update subworkflows

nf-core · Jan 25, 2024 · 38340ba · 38340ba
1 parent cb91dc8
commit 38340ba
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Showing 4 changed files with 5 additions and 5 deletions.
diff --git a/subworkflows/local/call_mobile_elements.nf b/subworkflows/local/call_mobile_elements.nf
@@ -76,7 +76,7 @@ workflow CALL_MOBILE_ELEMENTS {
 
         // Fix the vcf by adding header, sorting and indexing
         BCFTOOLS_REHEADER_ME (
-            RETROSEQ_CALL.out.vcf.map{ meta, vcf -> [ meta, vcf, [] ] },
+            RETROSEQ_CALL.out.vcf.map{ meta, vcf -> [ meta, vcf, [], [] ] },
             ch_genome_fai
         )
         BCFTOOLS_SORT_ME ( BCFTOOLS_REHEADER_ME.out.vcf )

diff --git a/subworkflows/local/call_repeat_expansions.nf b/subworkflows/local/call_repeat_expansions.nf
@@ -33,7 +33,7 @@ workflow CALL_REPEAT_EXPANSIONS {
 
         // Fix header and rename sample
         BCFTOOLS_REHEADER_EXP (
-            EXPANSIONHUNTER.out.vcf.map{ meta, vcf -> [ meta, vcf, [] ]},
+            EXPANSIONHUNTER.out.vcf.map{ meta, vcf -> [ meta, vcf, [], [] ]},
             ch_genome_fai
         )
         RENAMESAMPLE_EXP ( BCFTOOLS_REHEADER_EXP.out.vcf )

diff --git a/subworkflows/local/variant_calling/call_sv_manta.nf b/subworkflows/local/variant_calling/call_sv_manta.nf
@@ -32,13 +32,13 @@ workflow CALL_SV_MANTA {
                 .combine(bai_file_list)
                 .map { it -> it + [ [], [] ] }
                 .set { manta_input }
-            MANTA ( manta_input, ch_genome_fasta, ch_genome_fai )
+            MANTA ( manta_input, ch_genome_fasta, ch_genome_fai, [] )
         } else {
             ch_case_info.combine(bam_file_list)
                 .combine(bai_file_list)
                 .combine(bed_input)
                 .set { manta_input }
-            MANTA ( manta_input, ch_genome_fasta, ch_genome_fai )
+            MANTA ( manta_input, ch_genome_fasta, ch_genome_fai, [] )
         }
 
         ch_versions = MANTA.out.versions

diff --git a/subworkflows/local/variant_evaluation.nf b/subworkflows/local/variant_evaluation.nf
@@ -22,7 +22,7 @@ workflow VARIANT_EVALUATION {
             .map { row ->
                 evregions  = row.evaluationregions[0].isEmpty() ? [] : row.evaluationregions[0]
                 bedregions = row.bedregions[0].isEmpty()        ? [] : row.bedregions[0]
-                return [[samplename:row.samplename[0], bedregions:bedregions, evaluationregions:evregions], row.vcf[0], []]
+                return [[samplename:row.samplename[0], bedregions:bedregions, evaluationregions:evregions], row.vcf[0], [], []]
             }
             .set { ch_rtgvcfs_dbs }