == 'GRCh38' ? "${params.repository}/vepgrch38:${params.tag}" : "${params.repository}/vepgrch37:${params.tag}"}
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}
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withName:MapReads {
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container = "${params.repository}/sarek:${params.tag}"
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}
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withName:MarkDuplicates {
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container = "${params.repository}/sarek:${params.tag}"
79+
}
80+
withName:MergeBams {
81+
container = "${params.repository}/sarek:${params.tag}"
82+
}
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withName:RecalibrateBam {
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container = "${params.repository}/sarek:${params.tag}"
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}
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withName:RunAlleleCount {
87+
container = "${params.repository}/runallelecount:${params.tag}"
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}
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withName:RunAscat {
90+
container = "${params.repository}/r-base:${params.tag}"
91+
}
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withName:RunBamQC {
93+
container = "${params.repository}/sarek:${params.tag}"
94+
}
95+
withName:RunBcftoolsStats {
96+
container = "${params.repository}/sarek:${params.tag}"
97+
}
98+
withName:RunConvertAlleleCounts {
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container = "${params.repository}/r-base:${params.tag}"
100+
}
101+
withName:RunFastQC {
102+
container = "${params.repository}/sarek:${params.tag}"
103+
}
104+
withName:RunFreeBayes {
105+
container = "${params.repository}/sarek:${params.tag}"
106+
}
107+
withName:RunGenotypeGVCFs {
108+
container = "${params.repository}/sarek:${params.tag}"
109+
}
110+
withName:RunHaplotypecaller {
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container = "${params.repository}/sarek:${params.tag}"
112+
}
113+
withName:RunManta {
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container = "${params.repository}/sarek:${params.tag}"
115+
}
116+
withName:RunMultiQC {
117+
container = "${params.repository}/sarek:${params.tag}"
118+
}
119+
withName:RunMutect2 {
120+
container = "${params.repository}/sarek:${params.tag}"
121+
}
122+
withName:RunSamtoolsStats {
123+
container = "${params.repository}/sarek:${params.tag}"
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}
125+
withName:RunSingleManta {
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container = "${params.repository}/sarek:${params.tag}"
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}
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withName:RunSingleStrelka {
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container = "${params.repository}/sarek:${params.tag}"
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}
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withName:RunSnpeff {
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container = {params.genome == 'GRCh38' ? "${params.repository}/snpeffgrch38:${params.tag}" : "${params.repository}/snpeffgrch37:${params.tag}"}
133+
}
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withName:RunStrelka {
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container = "${params.repository}/sarek:${params.tag}"
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}
137+
withName:RunStrelkaBP {
138+
container = "${params.repository}/sarek:${params.tag}"
139+
}
140+
withName:RunVcftools {
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container = "${params.repository}/sarek:${params.tag}"
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}
143+
withName:RunVEP {
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container = {params.genome == 'GRCh38' ? "${params.repository}/vepgrch38:${params.tag}" : "${params.repository}/vepgrch37:${params.tag}"}
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}
56146
}

‎configuration/singularity-path.config‎

Lines changed: 141 additions & 47 deletions
Original file line numberDiff line numberDiff line change
@@ -13,51 +13,145 @@ singularity {
1313
}
1414

1515
process {
16-
$BuildBWAindexes.container = "${params.containerPath}/sarek-${params.tag}.img"
17-
$BuildReferenceIndex.container = "${params.containerPath}/sarek-${params.tag}.img"
18-
$BuildSAMToolsIndex.container = "${params.containerPath}/sarek-${params.tag}.img"
19-
$BuildVCFIndex.container = "${params.containerPath}/sarek-${params.tag}.img"
20-
$CompressVCF.container = "${params.containerPath}/sarek-${params.tag}.img"
21-
$ConcatVCF.container = "${params.containerPath}/sarek-${params.tag}.img"
22-
$CreateRecalibrationTable.container = "${params.containerPath}/sarek-${params.tag}.img"
23-
$GetVersionAll.container = "${params.containerPath}/sarek-${params.tag}.img"
24-
$GetVersionAlleleCount.container = "${params.containerPath}/runallelecount-${params.tag}.img"
25-
$GetVersionASCAT.container = "${params.containerPath}/r-base-${params.tag}.img"
26-
$GetVersionBamQC.container = "${params.containerPath}/sarek-${params.tag}.img"
27-
$GetVersionBCFtools.container = "${params.containerPath}/sarek-${params.tag}.img"
28-
$GetVersionBWAsamtools.container = "${params.containerPath}/sarek-${params.tag}.img"
29-
$GetVersionFastQC.container = "${params.containerPath}/sarek-${params.tag}.img"
30-
$GetVersionFreeBayes.container = "${params.containerPath}/sarek-${params.tag}.img"
31-
$GetVersionGATK.container = "${params.containerPath}/sarek-${params.tag}.img"
32-
$GetVersionManta.container = "${params.containerPath}/sarek-${params.tag}.img"
33-
$GetVersionSnpeff.container = {params.genome == 'GRCh38' ? "${params.containerPath}/snpeffgrch38-${params.tag}.img" : "${params.containerPath}/snpeffgrch37-${params.tag}.img"}
34-
$GetVersionStrelka.container = "${params.containerPath}/sarek-${params.tag}.img"
35-
$GetVersionVCFtools.container = "${params.containerPath}/sarek-${params.tag}.img"
36-
$GetVersionVEP.container = {params.genome == 'GRCh38' ? "${params.containerPath}/vepgrch38-${params.tag}.img" : "${params.containerPath}/vepgrch37-${params.tag}.img"}
37-
$IndelRealigner.container = "${params.containerPath}/sarek-${params.tag}.img"
38-
$MapReads.container = "${params.containerPath}/sarek-${params.tag}.img"
39-
$MarkDuplicates.container = "${params.containerPath}/sarek-${params.tag}.img"
40-
$MergeBams.container = "${params.containerPath}/sarek-${params.tag}.img"
41-
$RealignerTargetCreator.container = "${params.containerPath}/sarek-${params.tag}.img"
42-
$RecalibrateBam.container = "${params.containerPath}/sarek-${params.tag}.img"
43-
$RunAlleleCount.container = "${params.containerPath}/runallelecount-${params.tag}.img"
44-
$RunAscat.container = "${params.containerPath}/r-base-${params.tag}.img"
45-
$RunBamQC.container = "${params.containerPath}/sarek-${params.tag}.img"
46-
$RunBcftoolsStats.container = "${params.containerPath}/sarek-${params.tag}.img"
47-
$RunConvertAlleleCounts.container = "${params.containerPath}/r-base-${params.tag}.img"
48-
$RunFastQC.container = "${params.containerPath}/sarek-${params.tag}.img"
49-
$RunFreeBayes.container = "${params.containerPath}/sarek-${params.tag}.img"
50-
$RunGenotypeGVCFs.container = "${params.containerPath}/sarek-${params.tag}.img"
51-
$RunHaplotypecaller.container = "${params.containerPath}/sarek-${params.tag}.img"
52-
$RunManta.container = "${params.containerPath}/sarek-${params.tag}.img"
53-
$RunMultiQC.container = "${params.containerPath}/sarek-${params.tag}.img"
54-
$RunMutect2.container = "${params.containerPath}/sarek-${params.tag}.img"
55-
$RunSamtoolsStats.container = "${params.containerPath}/sarek-${params.tag}.img"
56-
$RunSingleManta.container = "${params.containerPath}/sarek-${params.tag}.img"
57-
$RunSingleStrelka.container = "${params.containerPath}/sarek-${params.tag}.img"
58-
$RunSnpeff.container = {params.genome == 'GRCh38' ? "${params.containerPath}/snpeffgrch38-${params.tag}.img" : "${params.containerPath}/snpeffgrch37-${params.tag}.img"}
59-
$RunStrelka.container = "${params.containerPath}/sarek-${params.tag}.img"
60-
$RunStrelkaBP.container = "${params.containerPath}/sarek-${params.tag}.img"
61-
$RunVcftools.container = "${params.containerPath}/sarek-${params.tag}.img"
62-
$RunVEP.container = {params.genome == 'GRCh38' ? "${params.containerPath}/vepgrch38-${params.tag}.img" : "${params.containerPath}/vepgrch37-${params.tag}.img"}
16+
withName:BuildBWAindexes {
17+
container = "${params.containerPath}/sarek-${params.tag}.img"
18+
}
19+
withName:BuildReferenceIndex {
20+
container = "${params.containerPath}/sarek-${params.tag}.img"
21+
}
22+
withName:BuildSAMToolsIndex {
23+
container = "${params.containerPath}/sarek-${params.tag}.img"
24+
}
25+
withName:BuildVCFIndex {
26+
container = "${params.containerPath}/sarek-${params.tag}.img"
27+
}
28+
withName:CompressVCF {
29+
container = "${params.containerPath}/sarek-${params.tag}.img"
30+
}
31+
withName:ConcatVCF {
32+
container = "${params.containerPath}/sarek-${params.tag}.img"
33+
}
34+
withName:CreateRecalibrationTable {
35+
container = "${params.containerPath}/sarek-${params.tag}.img"
36+
}
37+
withName:GetVersionAll {
38+
container = "${params.containerPath}/sarek-${params.tag}.img"
39+
}
40+
withName:GetVersionAlleleCount {
41+
container = "${params.containerPath}/runallelecount-${params.tag}.img"
42+
}
43+
withName:GetVersionASCAT {
44+
container = "${params.containerPath}/r-base-${params.tag}.img"
45+
}
46+
withName:GetVersionBamQC {
47+
container = "${params.containerPath}/sarek-${params.tag}.img"
48+
}
49+
withName:GetVersionBCFtools {
50+
container = "${params.containerPath}/sarek-${params.tag}.img"
51+
}
52+
withName:GetVersionBWAsamtools {
53+
container = "${params.containerPath}/sarek-${params.tag}.img"
54+
}
55+
withName:GetVersionFastQC {
56+
container = "${params.containerPath}/sarek-${params.tag}.img"
57+
}
58+
withName:GetVersionFreeBayes {
59+
container = "${params.containerPath}/sarek-${params.tag}.img"
60+
}
61+
withName:GetVersionGATK {
62+
container = "${params.containerPath}/sarek-${params.tag}.img"
63+
}
64+
withName:GetVersionManta {
65+
container = "${params.containerPath}/sarek-${params.tag}.img"
66+
}
67+
withName:GetVersionSnpeff {
68+
container = {params.genome == 'GRCh38' ? "${params.containerPath}/snpeffgrch38-${params.tag}.img" : "${params.containerPath}/snpeffgrch37-${params.tag}.img"}
69+
}
70+
withName:GetVersionStrelka {
71+
container = "${params.containerPath}/sarek-${params.tag}.img"
72+
}
73+
withName:GetVersionVCFtools {
74+
container = "${params.containerPath}/sarek-${params.tag}.img"
75+
}
76+
withName:GetVersionVEP {
77+
container = {params.genome == 'GRCh38' ? "${params.containerPath}/vepgrch38-${params.tag}.img" : "${params.containerPath}/vepgrch37-${params.tag}.img"}
78+
}
79+
withName:IndelRealigner {
80+
container = "${params.containerPath}/sarek-${params.tag}.img"
81+
}
82+
withName:MapReads {
83+
container = "${params.containerPath}/sarek-${params.tag}.img"
84+
}
85+
withName:MarkDuplicates {
86+
container = "${params.containerPath}/sarek-${params.tag}.img"
87+
}
88+
withName:MergeBams {
89+
container = "${params.containerPath}/sarek-${params.tag}.img"
90+
}
91+
withName:RealignerTargetCreator {
92+
container = "${params.containerPath}/sarek-${params.tag}.img"
93+
}
94+
withName:RecalibrateBam {
95+
container = "${params.containerPath}/sarek-${params.tag}.img"
96+
}
97+
withName:RunAlleleCount {
98+
container = "${params.containerPath}/runallelecount-${params.tag}.img"
99+
}
100+
withName:RunAscat {
101+
container = "${params.containerPath}/r-base-${params.tag}.img"
102+
}
103+
withName:RunBamQC {
104+
container = "${params.containerPath}/sarek-${params.tag}.img"
105+
}
106+
withName:RunBcftoolsStats {
107+
container = "${params.containerPath}/sarek-${params.tag}.img"
108+
}
109+
withName:RunConvertAlleleCounts {
110+
container = "${params.containerPath}/r-base-${params.tag}.img"
111+
}
112+
withName:RunFastQC {
113+
container = "${params.containerPath}/sarek-${params.tag}.img"
114+
}
115+
withName:RunFreeBayes {
116+
container = "${params.containerPath}/sarek-${params.tag}.img"
117+
}
118+
withName:RunGenotypeGVCFs {
119+
container = "${params.containerPath}/sarek-${params.tag}.img"
120+
}
121+
withName:RunHaplotypecaller {
122+
container = "${params.containerPath}/sarek-${params.tag}.img"
123+
}
124+
withName:RunManta {
125+
container = "${params.containerPath}/sarek-${params.tag}.img"
126+
}
127+
withName:RunMultiQC {
128+
container = "${params.containerPath}/sarek-${params.tag}.img"
129+
}
130+
withName:RunMutect2 {
131+
container = "${params.containerPath}/sarek-${params.tag}.img"
132+
}
133+
withName:RunSamtoolsStats {
134+
container = "${params.containerPath}/sarek-${params.tag}.img"
135+
}
136+
withName:RunSingleManta {
137+
container = "${params.containerPath}/sarek-${params.tag}.img"
138+
}
139+
withName:RunSingleStrelka {
140+
container = "${params.containerPath}/sarek-${params.tag}.img"
141+
}
142+
withName:RunSnpeff {
143+
container = {params.genome == 'GRCh38' ? "${params.containerPath}/snpeffgrch38-${params.tag}.img" : "${params.containerPath}/snpeffgrch37-${params.tag}.img"}
144+
}
145+
withName:RunStrelka {
146+
container = "${params.containerPath}/sarek-${params.tag}.img"
147+
}
148+
withName:RunStrelkaBP {
149+
container = "${params.containerPath}/sarek-${params.tag}.img"
150+
}
151+
withName:RunVcftools {
152+
container = "${params.containerPath}/sarek-${params.tag}.img"
153+
}
154+
withName:RunVEP {
155+
container = {params.genome == 'GRCh38' ? "${params.containerPath}/vepgrch38-${params.tag}.img" : "${params.containerPath}/vepgrch37-${params.tag}.img"}
156+
}
63157
}

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