Merge branch 'refactor_light' of github.com:maxulysse/nf-core_sarek i…

…nto refactor_light
nf-core · Apr 3, 2024 · 853f7d1 · 853f7d1
2 parents 0e86cc2 + 4575cba
commit 853f7d1
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Showing 3 changed files with 4 additions and 4 deletions.
diff --git a/main.nf b/main.nf
@@ -148,9 +148,9 @@ workflow NFCORE_SAREK {
 
     // Gather built indices or get them from the params
     // Built from the fasta file:
-    dict       = params.dict        ? Channel.fromPath(params.dict).map{ it -> [ [id:'dict'], it ] }
+    dict       = params.dict        ? Channel.fromPath(params.dict).map{ it -> [ [id:'dict'], it ] }.collect()
                                     : PREPARE_GENOME.out.dict
-    fasta_fai  = params.fasta_fai   ? Channel.fromPath(params.fasta_fai)
+    fasta_fai  = params.fasta_fai   ? Channel.fromPath(params.fasta_fai).collect()
                                     : PREPARE_GENOME.out.fasta_fai
     bwa        = params.bwa         ? Channel.fromPath(params.bwa).collect()
                                     : PREPARE_GENOME.out.bwa

diff --git a/subworkflows/local/samplesheet_to_channel/main.nf b/subworkflows/local/samplesheet_to_channel/main.nf
@@ -5,6 +5,7 @@ workflow  SAMPLESHEET_TO_CHANNEL{
     aligner                         //
     ascat_alleles                   //
     ascat_loci                      //
+    ascat_loci_gc                   //
     ascat_loci_rt                   //
     bcftools_annotations            //
     bcftools_annotations_tbi        //
@@ -306,5 +307,3 @@ def flowcellLaneFromFastq(path) {
     }
     return fcid
 }
-
-
diff --git a/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf b/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf
@@ -135,6 +135,7 @@ if (params.tools && (params.tools.split(',').contains('vep')    || params.tools.
         params.aligner,
         params.ascat_alleles,
         params.ascat_loci,
+        params.ascat_loci_gc,
         params.ascat_loci_rt,
         params.bcftools_annotations,
         params.bcftools_annotations_tbi,