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Enable multiple ploidy values for controlfreec #980

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Enable multiple ploidy values for controlfreec #980

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df60b0c
allow ploidy as list
FriederikeHanssen Mar 28, 2023
ddfe115
rename output according to ploidy
FriederikeHanssen Mar 28, 2023
812c99d
Merge branch 'dev' into issue_808
FriederikeHanssen Mar 28, 2023
383d62c
update changelog
FriederikeHanssen Mar 28, 2023
c38de89
update changelog
FriederikeHanssen Mar 28, 2023
75f1ffe
Reading the docs help, the ploidy is inferred by the script
FriederikeHanssen Mar 29, 2023
37c7819
remove changes
FriederikeHanssen Mar 29, 2023
4a0ec24
remove changes
FriederikeHanssen Mar 29, 2023
91ad680
[automated] Fix linting with Prettier
nf-core-bot Mar 29, 2023
b12878f
merge origin/dev
FriederikeHanssen May 29, 2023
08d314b
need ploidy as mandatory args afterall or channel magic won't work
FriederikeHanssen May 29, 2023
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -59,6 +59,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#941](https://github.com/nf-core/sarek/pull/941) - Fix json validation for `tools`, `skip_tools` and `use_gatk_spark` [#892](https://github.com/nf-core/sarek/issues/892)
- [#954](https://github.com/nf-core/sarek/pull/954) - Fix missing annotation keys with `snpeff` and `ensemblvep` for `hg19`
- [#957](https://github.com/nf-core/sarek/pull/957) - Add `failOnDuplicate` and `failOnMismatch` options to all `join()` operator where it was possible
- [#980](https://github.com/nf-core/sarek/pull/941) - Fix allowing multiple ploidy values for plotting of controlfreec output ([#808](https://github.com/nf-core/sarek/issues/808))
- [#982](https://github.com/nf-core/sarek/pull/982) - Remove usage of exit statements, using `Nextflow.error` instead
- [#985](https://github.com/nf-core/sarek/pull/985) - Cache correctly identifies when it needs to be updated
- [#988](https://github.com/nf-core/sarek/pull/988) - Updated ascat module to fix seed for reproducibility
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1 change: 0 additions & 1 deletion conf/modules/controlfreec.config
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Expand Up @@ -51,7 +51,6 @@ process {
}

withName: 'MAKEGRAPH' {
ext.args = { "${params.cf_ploidy}" }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/controlfreec/${meta.id}/" },
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4 changes: 2 additions & 2 deletions modules/nf-core/controlfreec/makegraph/main.nf
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4 changes: 3 additions & 1 deletion subworkflows/local/bam_variant_calling_somatic_all/main.nf
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Expand Up @@ -92,6 +92,7 @@ workflow BAM_VARIANT_CALLING_SOMATIC_ALL {
mpileup_pair = mpileup_normal.cross(mpileup_tumor).map{ normal, tumor -> [ normal[0], normal[1], tumor[1], [], [], [], [] ] }

length_file = cf_chrom_len ?: fasta_fai
ploidy = params.cf_ploidy && !params.cf_ploidy.toString().contains(",") ? [params.cf_ploidy] : params.cf_ploidy.split(',')
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BAM_VARIANT_CALLING_SOMATIC_CONTROLFREEC(
mpileup_pair,
Expand All @@ -101,7 +102,8 @@ workflow BAM_VARIANT_CALLING_SOMATIC_ALL {
dbsnp_tbi,
chr_files,
mappability,
intervals_bed_combined
intervals_bed_combined,
ploidy
)

versions = versions.mix(MPILEUP_NORMAL.out.versions)
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3 changes: 2 additions & 1 deletion subworkflows/local/bam_variant_calling_somatic_controlfreec/main.nf
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Expand Up @@ -14,6 +14,7 @@ workflow BAM_VARIANT_CALLING_SOMATIC_CONTROLFREEC {
chr_files // channel: [mandatory]
mappability // channel: [mandatory]
intervals_bed // channel: [optional] Contains a bed file of all intervals combined provided with the cram input(s). Should be empty for WGS
ploidy // channel: [mandatory] list of ploidy values

main:

Expand All @@ -24,7 +25,7 @@ workflow BAM_VARIANT_CALLING_SOMATIC_CONTROLFREEC {
ASSESS_SIGNIFICANCE(FREEC_SOMATIC.out.CNV.join(FREEC_SOMATIC.out.ratio, failOnDuplicate: true, failOnMismatch: true))
FREEC2BED(FREEC_SOMATIC.out.ratio)
FREEC2CIRCOS(FREEC_SOMATIC.out.ratio)
MAKEGRAPH(FREEC_SOMATIC.out.ratio.join(FREEC_SOMATIC.out.BAF, failOnDuplicate: true, failOnMismatch: true))
MAKEGRAPH(FREEC_SOMATIC.out.ratio.join(FREEC_SOMATIC.out.BAF, failOnDuplicate: true, failOnMismatch: true).combine(ploidy))

ch_versions = ch_versions.mix(FREEC_SOMATIC.out.versions)
ch_versions = ch_versions.mix(ASSESS_SIGNIFICANCE.out.versions)
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4 changes: 3 additions & 1 deletion subworkflows/local/bam_variant_calling_tumor_only_all/main.nf
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Expand Up @@ -60,6 +60,7 @@ workflow BAM_VARIANT_CALLING_TUMOR_ONLY_ALL {
// CONTROLFREEC (depends on MPILEUP)
if (tools.split(',').contains('controlfreec')) {
length_file = cf_chrom_len ?: fasta_fai
ploidy = params.cf_ploidy && !params.cf_ploidy.toString().contains(",") ? [params.cf_ploidy] : params.cf_ploidy.split(',')
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BAM_VARIANT_CALLING_TUMOR_ONLY_CONTROLFREEC(
// Remap channel to match module/subworkflow
Expand All @@ -70,7 +71,8 @@ workflow BAM_VARIANT_CALLING_TUMOR_ONLY_ALL {
dbsnp_tbi,
chr_files,
mappability,
intervals_bed_combined
intervals_bed_combined,
ploidy
)

versions = versions.mix(BAM_VARIANT_CALLING_TUMOR_ONLY_CONTROLFREEC.out.versions)
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3 changes: 2 additions & 1 deletion subworkflows/local/bam_variant_calling_tumor_only_controlfreec/main.nf
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Expand Up @@ -14,6 +14,7 @@ workflow BAM_VARIANT_CALLING_TUMOR_ONLY_CONTROLFREEC {
chr_files // channel: [mandatory]
mappability // channel: [mandatory]
intervals_bed // channel: [optional] Contains a bed file of all intervals combined provided with the cram input(s). Should be empty for WGS
ploidy // channel: [mandatory] list of ploidy values

main:

Expand All @@ -24,7 +25,7 @@ workflow BAM_VARIANT_CALLING_TUMOR_ONLY_CONTROLFREEC {
ASSESS_SIGNIFICANCE(FREEC_TUMORONLY.out.CNV.join(FREEC_TUMORONLY.out.ratio, failOnDuplicate: true, failOnMismatch: true))
FREEC2BED(FREEC_TUMORONLY.out.ratio)
FREEC2CIRCOS(FREEC_TUMORONLY.out.ratio)
MAKEGRAPH(FREEC_TUMORONLY.out.ratio.join(FREEC_TUMORONLY.out.BAF, failOnDuplicate: true, failOnMismatch: true))
MAKEGRAPH(FREEC_TUMORONLY.out.ratio.join(FREEC_TUMORONLY.out.BAF, failOnDuplicate: true, failOnMismatch: true).combine(ploidy))

ch_versions = ch_versions.mix(FREEC_TUMORONLY.out.versions)
ch_versions = ch_versions.mix(ASSESS_SIGNIFICANCE.out.versions)
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