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Merged
ramprasadn merged 5 commits into from
Jun 30, 2023
Merged

Gcnvcaller modules #3581

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ef89c33
update modules
ramprasadn Jun 27, 2023
40b27f8
update uri
ramprasadn Jun 27, 2023
bf4044f
review suggestions
ramprasadn Jun 28, 2023
daf7636
update germlinecnvcaller
ramprasadn Jun 30, 2023
753dbd7
Merge branch 'master' of https://github.com/nf-core/modules into gcnv…
ramprasadn Jun 30, 2023
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3 changes: 1 addition & 2 deletions modules/nf-core/gatk4/germlinecnvcaller/main.nf
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Expand Up @@ -11,9 +11,8 @@ process GATK4_GERMLINECNVCALLER {
}

input:
tuple val(meta), path(tsv), path(intervals)
tuple val(meta), path(tsv), path(intervals), path(ploidy)
tuple val(meta2), path(model)
tuple val(meta3), path(ploidy)

output:
tuple val(meta), path("*-cnv-calls/*-calls"), emit: calls, optional: true
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5 changes: 0 additions & 5 deletions modules/nf-core/gatk4/germlinecnvcaller/meta.yml
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Expand Up @@ -26,11 +26,6 @@ input:
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- meta3:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- tsv:
type: file
description: One or more count TSV files created with gatk/collectreadcounts
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14 changes: 7 additions & 7 deletions tests/modules/nf-core/gatk4/germlinecnvcaller/main.nf
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Expand Up @@ -48,17 +48,17 @@ workflow test_gatk4_germlinecnvcaller {
GATK4_BEDTOINTERVALLIST ( intervals, dict )

gcnvc_cohort_input = GATK4_COLLECTREADCOUNTS.out.tsv
.map({ meta, tsv -> return [[id:"test"], tsv ]})
.map({ meta, tsv -> [ [id:'test'], tsv ]})
.groupTuple()
.combine(GATK4_DETERMINEGERMLINECONTIGPLOIDY_COHORT.out.calls)
.combine(GATK4_BEDTOINTERVALLIST.out.interval_list)
.map({ meta, counts, meta2, bed -> [ meta, counts, bed ]})
.map({ meta, counts, meta2, calls, meta3, bed -> [ meta, counts, bed, calls ]})

GATK4_GERMLINECNVCALLER_COHORT ( gcnvc_cohort_input, [[],[]], GATK4_DETERMINEGERMLINECONTIGPLOIDY_COHORT.out.calls )
GATK4_GERMLINECNVCALLER_COHORT ( gcnvc_cohort_input, [[],[]] )

gcnvc_case_input = GATK4_COLLECTREADCOUNTS.out.tsv
.map({ meta, tsv -> [ [id:'test'], tsv ]})
.groupTuple()
.map({ meta, counts -> [ meta, counts, [] ]})
GATK4_GERMLINECNVCALLER_CASE ( gcnvc_case_input, GATK4_GERMLINECNVCALLER_COHORT.out.model, GATK4_DETERMINEGERMLINECONTIGPLOIDY_COHORT.out.calls )
.combine(GATK4_DETERMINEGERMLINECONTIGPLOIDY_COHORT.out.calls)
.map({ meta, counts, meta2, calls -> [ [id:'test'], counts, [], calls ]})
GATK4_GERMLINECNVCALLER_CASE ( gcnvc_case_input, GATK4_GERMLINECNVCALLER_COHORT.out.model )

}
14 changes: 7 additions & 7 deletions tests/modules/nf-core/gatk4/postprocessgermlinecnvcalls/main.nf
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Expand Up @@ -50,18 +50,18 @@ workflow test_gatk4_postprocessgermlinecnvcalls {
GATK4_BEDTOINTERVALLIST ( intervals, dict )
//
gcnvc_cohort_input = GATK4_COLLECTREADCOUNTS.out.tsv
.map({ meta, tsv -> return [[id:"test"], tsv ]})
.map({ meta, tsv -> [ [id:'test'], tsv ]})
.groupTuple()
.combine(GATK4_DETERMINEGERMLINECONTIGPLOIDY_COHORT.out.calls)
.combine(GATK4_BEDTOINTERVALLIST.out.interval_list)
.map({ meta, counts, meta2, bed -> [ meta, counts, bed ]})
.map({ meta, counts, meta2, calls, meta3, bed -> [ meta, counts, bed, calls ]})

GATK4_GERMLINECNVCALLER_COHORT ( gcnvc_cohort_input, [[],[]], GATK4_DETERMINEGERMLINECONTIGPLOIDY_COHORT.out.calls )
GATK4_GERMLINECNVCALLER_COHORT ( gcnvc_cohort_input, [[],[]] )

gcnvc_case_input = GATK4_COLLECTREADCOUNTS.out.tsv
.map({ meta, tsv -> [ [id:'test'], tsv ]})
.groupTuple()
.map({ meta, counts -> [ meta, counts, [] ]})
GATK4_GERMLINECNVCALLER_CASE ( gcnvc_case_input, GATK4_GERMLINECNVCALLER_COHORT.out.model, GATK4_DETERMINEGERMLINECONTIGPLOIDY_COHORT.out.calls )
.combine(GATK4_DETERMINEGERMLINECONTIGPLOIDY_COHORT.out.calls)
.map({ meta, counts, meta2, calls -> [ [id:'test'], counts, [], calls ]})
GATK4_GERMLINECNVCALLER_CASE ( gcnvc_case_input, GATK4_GERMLINECNVCALLER_COHORT.out.model )

GATK4_POSTPROCESSGERMLINECNVCALLS ( GATK4_DETERMINEGERMLINECONTIGPLOIDY_COHORT.out.calls,
GATK4_GERMLINECNVCALLER_COHORT.out.model,
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