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Don't pass in intervals file to freec #1214

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merged 5 commits into from
Sep 8, 2023
Merged

Don't pass in intervals file to freec #1214

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348cef4
Don't pass in intervals file to freec
FriederikeHanssen Sep 7, 2023
79c8e16
Update CHANGELOG.md
FriederikeHanssen Sep 7, 2023
4acf210
Fix caridanlity
FriederikeHanssen Sep 7, 2023
29eb2d6
Merge remote-tracking branch 'origin/controlfreec_bug' into controlfr…
FriederikeHanssen Sep 7, 2023
58457e8
Merge branch 'dev' into controlfreec_bug
maxulysse Sep 7, 2023
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -58,6 +58,7 @@ Rapaselet is a delta formed by the Rapaätno river between the Bielloriehppe mas
- [#1203](https://github.com/nf-core/sarek/pull/1203) - Fix issue with Singularity containers on test profiles
- [#1204](https://github.com/nf-core/sarek/pull/1204) - Fix issue with nf-validation: lane can be a requirement of bam too now
- [#1205](https://github.com/nf-core/sarek/pull/1205) - Less tests triggered
- [#](https://github.com/nf-core/sarek/pull/) - Don't pass in intervals file to ControlFREEC for WGS analysis
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### Dependencies

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5 changes: 4 additions & 1 deletion subworkflows/local/bam_variant_calling_somatic_all/main.nf
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Expand Up @@ -41,6 +41,7 @@ workflow BAM_VARIANT_CALLING_SOMATIC_ALL {
gc_file // channel: [optional] ascat gc content file
rt_file // channel: [optional] ascat rt file
joint_mutect2 // boolean: [mandatory] [default: false] run mutect2 in joint mode
wes // boolean: [mandatory] [default: false] whether targeted data is processed

main:
versions = Channel.empty()
Expand Down Expand Up @@ -94,6 +95,8 @@ workflow BAM_VARIANT_CALLING_SOMATIC_ALL {

length_file = cf_chrom_len ?: fasta_fai

intervals_controlfreec = wes ? intervals_bed_combined : []

BAM_VARIANT_CALLING_SOMATIC_CONTROLFREEC(
mpileup_pair,
fasta,
Expand All @@ -102,7 +105,7 @@ workflow BAM_VARIANT_CALLING_SOMATIC_ALL {
dbsnp_tbi,
chr_files,
mappability,
intervals_bed_combined
intervals_controlfreec
)

versions = versions.mix(MPILEUP_NORMAL.out.versions)
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5 changes: 3 additions & 2 deletions subworkflows/local/bam_variant_calling_tumor_only_all/main.nf
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Expand Up @@ -61,7 +61,8 @@ workflow BAM_VARIANT_CALLING_TUMOR_ONLY_ALL {

// CONTROLFREEC (depends on MPILEUP)
if (tools.split(',').contains('controlfreec')) {
length_file = cf_chrom_len ?: fasta_fai
length_file = cf_chrom_len ?: fasta_fai
intervals_controlfreec = wes ? intervals_bed_combined : []

BAM_VARIANT_CALLING_TUMOR_ONLY_CONTROLFREEC(
// Remap channel to match module/subworkflow
Expand All @@ -72,7 +73,7 @@ workflow BAM_VARIANT_CALLING_TUMOR_ONLY_ALL {
dbsnp_tbi,
chr_files,
mappability,
intervals_bed_combined
intervals_controlfreec
)

versions = versions.mix(BAM_VARIANT_CALLING_TUMOR_ONLY_CONTROLFREEC.out.versions)
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6 changes: 4 additions & 2 deletions workflows/sarek.nf
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Expand Up @@ -1146,7 +1146,8 @@ workflow SAREK {
mappability,
pon,
pon_tbi,
params.joint_mutect2
params.joint_mutect2,
params.wes
)

// PAIR VARIANT CALLING
Expand Down Expand Up @@ -1175,7 +1176,8 @@ workflow SAREK {
loci_files,
gc_file,
rt_file,
params.joint_mutect2
params.joint_mutect2,
params.wes
)

// POST VARIANTCALLING
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