Merge pull request #444 from JoseEspinosa/fixes

Fix GFFREAD when gff file provided by user (add empty map to channel) @JoseEspinosa
nf-core · Dec 24, 2024 · 5908238 · 5908238
2 parents 73a5304 + 3153907
commit 5908238
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -9,6 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - [[PR #434](https://github.com/nf-core/chipseq/pull/434)] - Prevent pipeline fails from erroneous param validation when igenomes is used.
 - [[#432](https://github.com/nf-core/chipseq/issues/432)] - Fix `GFFREAD` call to have the two expected input channels.
+- [[PR #444](https://github.com/nf-core/chipseq/pull/444)] - Add empty map to ch_gff so that when provided by the user `GFFREAD` works.
 
 ### Parameters
 

diff --git a/subworkflows/local/prepare_genome.nf b/subworkflows/local/prepare_genome.nf
@@ -71,9 +71,9 @@ workflow PREPARE_GENOME {
     } else if (gff) {
         if (gff.endsWith('.gz')) {
             ch_gff      = GUNZIP_GFF([[:], file(gff, checkIfExists: true)]).gunzip.map { it[1] }
-            ch_versions = ch_versions.mix(GUNZIP_GFF.out.versions).map { [ [:], it ] }
+            ch_versions = ch_versions.mix(GUNZIP_GFF.out.versions)
         } else {
-            ch_gff = Channel.value(file(gff, checkIfExists: true))
+            ch_gff = Channel.value(file(gff, checkIfExists: true)).map { [ [:], it ] }
         }
 
         ch_gtf      = GFFREAD(ch_gff, []).gtf.map { it[1] }