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Dealing with optional and mandatory GATK resource files #592

Merged
merged 22 commits into from
Jun 20, 2022
Merged

Dealing with optional and mandatory GATK resource files #592

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f217e6a
Add error message if dbsnp or known_indels is not supplied for bqsr o…
FriederikeHanssen Jun 16, 2022
2d811ff
multi-line not supported, use \n instead
FriederikeHanssen Jun 16, 2022
dd54c4c
Make PON optional
FriederikeHanssen Jun 16, 2022
a49df17
Make germline_resource optional for mutect2
FriederikeHanssen Jun 16, 2022
30b368c
Update getpileup, deal with optional dbsnp, germline, knwon_indels
FriederikeHanssen Jun 16, 2022
f3796c1
Formatting
FriederikeHanssen Jun 16, 2022
63e8e7d
Formatting
FriederikeHanssen Jun 16, 2022
f0805af
Merge remote-tracking branch 'upstream/dev' into gatk_resource
FriederikeHanssen Jun 17, 2022
37043a0
Add suggestion on value channels to handle optional input
FriederikeHanssen Jun 17, 2022
3d34ae7
make germline_resource work again
FriederikeHanssen Jun 17, 2022
c6210fa
remove test code
FriederikeHanssen Jun 17, 2022
a72ce06
add mutect2 no intervals tests
FriederikeHanssen Jun 17, 2022
1d6e363
some indents
FriederikeHanssen Jun 17, 2022
7fd12ab
more channel :sparkles: magic
FriederikeHanssen Jun 17, 2022
17d3d72
Merge remote-tracking branch 'upstream/dev' into gatk_resource
FriederikeHanssen Jun 17, 2022
ae9eb2f
add config for mutect2 tests
FriederikeHanssen Jun 17, 2022
f8a0e12
not sure what is going with mutect2
FriederikeHanssen Jun 20, 2022
7216964
Fix getpileupsummaries output
FriederikeHanssen Jun 20, 2022
ed7c724
Update conf/modules.config
FriederikeHanssen Jun 20, 2022
975e71c
Try to request more memory
FriederikeHanssen Jun 20, 2022
26d52d4
Revert this, everything is red
FriederikeHanssen Jun 20, 2022
2aa1e2f
try .5
FriederikeHanssen Jun 20, 2022
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27 changes: 18 additions & 9 deletions conf/modules.config
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Original file line number Diff line number Diff line change
Expand Up @@ -808,8 +808,8 @@ process{
ext.args = { "-tumor-segmentation ${meta.id}.segmentation.table" }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/${meta.id}/mutect2" },
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
path: { "${params.outdir}/variant_calling/" },
saveAs: { filename -> filename.equals('versions.yml') ? null : "${meta.id}/mutect2/${filename}" }
]
}

Expand All @@ -825,8 +825,8 @@ process{
ext.prefix = {"${meta.id}.filtered"}
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/${meta.id}/mutect2" },
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
path: { "${params.outdir}/variant_calling/" },
saveAs: { filename -> filename.equals('versions.yml') ? null : "${meta.id}/mutect2/${filename}" }
]
}

Expand All @@ -846,13 +846,22 @@ process{
]
}

withName: 'GETPILEUPSUMMARIES.*' {
withName: 'GETPILEUPSUMMARIES.*' {
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ext.prefix = { meta.num_intervals <= 1 ? meta.id : "${meta.id}_${intervals.simpleName}" }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/${meta.id}/" },
path: { "${params.outdir}/variant_calling/" },
pattern: "*.table",
saveAs: { meta.num_intervals > 1 ? null : "${meta.id}/mutect2/${it}" }
]
}

withName: 'GETPILEUPSUMMARIES_.*' {
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publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/" },
pattern: "*.table",
saveAs: { meta.num_intervals > 1 ? null : "mutect2/${it}" }
saveAs: { meta.num_intervals > 1 ? null : "${meta.tumor_id}_vs_${meta.normal_id}/mutect2/${it}" }
]
}

Expand Down Expand Up @@ -880,9 +889,9 @@ process{
ext.args = { params.ignore_soft_clipped_bases ? "--dont-use-soft-clipped-bases true --f1r2-tar-gz ${task.ext.prefix}.f1r2.tar.gz" : "--f1r2-tar-gz ${task.ext.prefix}.f1r2.tar.gz" }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/${meta.id}/" },
path: { "${params.outdir}/variant_calling/" },
pattern: "*{vcf.gz,vcf.gz.tbi,stats}",
saveAs: { meta.num_intervals > 1 ? null : "mutect2/${it}" }
saveAs: { meta.num_intervals > 1 ? null : "${meta.id}/mutect2/${it}" }
]
}

Expand Down