fix dict channel issue when using --dict

nf-core · May 25, 2023 · f26f49b · f26f49b
1 parent 9b933a1
commit f26f49b
Show file tree

Hide file tree

Showing 2 changed files with 12 additions and 6 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -64,6 +64,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#1014](https://github.com/nf-core/sarek/pull/1014) - Fix calls to `ensemblvep` and `snpeff` containers
 - [#1022](https://github.com/nf-core/sarek/pull/1022) - Fix call to variantrecalibrator. (Making sure that dbsnp_vqsr, known_indels_vqsr and known_snps_vqsr are channels, and not strings.)
 - [#1039](https://github.com/nf-core/sarek/pull/1039) - Remove concatenate_vcfs tests with singularity, as they are failing due to not enough space on GHA runners
+- [#1040](https://github.com/nf-core/sarek/pull/1040) - Fix dict channel issue due to [#1032](https://github.com/nf-core/sarek/pull/1032)
 
 ### Deprecated
 

diff --git a/workflows/sarek.nf b/workflows/sarek.nf
@@ -329,12 +329,17 @@ workflow SAREK {
 
     // Gather built indices or get them from the params
     // Built from the fasta file:
-    dict                   = params.dict                    ? Channel.fromPath(params.dict).collect()      : PREPARE_GENOME.out.dict
-    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
-    bwamem2                = params.bwamem2                 ? Channel.fromPath(params.bwamem2).collect()   : PREPARE_GENOME.out.bwamem2
-    dragmap                = params.dragmap                 ? Channel.fromPath(params.dragmap).collect()   : PREPARE_GENOME.out.hashtable
+    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).collect()
+                                                            : PREPARE_GENOME.out.fasta_fai
+
+    bwa                    = params.bwa                     ? Channel.fromPath(params.bwa).collect()
+                                                            : PREPARE_GENOME.out.bwa
+    bwamem2                = params.bwamem2                 ? Channel.fromPath(params.bwamem2).collect()
+                                                            : PREPARE_GENOME.out.bwamem2
+    dragmap                = params.dragmap                 ? Channel.fromPath(params.dragmap).collect()
+                                                            : PREPARE_GENOME.out.hashtable
     // Gather index for mapping given the chosen aligner
     index_alignement = params.aligner == "bwa-mem" ? bwa :
         params.aligner == "bwa-mem2" ? bwamem2 :