Implemented Joses PR review suggestions

Author: Kevin-Brockers

modules/local/gtf2bed/main.nf

@@ -12,8 +12,7 @@ process GTF2BED {
 
     output:
     path '*.bed'       , emit: bed
-    tuple val({"${task.process}"}), val('perl'), eval("perl -V:version | sed \"s/version='//; s/';//\""), topic:versions, emit: versions_perl
-
+    tuple val("${task.process}"), val('perl'), eval("perl -V:version | sed \"s/version='//; s/';//\""), topic:versions, emit: versions_perl
 
     when:
     task.ext.when == null || task.ext.when

modules/local/multiqc_custom_phantompeakqualtools/main.nf

@@ -1,6 +1,6 @@
 process MULTIQC_CUSTOM_PHANTOMPEAKQUALTOOLS {
     tag "$meta.id"
-    conda "conda-forge::r-base=4.3.3"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c7/c73daa0b0040137fbea15fc8ee54c9bf4e0a9c5e9412cc7c13f7b38cc9c8bbd9/data':
         'community.wave.seqera.io/library/r-base:4.5.3--6814a4ccafc04d08' }"

subworkflows/local/bam_peaks_call_qc_annotate_macs3_homer/main.nf

@@ -98,6 +98,7 @@ workflow BAM_PEAKS_CALL_QC_ANNOTATE_MACS3_HOMER {
             ch_gtf
         )
         ch_homer_annotatepeaks = HOMER_ANNOTATEPEAKS.out.txt
+        ch_versions = ch_versions.mix(HOMER_ANNOTATEPEAKS.out.versions.first())
 
         if (!skip_peak_qc) {
             //