feat: convert to bam

nf-core · Dec 4, 2024 · a5ec509 · a5ec509
1 parent 66bc786
commit a5ec509
Showing 1 changed file with 37 additions and 1 deletion.
diff --git a/subworkflows/local/bam_variant_calling_somatic_muse/main.nf b/subworkflows/local/bam_variant_calling_somatic_muse/main.nf
@@ -6,19 +6,53 @@
 
 include { MUSE_CALL } from '../../../modules/nf-core/muse/call/main'
 include { MUSE_SUMP } from '../../../modules/nf-core/muse/sump/main'
+include { SAMTOOLS_CONVERT as CRAM_TO_BAM_TUMOR } from '../../../modules/nf-core/samtools/convert/main'
+include { SAMTOOLS_CONVERT as CRAM_TO_BAM_NORMAL } from '../../../modules/nf-core/samtools/convert/main'
 
 workflow BAM_VARIANT_CALLING_SOMATIC_MUSE {
     take:
     cram          // channel: [mandatory] [ meta, normal_cram, normal_crai, tumor_cram, tumor_crai ]
     fasta         // channel: [mandatory] [ meta, fasta ]
+    fai           // channel: [mandatory] [ meta, fai ]
     dbsnp         // channel: [optional] [ dbsnp ]
     dbsnp_tbi     // channel: [optional] [ dbsnp_tbi ]
 
     main:
     versions = Channel.empty()
 
+    CRAM_TO_BAM_TUMOR(
+        cram.map{ meta, normal_cram, normal_crai,tumor_cram, tumor_crai -> [ meta + [ tobam: 'tumor' ], tumor_cram, tumor_crai ] },
+        fasta,
+        fai
+    )
+
+    CRAM_TO_BAM_NORMAL(
+        cram.map{ meta, normal_cram, normal_crai,tumor_cram, tumor_crai -> [ meta + [ tobam: 'normal' ], normal_cram, normal_crai ] },
+        fasta,
+        fai
+    )
+
+    ch_normal_bam = CRAM_TO_BAM_NORMAL.out.bam
+    ch_normal_bai = CRAM_TO_BAM_NORMAL.out.bai
+    ch_tumor_bam = CRAM_TO_BAM_TUMOR.out.bam
+    ch_tumor_bai = CRAM_TO_BAM_TUMOR.out.bai
+
+    // Combine normal BAM and BAI
+    ch_normal = ch_normal_bam.join(ch_normal_bai, by: [0])  // Join by meta
+
+    // Combine tumor BAM and BAI
+    ch_tumor = ch_tumor_bam.join(ch_tumor_bai, by: [0])  // Join by meta
+
+    // Combine normal and tumor data
+    ch_combined = ch_normal.join(ch_tumor, by: [0])  // Join by meta
+
+    // Rearrange the elements to match the desired output
+    ch_bam = ch_combined.map { meta, normal_bam, normal_bai, tumor_bam, tumor_bai ->
+        [meta, normal_bam, normal_bai, tumor_bam, tumor_bai]
+    }
+
     MUSE_CALL(
-        cram,
+        ch_bam,
         fasta
     )
 
@@ -31,6 +65,8 @@ workflow BAM_VARIANT_CALLING_SOMATIC_MUSE {
     vcf = Channel.empty().mix(MUSE_SUMP.out.vcf)
         .map{ meta, vcf -> [ meta + [ variantcaller: 'muse' ], vcf ] }
 
+    versions = versions.mix(CRAM_TO_BAM_NORMAL.out.versions)
+    versions = versions.mix(CRAM_TO_BAM_TUMOR.out.versions)
     versions = versions.mix(MUSE_CALL.out.versions)
     versions = versions.mix(MUSE_SUMP.out.versions)