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Fix null value for joint calling with Mutect2 #1277

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merged 5 commits into from
Oct 11, 2023
Merged

Fix null value for joint calling with Mutect2 #1277

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7387c6a
remove normal id later
FriederikeHanssen Oct 10, 2023
9c8d02d
update changelog [skip actions]
FriederikeHanssen Oct 10, 2023
0b81e81
trigger tests
FriederikeHanssen Oct 10, 2023
09fbd09
only remove normal id when joint calling
FriederikeHanssen Oct 11, 2023
2db3cbd
Merge remote-tracking branch 'origin/issue_1274' into issue_1274
FriederikeHanssen Oct 11, 2023
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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -16,6 +16,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### Fixed

- [#1277](https://github.com/nf-core/sarek/pull/1277) - Fix null value issue for Mutect2 joint calling

### Dependencies

| Dependency | Old version | New version |
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20 changes: 14 additions & 6 deletions subworkflows/local/bam_variant_calling_somatic_mutect2/main.nf
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Expand Up @@ -44,8 +44,8 @@ workflow BAM_VARIANT_CALLING_SOMATIC_MUTECT2 {
// Separate normal cram files
// Extract tumor cram files
ch_cram = input.multiMap{ meta, cram, crai ->
normal: [ meta - meta.subMap('normal_id', 'tumor_id') , cram[0], crai[0] ]
tumor: [ meta - meta.subMap('normal_id', 'tumor_id') , cram[1], crai[1] ]
normal: [ meta - meta.subMap('tumor_id') , cram[0], crai[0] ]
tumor: [ meta - meta.subMap('tumor_id') , cram[1], crai[1] ]
}

// Remove duplicates from normal channel and merge normal and tumor crams by patient
Expand Down Expand Up @@ -102,10 +102,18 @@ workflow BAM_VARIANT_CALLING_SOMATIC_MUTECT2 {
MERGEMUTECTSTATS(stats_to_merge)

// Mix intervals and no_intervals channels together and remove no longer necessary field: normal_id, tumor_id, num_intervals
vcf = Channel.empty().mix(MERGE_MUTECT2.out.vcf, vcf_branch.no_intervals).map{ meta, vcf -> [ meta - meta.subMap('num_intervals'), vcf ]}
tbi = Channel.empty().mix(MERGE_MUTECT2.out.tbi, tbi_branch.no_intervals).map{ meta, tbi -> [ meta - meta.subMap('num_intervals'), tbi ]}
stats = Channel.empty().mix(MERGEMUTECTSTATS.out.stats, stats_branch.no_intervals).map{ meta, stats -> [ meta - meta.subMap('num_intervals'), stats ]}
f1r2 = Channel.empty().mix(f1r2_to_merge, f1r2_branch.no_intervals).map{ meta, f1r2 -> [ meta - meta.subMap('num_intervals'), f1r2 ]}
vcf = Channel.empty().mix(MERGE_MUTECT2.out.vcf, vcf_branch.no_intervals).map{ meta, vcf ->
[ joint_mutect2 ? meta - meta.subMap('normal_id', 'num_intervals') : meta - meta.subMap('num_intervals') , vcf ]
}
tbi = Channel.empty().mix(MERGE_MUTECT2.out.tbi, tbi_branch.no_intervals).map{ meta, tbi->
[ joint_mutect2 ? meta - meta.subMap('normal_id', 'num_intervals') : meta - meta.subMap('num_intervals'), tbi ]
}
stats = Channel.empty().mix(MERGEMUTECTSTATS.out.stats, stats_branch.no_intervals).map{ meta, stats ->
[ joint_mutect2 ? meta - meta.subMap('normal_id', 'num_intervals') : meta - meta.subMap('num_intervals'), stats ]
}
f1r2 = Channel.empty().mix(f1r2_to_merge, f1r2_branch.no_intervals).map{ meta, f1r2->
[ joint_mutect2 ? meta - meta.subMap('normal_id', 'num_intervals') : meta - meta.subMap('num_intervals') , f1r2 ]
}

// Generate artifactpriors using learnreadorientationmodel on the f1r2 output of mutect2
LEARNREADORIENTATIONMODEL(f1r2)
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