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TMB #616

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TMB #616

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3587591
come up with a structure to support all tools for tmb
FriederikeHanssen Jul 4, 2022
f3ceb55
Add lib script
FriederikeHanssen Jul 5, 2022
bef4ff1
Merge usptream/dev
FriederikeHanssen Aug 3, 2022
367fc77
poc
FriederikeHanssen Aug 5, 2022
2d2bd26
add to possible tool input
FriederikeHanssen Aug 11, 2022
b9b1191
first working version, lots still hardcoded
FriederikeHanssen Aug 11, 2022
e918016
remove projectdir from groovy function, can't be resolved
FriederikeHanssen Aug 11, 2022
ae380e3
add sample name
FriederikeHanssen Aug 11, 2022
9c4bca2
Merge remote-tracking branch 'upstream/dev' into tmb_curie
FriederikeHanssen Oct 11, 2022
f3056cd
Merge remote-tracking branch 'origin/tmb_curie' into tmb_curie
FriederikeHanssen Oct 11, 2022
d732f4d
merge upstream/dev
FriederikeHanssen Nov 10, 2022
ccac196
remove old modules.config
FriederikeHanssen Nov 10, 2022
a36d349
remove files not part of this PR
FriederikeHanssen Nov 10, 2022
01e06ea
update modules
FriederikeHanssen Nov 10, 2022
500543c
add new step to handle vcf&tbi combi
FriederikeHanssen Nov 10, 2022
ea51471
reorganize code
FriederikeHanssen Nov 10, 2022
c00837d
this works :tada:
FriederikeHanssen Nov 10, 2022
44d56a1
add selection function back in
FriederikeHanssen Nov 10, 2022
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add new step to handle vcf&tbi combi
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@FriederikeHanssen
FriederikeHanssen committed Nov 10, 2022
commit 500543c7023f010d8842efc0c056544649caa35c
3 changes: 2 additions & 1 deletion nextflow_schema.json
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Original file line number Diff line number Diff line change
Expand Up @@ -24,7 +24,8 @@
"prepare_recalibration",
"recalibrate",
"variant_calling",
"annotate"
"annotate",
"post-process"
]
},
"input": {
Expand Down
37 changes: 28 additions & 9 deletions workflows/sarek.nf
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Expand Up @@ -280,7 +280,7 @@ include { VCF_QC_BCFTOOLS_VCFTOOLS } from '../subworkflows
include { VCF_ANNOTATE_ALL } from '../subworkflows/local/vcf_annotate_all/main'

// Tumor mutational burden
include { TUMOR_MUTATIONAL_BURDEN } from '../subworkflows/nf-core/tumor_mutational_burden'
include { TUMOR_MUTATIONAL_BURDEN } from '../subworkflows/local/tumor_mutational_burden'

// REPORTING VERSIONS OF SOFTWARE USED
include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoftwareversions/main'
Expand Down Expand Up @@ -869,7 +869,7 @@ workflow SAREK {

if (params.tools) {

if (params.step == 'annotate') ch_cram_variant_calling = Channel.empty()
if (params.step == 'annotate' || params.step == 'post-process') ch_cram_variant_calling = Channel.empty()

//
// Logic to separate germline samples, tumor samples with no matched normal, and combine tumor-normal pairs
Expand Down Expand Up @@ -1054,16 +1054,22 @@ workflow SAREK {
vep_cache,
vep_extra_files)

vcf_to_postprocess = VCF_ANNOTATE_ALL.out.vcf_ann

// Gather used softwares versions
ch_versions = ch_versions.mix(VCF_ANNOTATE_ALL.out.versions)
ch_reports = ch_reports.mix(VCF_ANNOTATE_ALL.out.reports)
}

if(params.tools && params.tools.contains('tmb')){
vcf_to_tmb = vcf_to_annotate //TODO: proper input ANNOTATE.out.vcf_ann
// Post-process
if (params.step == 'post-process') vcf_to_postprocess = ch_input_sample

if (params.tools.split(',').contains('tmb') ) {

TUMOR_MUTATIONAL_BURDEN(vcf_to_postprocess, fasta, intervals_bed_combined)

ch_versions = ch_versions.mix(TUMOR_MUTATIONAL_BURDEN.out.versions)

intervals_bed_combined.view()
TUMOR_MUTATIONAL_BURDEN(vcf_to_tmb, fasta, intervals_bed_combined)
}
}

Expand Down Expand Up @@ -1333,7 +1339,20 @@ def extract_csv(csv_file) {
}

// annotation
} else if (row.vcf) {
} else if (row.vcf && !row.tbi) {
meta.id = meta.sample
def vcf = file(row.vcf, checkIfExists: true)

meta.data_type = 'vcf'
meta.variantcaller = row.variantcaller ?: ''

if (params.step == 'annotate') return [meta, vcf]
else {
log.error "Samplesheet contains vcf files but step is `$params.step`. Please check your samplesheet or adjust the step parameter.\nhttps://nf-co.re/sarek/usage#input-samplesheet-configurations"
System.exit(1)
}
// post-process
} else if (row.tbi) {
meta.id = meta.sample
def vcf = file(row.vcf, checkIfExists: true)
def tbi = file(row.tbi, checkIfExists: true)
Expand All @@ -1342,9 +1361,9 @@ def extract_csv(csv_file) {
meta.variantcaller = row.variantcaller ?: ''
meta.annotation = row.annotation ?: ''

if (params.step == 'annotate') return [meta, vcf, tbi]
if (params.step == 'post-process') return [meta, vcf, tbi]
else {
log.error "Samplesheet contains vcf files but step is `$params.step`. Please check your samplesheet or adjust the step parameter.\nhttps://nf-co.re/sarek/usage#input-samplesheet-configurations"
log.error "Samplesheet contains vcf & tbi files but step is `$params.step`. Please check your samplesheet or adjust the step parameter.\nhttps://nf-co.re/sarek/usage#input-samplesheet-configurations"
System.exit(1)
}
} else {
Expand Down