Finish hooking up the pipeline and fix linting

nf-core · Oct 29, 2024 · fc426df · fc426df
1 parent 25b55df
commit fc426df
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Showing 2 changed files with 27 additions and 1 deletion.
diff --git a/subworkflows/local/bam_variant_calling_somatic_all/main.nf b/subworkflows/local/bam_variant_calling_somatic_all/main.nf
@@ -13,6 +13,9 @@ include { BAM_VARIANT_CALLING_SOMATIC_MUTECT2           } from '../bam_variant_c
 include { BAM_VARIANT_CALLING_SOMATIC_STRELKA           } from '../bam_variant_calling_somatic_strelka/main'
 include { BAM_VARIANT_CALLING_SOMATIC_TIDDIT            } from '../bam_variant_calling_somatic_tiddit/main'
 include { MSISENSORPRO_MSISOMATIC                       } from '../../../modules/nf-core/msisensorpro/msisomatic/main'
+include { PURECN_INTERVALFILE                           } from '../../../modules/nf-core/purecn/intervalfile/main'
+include { PURECN_INTERVALFILE } from '../../../../nf-core-modules/modules/nf-core/purecn/intervalfile/main.nf'
+include { BAM_VARIANT_CALLING_SOMATIC_PURECN } from '../bam_variant_calling_somatic_purecn/main.nf'
 
 workflow BAM_VARIANT_CALLING_SOMATIC_ALL {
     take:
@@ -42,6 +45,8 @@ workflow BAM_VARIANT_CALLING_SOMATIC_ALL {
     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
+    purecn_gatk_pon               // channel: [optional] PoN made from GATK4 for PureCN
+    purecn_normaldb               // channel: [optional] NormalDB generated by PureCN
 
     main:
     versions          = Channel.empty()
@@ -223,6 +228,28 @@ workflow BAM_VARIANT_CALLING_SOMATIC_ALL {
         versions = versions.mix(BAM_VARIANT_CALLING_SOMATIC_TIDDIT.out.versions)
     }
 
+    //PURECN
+    if (tools.split(',').contains('purecn')) {
+        ch_bed = [["id": "intervals_bed"], intervals]
+        ch_fasta = [["id": "fasta"], fasta]
+        PURECN_INTERVALFILE(ch_bed, ch_fasta)
+        versions = versions.mix(PURECN_INTERVALFILE.out.versions)
+
+        BAM_VARIANT_CALLING_SOMATIC_PURECN(cram.map{
+            // Remap channel to match module/subworkflow
+            meta, normal_cram, normal_crai, tumor_cram, tumor_crai -> [meta, tumor_cram, tumor_crai]},
+            fasta,
+            fasta_fai,
+            dict,
+            file(purecn_normaldb),
+            file(purecn_gatk_pon),
+            PURECN_INTERVALFILE.out.txt,
+            PURECN_INTERVALFILE.out.bed
+            )
+        versions = versions.mix(BAM_VARIANT_CALLING_SOMATIC_PURECN.out.versions)
+    }
+
+
     vcf_all = Channel.empty().mix(
         vcf_freebayes,
         vcf_manta,

diff --git a/subworkflows/local/bam_variant_calling_somatic_purecn/main.nf b/subworkflows/local/bam_variant_calling_somatic_purecn/main.nf
@@ -45,7 +45,6 @@ workflow BAM_VARIANT_CALLING_SOMATIC_PURECN {
         meta, denoised -> [meta, denoised, intervals_purecn]
     }
 
-    //FIXME: PURECN_RUN upstream should require a VCF file here
     PURECN_RUN(ch_purecn_in, normaldb)
     ch_versions = ch_versions.mix(PURECN_RUN.out.versions)