correct merging error

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.
+- [[#428](https://github.com/nf-core/chipseq/issues/428)] - Bump MultiQC version to 1.25.1
 
 ### Parameters
 

modules/local/multiqc.nf

@@ -1,70 +1,69 @@
 process MULTIQC {
     label 'process_medium'
-
-    conda "bioconda::multiqc=1.23"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.23--pyhdfd78af_0' :
-        'biocontainers/multiqc:1.23--pyhdfd78af_0' }"
+    conda "bioconda::multiqc=1.25.1"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://depot.galaxyproject.org/singularity/multiqc:1.25.1--pyhdfd78af_0'
+        : 'biocontainers/multiqc:1.25.1--pyhdfd78af_0'}"
 
     input:
     path workflow_summary
     path multiqc_config
     path mqc_custom_config
     path logo
 
-    path ('fastqc/*')
-    path ('trimgalore/fastqc/*')
-    path ('trimgalore/*')
+    path 'fastqc/*'
+    path 'trimgalore/fastqc/*'
+    path 'trimgalore/*'
 
-    path ('alignment/library/*')
-    path ('alignment/library/*')
-    path ('alignment/library/*')
+    path 'alignment/library/*'
+    path 'alignment/library/*'
+    path 'alignment/library/*'
 
-    path ('alignment/merged_library/unfiltered/*')
-    path ('alignment/merged_library/unfiltered/*')
-    path ('alignment/merged_library/unfiltered/*')
-    path ('alignment/merged_library/unfiltered/picard_metrics/*')
+    path 'alignment/merged_library/unfiltered/*'
+    path 'alignment/merged_library/unfiltered/*'
+    path 'alignment/merged_library/unfiltered/*'
+    path 'alignment/merged_library/unfiltered/picard_metrics/*'
 
-    path ('alignment/merged_library/filtered/*')
-    path ('alignment/merged_library/filtered/*')
-    path ('alignment/merged_library/filtered/*')
-    path ('alignment/merged_library/filtered/picard_metrics/*')
+    path 'alignment/merged_library/filtered/*'
+    path 'alignment/merged_library/filtered/*'
+    path 'alignment/merged_library/filtered/*'
+    path 'alignment/merged_library/filtered/picard_metrics/*'
 
-    path ('preseq/*')
+    path 'preseq/*'
 
-    path ('deeptools/*')
-    path ('deeptools/*')
+    path 'deeptools/*'
+    path 'deeptools/*'
 
-    path ('phantompeakqualtools/*')
-    path ('phantompeakqualtools/*')
-    path ('phantompeakqualtools/*')
-    path ('phantompeakqualtools/*')
+    path 'phantompeakqualtools/*'
+    path 'phantompeakqualtools/*'
+    path 'phantompeakqualtools/*'
+    path 'phantompeakqualtools/*'
 
-    path ('macs3/peaks/*')
-    path ('macs3/peaks/*')
-    path ('macs3/annotation/*')
-    path ('macs3/featurecounts/*')
+    path 'macs3/peaks/*'
+    path 'macs3/peaks/*'
+    path 'macs3/annotation/*'
+    path 'macs3/featurecounts/*'
 
-    path ('deseq2/*')
-    path ('deseq2/*')
+    path 'deseq2/*'
+    path 'deseq2/*'
 
     output:
     path "*multiqc_report.html", emit: report
     path "*_data"              , emit: data
-    path "*_plots"             , optional:true, emit: plots
+    path "*_plots"             , optional: true, emit: plots
     path "versions.yml"        , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
     def args          = task.ext.args ?: ''
-    def custom_config = params.multiqc_config ? "--config $mqc_custom_config" : ''
+    def custom_config = params.multiqc_config ? "--config ${mqc_custom_config}" : ''
     """
     multiqc \\
         -f \\
-        $args \\
-        $custom_config \\
+        ${args} \\
+        ${custom_config} \\
         .
 
     cat <<-END_VERSIONS > versions.yml

subworkflows/local/prepare_genome.nf

@@ -73,7 +73,7 @@ workflow PREPARE_GENOME {
             ch_gff      = GUNZIP_GFF([[:], file(gff, checkIfExists: true)]).gunzip.map { it[1] }
             ch_versions = ch_versions.mix(GUNZIP_GFF.out.versions).map { [ [:], it ] }
         } 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] }