Merge branch 'dev' into fix-multiqc-shared-mem-error

Author: JoseEspinosa

CHANGELOG.md

@@ -7,9 +7,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Enhancements & fixes
 
+- [[#428](https://github.com/nf-core/chipseq/issues/428)] - Bump MultiQC version to 1.25.1
 - [[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.
-- [[#428](https://github.com/nf-core/chipseq/issues/428)] - Bump MultiQC version to 1.25.1
+- [[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
 

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] }

workflows/chipseq.nf

@@ -524,6 +524,8 @@ workflow CHIPSEQ {
     //
     // MODULE: MultiQC
     //
+    ch_multiqc_report = Channel.empty()
+
     if (!params.skip_multiqc) {
         ch_multiqc_config        = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true)
         ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath( params.multiqc_config ): Channel.empty()
@@ -578,7 +580,8 @@ workflow CHIPSEQ {
         ch_multiqc_report = MULTIQC.out.report
     }
 
-    emit:multiqc_report = MULTIQC.out.report.toList() // channel: /path/to/multiqc_report.html
+    emit:
+    multiqc_report = ch_multiqc_report.toList()  // channel: /path/to/multiqc_report.html
     versions       = ch_versions                 // channel: [ path(versions.yml) ]
 
 }