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feat: add annotation to ffpe output
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@dnousome
dnousome committed Dec 31, 2024
1 parent fd7581f commit 95be395
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Showing 2 changed files with 298 additions and 35 deletions.
214 changes: 183 additions & 31 deletions subworkflows/local/workflows.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -50,8 +50,8 @@ include {combineVariants as combineVariants_vardict; combineVariants as combineV
combineVariants_alternative as combineVariants_lofreq; combineVariants as combineVariants_muse;
combineVariants_alternative as combineVariants_octopus;
combineVariants_alternative as combineVariants_octopus_tonly;
combinemafs_tn; somaticcombine;
combinemafs_tonly;somaticcombine_tonly} from '../../modules/local/combinefilter.nf'
combinemafs_tn; somaticcombine; somaticcombine as somaticcombine_ffpe;
combinemafs_tonly;somaticcombine_tonly; somaticcombine_tonly as somaticcombine_tonly_ffpe} from '../../modules/local/combinefilter.nf'

include {sobdetect_pass1 as sobdetect_pass1_mutect2; sobdetect_pass2 as sobdetect_pass2_mutect2;
sobdetect_metrics as sobdetect_metrics_mutect2; sobdetect_cohort_params as sobdetect_cohort_params_mutect2;
Expand All @@ -67,9 +67,30 @@ include {sobdetect_pass1 as sobdetect_pass1_mutect2; sobdetect_pass2 as sobdetec
sobdetect_metrics as sobdetect_metrics_vardict; sobdetect_cohort_params as sobdetect_cohort_params_vardict;
sobdetect_pass1 as sobdetect_pass1_varscan; sobdetect_pass2 as sobdetect_pass2_varscan;
sobdetect_metrics as sobdetect_metrics_varscan; sobdetect_cohort_params as sobdetect_cohort_params_varscan;
//Tumor Only
sobdetect_pass1 as sobdetect_pass1_mutect2_tonly; sobdetect_pass2 as sobdetect_pass2_mutect2_tonly;
sobdetect_metrics as sobdetect_metrics_mutect2_tonly; sobdetect_cohort_params as sobdetect_cohort_params_mutect2_tonly;
sobdetect_pass1 as sobdetect_pass1_octopus_tonly; sobdetect_pass2 as sobdetect_pass2_octopus_tonly;
sobdetect_metrics as sobdetect_metrics_octopus_tonly; sobdetect_cohort_params as sobdetect_cohort_params_octopus_tonly;
sobdetect_pass1 as sobdetect_pass1_vardict_tonly; sobdetect_pass2 as sobdetect_pass2_vardict_tonly;
sobdetect_metrics as sobdetect_metrics_vardict_tonly; sobdetect_cohort_params as sobdetect_cohort_params_vardict_tonly;
sobdetect_pass1 as sobdetect_pass1_varscan_tonly; sobdetect_pass2 as sobdetect_pass2_varscan_tonly;
sobdetect_metrics as sobdetect_metrics_varscan_tonly; sobdetect_cohort_params as sobdetect_cohort_params_varscan_tonly

} from "../../modules/local/ffpe.nf"


include {annotvep_tn as annotvep_tn_mut2_ffpe; annotvep_tn as annotvep_tn_strelka_ffpe;
annotvep_tn as annotvep_tn_varscan_ffpe; annotvep_tn as annotvep_tn_vardict_ffpe; annotvep_tn as annotvep_tn_octopus_ffpe;
annotvep_tn as annotvep_tn_lofreq_ffpe; annotvep_tn as annotvep_tn_muse_ffpe; annotvep_tn as annotvep_tn_sage_ffpe;
annotvep_tn as annotvep_tn_deepsomatic_ffpe;
annotvep_tn as annotvep_tn_combined_ffpe;
annotvep_tonly as annotvep_tonly_varscan_ffpe; annotvep_tonly as annotvep_tonly_vardict_ffpe;
annotvep_tonly as annotvep_tonly_mut2_ffpe; annotvep_tonly as annotvep_tonly_octopus_ffpe;
annotvep_tonly as annotvep_tonly_sage_ffpe; annotvep_tonly as annotvep_tonly_deepsomatic_ffpe;
annotvep_tonly as annotvep_tonly_combined_ffpe} from '../../modules/local/annotvep.nf'


include {annotvep_tn as annotvep_tn_mut2; annotvep_tn as annotvep_tn_strelka;
annotvep_tn as annotvep_tn_varscan; annotvep_tn as annotvep_tn_vardict; annotvep_tn as annotvep_tn_octopus;
annotvep_tn as annotvep_tn_lofreq; annotvep_tn as annotvep_tn_muse; annotvep_tn as annotvep_tn_sage;
Expand Down Expand Up @@ -520,30 +541,7 @@ workflow VC {

}


//Combine All Variants Using VCF -> Annotate
if (call_list.size()>1){
vc_all | groupTuple(by:[0,1])
| somaticcombine
| map{tumor,normal,vcf,index ->tuple(tumor,normal,"combined",vcf,index)}
| annotvep_tn_combined

if (!params.no_tonly & call_list_tonly.size()>1){
vc_tonly | groupTuple()
| somaticcombine_tonly
| map{tumor,vcf,index ->tuple(tumor,"combined_tonly",vcf,index)}
| annotvep_tonly_combined
}
}

if("sage" in call_list){
somaticcall_input=sage_in
}else if("mutect2" in call_list){
somaticcall_input=mutect2_in
}else{
somaticcall_input=Channel.empty()
}


//FFPE Steps
if(params.ffpe){
vc_ffpe_paired=Channel.empty()
Expand All @@ -563,9 +561,37 @@ workflow VC {
| map{tumor,normal,tbam,tbai,nbam,nbai,vc,normvcf,tbi->tuple("${tumor}_vs_${normal}",normvcf,tbam,vc)}
| combine(sobdetect_cohort_params_mutect2.out)
| sobdetect_pass2_mutect2
mutect2_p1_vcfs=mutect2_p1 | map{sample,vcf,info->vcf} |collect
mutect2_p2_vcfs=mutect2_p2 | map{sample,vcf,info,filtvcf,vcftbi->vcf} |collect
mutect2_p1_vcfs=mutect2_p1 | map{sample,vcf,info->vcf} | collect
mutect2_p2_vcfs=mutect2_p2 | map{sample,vcf,info,filtvcf,vcftbi->vcf} | collect
sobdetect_metrics_mutect2(mutect2_p1_vcfs,mutect2_p2_vcfs)

mutect2_ffpe_out=mutect2_p2 | map{sample,vcf,info,filtvcf,vcftbi->tuple(sample.split("_vs_")[0],sample.split("_vs_")[1],"mutect2",filtvcf,vcftbi)}
annotvep_tn_mut2_ffpe(mutect2_ffpe_out)
vc_ffpe_paired=vc_ffpe_paired |concat(mutect2_ffpe_out)

if (!params.no_tonly){
mutect2_tonly_p1=bamwithsample1 | join(mutect2_in_tonly)
| map{tumor,normal,tbam,tbai,nbam,nbai,vc,normvcf,tbi->tuple(tumor,normvcf,tbam,vc)}
| sobdetect_pass1_mutect2_tonly
mutect2_tonly_p1 | map{sample,vcf,info->info}
| collect
| sobdetect_cohort_params_mutect2_tonly

mutect2_tonly_p2 = bamwithsample1
| join(mutect2_in_tonly)
| map{tumor,normal,tbam,tbai,nbam,nbai,vc,normvcf,tbi->tuple(tumor,normvcf,tbam,vc)}
| combine(sobdetect_cohort_params_mutect2_tonly.out)
| sobdetect_pass2_mutect2_tonly
mutect2_tonly_p1_vcfs=mutect2_tonly_p1 | map{sample,vcf,info->vcf} |collect
mutect2_tonly_p2_vcfs=mutect2_tonly_p2 | map{sample,vcf,info,filtvcf,vcftbi->vcf} |collect
sobdetect_metrics_mutect2_tonly(mutect2_tonly_p1_vcfs,mutect2_tonly_p2_vcfs)

mutect2_tonly_ffpe_out=mutect2_tonly_p2 | map{sample,vcf,info,filtvcf,vcftbi->tuple(sample,"mutect2_tonly",filtvcf,vcftbi)}
annotvep_tonly_mut2_ffpe(mutect2_tonly_ffpe_out)
vc_ffpe_tonly=vc_ffpe_tonly |concat(mutect2_tonly_ffpe_out)

}

}

if('octopus' in call_list){
Expand All @@ -580,9 +606,35 @@ workflow VC {
| map{tumor,normal,tbam,tbai,nbam,nbai,vc,normvcf,tbi->tuple("${tumor}_vs_${normal}",normvcf,tbam,vc)}
| combine(sobdetect_cohort_params_octopus.out)
| sobdetect_pass2_octopus
octopus_p1_vcfs=octopus_p1 | map{sample,vcf,info->vcf} |collect
octopus_p2_vcfs=octopus_p2 | map{sample,vcf,info,filtvcf,vcftbi->vcf} |collect
octopus_p1_vcfs=octopus_p1 | map{sample,vcf,info->vcf} | collect
octopus_p2_vcfs=octopus_p2 | map{sample,vcf,info,filtvcf,vcftbi->vcf} | collect
sobdetect_metrics_octopus(octopus_p1_vcfs,octopus_p2_vcfs)

octopus_ffpe_out=octopus_p2 | map{sample,vcf,info,filtvcf,vcftbi->tuple(sample.split("_vs_")[0],sample.split("_vs_")[1],"octopus",filtvcf,vcftbi)}
annotvep_tn_octopus_ffpe(octopus_ffpe_out)
vc_ffpe_paired=vc_ffpe_paired |concat(octopus_ffpe_out)

if (!params.no_tonly){
octopus_tonly_p1=bamwithsample1 | join(octopus_in_tonly)
| map{tumor,normal,tbam,tbai,nbam,nbai,vc,normvcf,tbi->tuple(tumor,normvcf,tbam,vc)}
| sobdetect_pass1_octopus_tonly
octopus_tonly_p1 | map{sample,vcf,info->info}
| collect
| sobdetect_cohort_params_octopus_tonly

octopus_tonly_p2 = bamwithsample1
| join(octopus_in_tonly)
| map{tumor,normal,tbam,tbai,nbam,nbai,vc,normvcf,tbi->tuple(tumor,normvcf,tbam,vc)}
| combine(sobdetect_cohort_params_octopus_tonly.out)
| sobdetect_pass2_octopus_tonly
octopus_tonly_p1_vcfs=octopus_tonly_p1 | map{sample,vcf,info->vcf} |collect
octopus_tonly_p2_vcfs=octopus_tonly_p2 | map{sample,vcf,info,filtvcf,vcftbi->vcf} |collect
sobdetect_metrics_octopus_tonly(octopus_tonly_p1_vcfs,octopus_tonly_p2_vcfs)

octopus_tonly_ffpe_out=octopus_tonly_p2 | map{sample,vcf,info,filtvcf,vcftbi->tuple(sample,"octopus_tonly",filtvcf,vcftbi)}
annotvep_tonly_octopus_ffpe(octopus_tonly_ffpe_out)
vc_ffpe_tonly=vc_ffpe_tonly |concat(octopus_tonly_ffpe_out)
}
}

if('strelka' in call_list){
Expand All @@ -600,9 +652,12 @@ workflow VC {

strelka_p1_vcfs=strelka_p1 | map{sample,vcf,info->vcf} |collect
strelka_p2_vcfs=strelka_p2 | map{sample,vcf,info,filtvcf,vcftbi->vcf} | collect

sobdetect_metrics_strelka(strelka_p1_vcfs,strelka_p2_vcfs)

strelka_ffpe_out=strelka_p2 | map{sample,vcf,info,filtvcf,vcftbi->tuple(sample.split("_vs_")[0],sample.split("_vs_")[1],"strelka",filtvcf,vcftbi)}
annotvep_tn_strelka_ffpe(strelka_ffpe_out)
vc_ffpe_paired=vc_ffpe_paired |concat(strelka_ffpe_out)

}

if('lofreq' in call_list){
Expand All @@ -620,6 +675,10 @@ workflow VC {
lofreq_p1_vcfs=lofreq_p1 | map{sample,vcf,info->vcf} |collect
lofreq_p2_vcfs=lofreq_p2 | map{sample,vcf,info,filtvcf,vcftbi->vcf} |collect
sobdetect_metrics_lofreq(lofreq_p1_vcfs,lofreq_p2_vcfs)

lofreq_ffpe_out=lofreq_p2 | map{sample,vcf,info,filtvcf,vcftbi->tuple(sample.split("_vs_")[0],sample.split("_vs_")[1],"lofreq",filtvcf,vcftbi)}
annotvep_tn_lofreq_ffpe(lofreq_ffpe_out)
vc_ffpe_paired=vc_ffpe_paired |concat(lofreq_ffpe_out)
}

if('muse' in call_list){
Expand All @@ -637,6 +696,10 @@ workflow VC {
muse_p1_vcfs=muse_p1 | map{sample,vcf,info->vcf} |collect
muse_p2_vcfs=muse_p2 | map{sample,vcf,info,filtvcf,vcftbi->vcf} |collect
sobdetect_metrics_muse(muse_p1_vcfs,muse_p2_vcfs)

muse_ffpe_out=muse_p2 | map{sample,vcf,info,filtvcf,vcftbi->tuple(sample.split("_vs_")[0],sample.split("_vs_")[1],"muse",filtvcf,vcftbi)}
annotvep_tn_muse_ffpe(muse_ffpe_out)
vc_ffpe_paired=vc_ffpe_paired |concat(muse_ffpe_out)
}

if('vardict' in call_list){
Expand All @@ -654,6 +717,32 @@ workflow VC {
vardict_p1_vcfs=vardict_p1 | map{sample,vcf,info->vcf} |collect
vardict_p2_vcfs=vardict_p2 | map{sample,vcf,info,filtvcf,vcftbi->vcf} |collect
sobdetect_metrics_vardict(vardict_p1_vcfs,vardict_p2_vcfs)

vardict_ffpe_out=vardict_p2 | map{sample,vcf,info,filtvcf,vcftbi->tuple(sample.split("_vs_")[0],sample.split("_vs_")[1],"vardict",filtvcf,vcftbi)}
annotvep_tn_vardict_ffpe(vardict_ffpe_out)
vc_ffpe_paired=vc_ffpe_paired |concat(vardict_ffpe_out)

if (!params.no_tonly){
vardict_tonly_p1=bamwithsample1 | join(vardict_in_tonly)
| map{tumor,normal,tbam,tbai,nbam,nbai,vc,normvcf,tbi->tuple(tumor,normvcf,tbam,vc)}
| sobdetect_pass1_vardict_tonly
vardict_tonly_p1 | map{sample,vcf,info->info}
| collect
| sobdetect_cohort_params_vardict_tonly

vardict_tonly_p2 = bamwithsample1
| join(vardict_in_tonly)
| map{tumor,normal,tbam,tbai,nbam,nbai,vc,normvcf,tbi->tuple(tumor,normvcf,tbam,vc)}
| combine(sobdetect_cohort_params_vardict_tonly.out)
| sobdetect_pass2_vardict_tonly
vardict_tonly_p1_vcfs=vardict_tonly_p1 | map{sample,vcf,info->vcf} |collect
vardict_tonly_p2_vcfs=vardict_tonly_p2 | map{sample,vcf,info,filtvcf,vcftbi->vcf} |collect
sobdetect_metrics_vardict_tonly(vardict_tonly_p1_vcfs,vardict_tonly_p2_vcfs)

vardict_tonly_ffpe_out=vardict_tonly_p2 | map{sample,vcf,info,filtvcf,vcftbi->tuple(sample,"vardict_tonly",filtvcf,vcftbi)}
annotvep_tonly_vardict_ffpe(vardict_tonly_ffpe_out)
vc_ffpe_tonly=vc_ffpe_tonly |concat(vardict_tonly_ffpe_out)
}
}

if('varscan' in call_list){
Expand All @@ -671,6 +760,69 @@ workflow VC {
varscan_p1_vcfs=varscan_p1 | map{sample,vcf,info->vcf} |collect
varscan_p2_vcfs=varscan_p2 | map{sample,vcf,info,filtvcf,vcftbi->vcf} |collect
sobdetect_metrics_varscan(varscan_p1_vcfs,varscan_p2_vcfs)

varscan_ffpe_out=varscan_p2 | map{sample,vcf,info,filtvcf,vcftbi->tuple(sample.split("_vs_")[0],sample.split("_vs_")[1],"varscan",filtvcf,vcftbi)}
annotvep_tn_varscan_ffpe(varscan_ffpe_out)
vc_ffpe_paired=vc_ffpe_paired | concat(varscan_ffpe_out)

if (!params.no_tonly){
varscan_tonly_p1=bamwithsample1 | join(varscan_in_tonly)
| map{tumor,normal,tbam,tbai,nbam,nbai,vc,normvcf,tbi->tuple(tumor,normvcf,tbam,vc)}
| sobdetect_pass1_varscan_tonly
varscan_tonly_p1 | map{sample,vcf,info->info}
| collect
| sobdetect_cohort_params_varscan_tonly

varscan_tonly_p2 = bamwithsample1
| join(varscan_in_tonly)
| map{tumor,normal,tbam,tbai,nbam,nbai,vc,normvcf,tbi->tuple(tumor,normvcf,tbam,vc)}
| combine(sobdetect_cohort_params_varscan_tonly.out)
| sobdetect_pass2_varscan_tonly
varscan_tonly_p1_vcfs=varscan_tonly_p1 | map{sample,vcf,info->vcf} |collect
varscan_tonly_p2_vcfs=varscan_tonly_p2 | map{sample,vcf,info,filtvcf,vcftbi->vcf} |collect
sobdetect_metrics_varscan_tonly(varscan_tonly_p1_vcfs,varscan_tonly_p2_vcfs)

varscan_tonly_ffpe_out=varscan_tonly_p2 | map{sample,vcf,info,filtvcf,vcftbi->tuple(sample,"varscan_tonly",filtvcf,vcftbi)}
annotvep_tonly_varscan_ffpe(varscan_tonly_ffpe_out)
vc_ffpe_tonly=vc_ffpe_tonly |concat(varscan_tonly_ffpe_out)
}
}


//Combine All Variants Using VCF -> Annotate
if (call_list.size()>1){
vc_all | groupTuple(by:[0,1])
| somaticcombine
| map{tumor,normal,vcf,index ->tuple(tumor,normal,"combined",vcf,index)}
| annotvep_tn_combined
if(params.ffpe){
vc_ffpe_paired | groupTuple(by:[0,1])
| somaticcombine_ffpe
| map{tumor,normal,vcf,index ->tuple(tumor,normal,"combined_ffpe",vcf,index)}
| annotvep_tn_combined_ffpe
}
if (!params.no_tonly & call_list_tonly.size()>1){
vc_tonly | groupTuple()
| somaticcombine_tonly
| map{tumor,vcf,index ->tuple(tumor,"combined_tonly",vcf,index)}
| annotvep_tonly_combined
}
if (!params.no_tonly & call_list_tonly.size()>1 & params.ffpe){
vc_ffpe_tonly | groupTuple()
| somaticcombine_tonly_ffpe
| map{tumor,vcf,index ->tuple(tumor,"combined_tonly_ffpe",vcf,index)}
| annotvep_tonly_combined_ffpe
}
}

if("sage" in call_list){
somaticcall_input=sage_in
}else if("mutect2" in call_list){
somaticcall_input=mutect2_in
}else if("mutect2" in call_list & params.ffpe){
somaticcall_input=mutect2_ffpe_out
}else{
somaticcall_input=Channel.empty()
}
}

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