fix channels for manta

Author: maxulysse

subworkflows/local/bam_variant_calling_germline_all/main.nf

@@ -181,8 +181,8 @@ workflow BAM_VARIANT_CALLING_GERMLINE_ALL {
     if (tools.split(',').contains('manta')) {
         BAM_VARIANT_CALLING_GERMLINE_MANTA (
             cram,
-            fasta,
-            fasta_fai,
+            fasta.map{ it -> [ [ id:'fasta' ], it ] },
+            fasta_fai.map{ it -> [ [ id:'fasta_fai' ], it ] },
             intervals_bed_gz_tbi_combined
         )
 

subworkflows/local/bam_variant_calling_germline_manta/main.nf

@@ -10,8 +10,8 @@ include { MANTA_GERMLINE } from '../../../modules/nf-core/manta/germline/main'
 workflow BAM_VARIANT_CALLING_GERMLINE_MANTA {
     take:
     cram          // channel: [mandatory] [ meta, cram, crai ]
-    fasta         // channel: [mandatory] [ fasta ]
-    fasta_fai     // channel: [mandatory] [ fasta_fai ]
+    fasta         // channel: [mandatory] [ meta, fasta ]
+    fasta_fai     // channel: [mandatory] [ meta, fasta_fai ]
     intervals     // channel: [mandatory] [ interval.bed.gz, interval.bed.gz.tbi] or [ [], []] if no intervals; intervals file contains all intervals
 
     main:
@@ -25,7 +25,7 @@ workflow BAM_VARIANT_CALLING_GERMLINE_MANTA {
         [it[0], it[1], it[2], bed_gz, bed_tbi]
     }
 
-    MANTA_GERMLINE(cram_intervals, fasta.map{ fasta -> [ [ id:fasta.baseName ], fasta ] }, fasta_fai.map{ fasta_fai -> [ [ id:fasta_fai.baseName ], fasta_fai ] })
+    MANTA_GERMLINE(cram_intervals, fasta, fasta_fai, [])
 
     small_indels_vcf = MANTA_GERMLINE.out.candidate_small_indels_vcf
     sv_vcf = MANTA_GERMLINE.out.candidate_sv_vcf

subworkflows/local/bam_variant_calling_somatic_all/main.nf

@@ -145,8 +145,8 @@ workflow BAM_VARIANT_CALLING_SOMATIC_ALL {
     if (tools.split(',').contains('manta')) {
         BAM_VARIANT_CALLING_SOMATIC_MANTA(
             cram,
-            fasta,
-            fasta_fai,
+            fasta.map{ it -> [ [ id:'fasta' ], it ] },
+            fasta_fai.map{ it -> [ [ id:'fasta_fai' ], it ] },
             intervals_bed_gz_tbi_combined
         )
 

subworkflows/local/bam_variant_calling_somatic_manta/main.nf

@@ -9,8 +9,8 @@ include { MANTA_SOMATIC } from '../../../modules/nf-core/manta/somatic/main'
 workflow BAM_VARIANT_CALLING_SOMATIC_MANTA {
     take:
     cram          // channel: [mandatory] [ meta, cram1, crai1, cram2, crai2 ]
-    fasta         // channel: [mandatory] [ fasta ]
-    fasta_fai     // channel: [mandatory] [ fasta_fai ]
+    fasta         // channel: [mandatory] [ meta, fasta ]
+    fasta_fai     // channel: [mandatory] [ meta, fasta_fai ]
     intervals     // channel: [mandatory] [ interval.bed.gz, interval.bed.gz.tbi ] or [ [], [] ] if no intervals
 
     main:
@@ -24,7 +24,7 @@ workflow BAM_VARIANT_CALLING_SOMATIC_MANTA {
         [it[0], it[1], it[2], it[3], it[4], bed_gz, bed_tbi]
     }
 
-    MANTA_SOMATIC(cram_intervals, fasta, fasta_fai)
+    MANTA_SOMATIC(cram_intervals, fasta, fasta_fai, [])
 
     candidate_small_indels_vcf = MANTA_SOMATIC.out.candidate_small_indels_vcf
     candidate_small_indels_vcf_tbi = MANTA_SOMATIC.out.candidate_small_indels_vcf_tbi

subworkflows/local/bam_variant_calling_tumor_only_all/main.nf

@@ -141,9 +141,8 @@ workflow BAM_VARIANT_CALLING_TUMOR_ONLY_ALL {
         BAM_VARIANT_CALLING_TUMOR_ONLY_MANTA(
             cram,
             // Remap channel to match module/subworkflow
-            dict.map{ it -> [ [ id:'dict' ], it ] },
-            fasta,
-            fasta_fai,
+            fasta.map{ it -> [ [ id:'fasta' ], it ] },
+            fasta_fai.map{ it -> [ [ id:'fasta_fai' ], it ] },
             intervals_bed_gz_tbi_combined
 
         )

subworkflows/local/bam_variant_calling_tumor_only_manta/main.nf

@@ -10,9 +10,8 @@ include { MANTA_TUMORONLY } from '../../../modules/nf-core/manta/tumoronly/main'
 workflow BAM_VARIANT_CALLING_TUMOR_ONLY_MANTA {
     take:
     cram          // channel: [mandatory] [ meta, cram, crai ]
-    dict          // channel: [optional]  [ meta, dict ]
-    fasta         // channel: [mandatory] [ fasta ]
-    fasta_fai     // channel: [mandatory] [ fasta_fai ]
+    fasta         // channel: [mandatory] [ meta, fasta ]
+    fasta_fai     // channel: [mandatory] [ meta, fasta_fai ]
     intervals     // channel: [mandatory] [ interval.bed.gz, interval.bed.gz.tbi ] or [ [], [] ] if no intervals
 
     main:
@@ -26,7 +25,7 @@ workflow BAM_VARIANT_CALLING_TUMOR_ONLY_MANTA {
         [it[0], it[1], it[2], bed_gz, bed_tbi]
     }
 
-    MANTA_TUMORONLY(cram_intervals, fasta, fasta_fai)
+    MANTA_TUMORONLY(cram_intervals, fasta, fasta_fai, [])
 
     small_indels_vcf = MANTA_TUMORONLY.out.candidate_small_indels_vcf
     candidate_sv_vcf = MANTA_TUMORONLY.out.candidate_sv_vcf