Merge pull request #149 from nschcolnicov/dev

ch_fasta_fai and ch_gtf fix after nf-core/tools v2.14.1 merge

Author: maxulysse

CHANGELOG.md

@@ -30,6 +30,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#138](https://github.com/nf-core/rnavar/pull/138) - Proper usage of GVCF
 - [#142](https://github.com/nf-core/rnavar/pull/142) - Fix dbsnp channels
 - [#143](https://github.com/nf-core/rnavar/pull/143) - Use `DROP_MISSING_CONTIGS` by default in `GATK4_BEDTOINTERVALLIST`
+- [#145](https://github.com/nf-core/rnavar/pull/145) - Updated ch_gtf and ch_fasta_fai channels emitted by main.nf
 
 ### Dependencies
 

main.nf

@@ -111,14 +111,13 @@ workflow NFCORE_RNAVAR {
 
     ch_fasta            = PREPARE_GENOME.out.fasta
     ch_star_index       = PREPARE_GENOME.out.star_index
+    ch_gtf              = PREPARE_GENOME.out.gtf
     ch_dict             = params.dict           ? Channel.fromPath(params.dict).map{ it -> [ [id:'dict'], it ] }.collect()
                                                 : PREPARE_GENOME.out.dict
-    ch_fasta_fai        = params.fasta_fai      ? Channel.fromPath(params.fasta_fai).map{ it -> [ [id:'fai'], it ] }.collect()
+    ch_fasta_fai        = params.fasta_fai      ? Channel.fromPath(params.fasta_fai)
                                                 : PREPARE_GENOME.out.fasta_fai
     ch_exon_bed         = params.exon_bed       ? Channel.fromPath(params.exon_bed).map{ it -> [ [id:'exon_bed'], it ] }.collect()
                                                 : PREPARE_GENOME.out.exon_bed
-    ch_gtf              = params.gtf            ? Channel.fromPath(params.gtf).map{ it -> [ [id:'gtf'], it ] }.collect()
-                                                : PREPARE_GENOME.out.gtf
     ch_dbsnp_tbi        = params.dbsnp          ? params.dbsnp_tbi ? Channel.fromPath(params.dbsnp_tbi).collect()
                                                 : PREPARE_GENOME.out.dbsnp_tbi : Channel.value([])
     ch_known_indels_tbi = params.known_indels   ? params.known_indels_tbi ? Channel.fromPath(params.known_indels_tbi).collect()