diff --git a/conf/modules.config b/conf/modules.config
index 6e28f549b..764838d01 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -19,8 +19,7 @@ def rseqc_modules = params.rseqc_modules ? params.rseqc_modules.split(',').colle
 process {
     publishDir = [
         path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        mode: params.publish_dir_mode
     ]
 
     withName: 'CUSTOM_DUMPSOFTWAREVERSIONS' {
@@ -41,7 +40,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/genome" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
+            saveAs: { filename -> params.save_reference ? filename : null }
         ]
     }
 
@@ -53,7 +52,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/genome/index" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
+            saveAs: { filename -> params.save_reference ? filename : null }
         ]
     }
 
@@ -62,7 +61,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/genome" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
+            saveAs: { filename -> params.save_reference ? filename : null }
         ]
     }
 
@@ -70,7 +69,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/genome/index" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
+            saveAs: { filename -> params.save_reference ? filename : null }
         ]
     }
 
@@ -79,7 +78,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/genome/index" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
+            saveAs: { filename -> params.save_reference ? filename : null }
         ]
     }
 
@@ -88,7 +87,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/genome/index" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
+            saveAs: { filename -> params.save_reference ? filename : null }
         ]
     }
 
@@ -97,7 +96,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/genome/index" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
+            saveAs: { filename -> params.save_reference ? filename : null }
         ]
     }
 
@@ -105,7 +104,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/genome" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
+            saveAs: { filename -> params.save_reference ? filename : null }
         ]
     }
 
@@ -113,7 +112,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/genome" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
+            saveAs: { filename -> params.save_reference ? filename : null }
         ]
     }
 
@@ -122,7 +121,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/genome" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
+            saveAs: { filename -> params.save_reference ? filename : null }
         ]
     }
 
@@ -130,7 +129,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/genome" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
+            saveAs: { filename -> params.save_reference ? filename : null }
         ]
     }
 
@@ -138,7 +137,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/fastq" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_merged_fastq ? filename : null }
+            saveAs: { params.save_merged_fastq ? filename : null }
         ]
     }
 }
@@ -150,7 +149,7 @@ if (!params.skip_bbsplit && params.bbsplit_fasta_list) {
             publishDir = [
                 path: { "${params.outdir}/genome/index" },
                 mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
+                saveAs: { filename -> params.save_reference ? filename : null }
             ]
         }
     }
@@ -200,8 +199,7 @@ if (!(params.skip_fastqc || params.skip_qc)) {
                 ext.args   = '--quiet'
                 publishDir = [
                     path: { "${params.outdir}/${params.trimmer}/fastqc" },
-                    mode: params.publish_dir_mode,
-                    saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+                    mode: params.publish_dir_mode
                 ]
             }
         }
@@ -485,8 +483,7 @@ if (!params.skip_alignment) {
                 ext.prefix = { "${meta.id}.forward" }
                 publishDir = [
                     path: { "${params.outdir}/${params.aligner}/bigwig" },
-                    mode: params.publish_dir_mode,
-                    saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+                    mode: params.publish_dir_mode
                 ]
             }
 
@@ -501,8 +498,7 @@ if (!params.skip_alignment) {
                 ext.prefix = { "${meta.id}.reverse" }
                 publishDir = [
                     path: { "${params.outdir}/${params.aligner}/bigwig" },
-                    mode: params.publish_dir_mode,
-                    saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+                    mode: params.publish_dir_mode
                 ]
             }
         }
@@ -517,8 +513,7 @@ if (!params.skip_alignment) {
                 ].join(' ').trim() }
                 publishDir = [
                     path: { "${params.outdir}/${params.aligner}/stringtie" },
-                    mode: params.publish_dir_mode,
-                    saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+                    mode: params.publish_dir_mode
                 ]
             }
         }
@@ -572,15 +567,14 @@ if (!params.skip_alignment && params.aligner == 'star_salmon') {
             publishDir = [
                 path: { "${params.outdir}/${params.aligner}" },
                 mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') || filename.endsWith('_meta_info.json') ? null : filename }
+                saveAs: { filename -> filename.endsWith('_meta_info.json') ? null : filename }
             ]
         }
 
         withName: '.*:QUANTIFY_STAR_SALMON:TX2GENE' {
             publishDir = [
                 path: { "${params.outdir}/${params.aligner}" },
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+                mode: params.publish_dir_mode
             ]
         }
 
@@ -588,16 +582,14 @@ if (!params.skip_alignment && params.aligner == 'star_salmon') {
             ext.prefix = { "${quant_type}.merged" }
             publishDir = [
                 path: { "${params.outdir}/${params.aligner}" },
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+                mode: params.publish_dir_mode
             ]
         }
 
         withName: '.*:QUANTIFY_STAR_SALMON:SE_.*' {
             publishDir = [
                 path: { "${params.outdir}/${params.aligner}" },
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+                mode: params.publish_dir_mode
             ]
         }
     }
@@ -760,8 +752,7 @@ if (!params.skip_alignment && params.aligner == 'star_rsem') {
         withName: '.*:QUANTIFY_RSEM:RSEM_MERGE_COUNTS' {
             publishDir = [
                 path: { "${params.outdir}/${params.aligner}" },
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+                mode: params.publish_dir_mode
             ]
         }
     }
@@ -847,8 +838,7 @@ if (!params.skip_alignment && !params.skip_qc) {
             withName: 'QUALIMAP_RNASEQ' {
                 publishDir = [
                     path: { "${params.outdir}/${params.aligner}/qualimap" },
-                    mode: params.publish_dir_mode,
-                    saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+                    mode: params.publish_dir_mode
                 ]
             }
         }
@@ -898,16 +888,14 @@ if (!params.skip_alignment && !params.skip_qc) {
                 ].join(' ').trim() }
                 publishDir = [
                     path: { "${params.outdir}/${params.aligner}/featurecounts" },
-                    mode: params.publish_dir_mode,
-                    saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+                    mode: params.publish_dir_mode
                 ]
             }
 
             withName: 'MULTIQC_CUSTOM_BIOTYPE' {
                 publishDir = [
                     path: { "${params.outdir}/${params.aligner}/featurecounts" },
-                    mode: params.publish_dir_mode,
-                    saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+                    mode: params.publish_dir_mode
                 ]
             }
         }
@@ -918,8 +906,7 @@ if (!params.skip_alignment && !params.skip_qc) {
             withName: '.*:BAM_RSEQC:RSEQC_BAMSTAT' {
                 publishDir = [
                     path: { "${params.outdir}/${params.aligner}/rseqc/bam_stat" },
-                    mode: params.publish_dir_mode,
-                    saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+                    mode: params.publish_dir_mode
                 ]
             }
         }
@@ -930,8 +917,7 @@ if (!params.skip_alignment && !params.skip_qc) {
             withName: '.*:BAM_RSEQC:RSEQC_INFEREXPERIMENT' {
                 publishDir = [
                     path: { "${params.outdir}/${params.aligner}/rseqc/infer_experiment" },
-                    mode: params.publish_dir_mode,
-                    saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+                    mode: params.publish_dir_mode
                 ]
             }
         }
@@ -1019,8 +1005,7 @@ if (!params.skip_alignment && !params.skip_qc) {
             withName: '.*:BAM_RSEQC:RSEQC_READDISTRIBUTION' {
                 publishDir = [
                     path: { "${params.outdir}/${params.aligner}/rseqc/read_distribution" },
-                    mode: params.publish_dir_mode,
-                    saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+                    mode: params.publish_dir_mode
                 ]
             }
         }
@@ -1033,8 +1018,7 @@ if (!params.skip_alignment && !params.skip_qc) {
                     [
                         path: { "${params.outdir}/${params.aligner}/rseqc/inner_distance/txt" },
                         mode: params.publish_dir_mode,
-                        pattern: '*.txt',
-                        saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+                        pattern: '*.txt'
                     ],
                     [
                         path: { "${params.outdir}/${params.aligner}/rseqc/inner_distance/pdf" },
@@ -1056,8 +1040,7 @@ if (!params.skip_alignment && !params.skip_qc) {
             withName: '.*:BAM_RSEQC:RSEQC_TIN' {
                 publishDir = [
                     path: { "${params.outdir}/${params.aligner}/rseqc/tin" },
-                    mode: params.publish_dir_mode,
-                    saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+                    mode: params.publish_dir_mode
                 ]
             }
         }
@@ -1074,8 +1057,7 @@ if (!params.skip_multiqc) {
                     "${params.outdir}/multiqc",
                     params.skip_alignment? '' : "/${params.aligner}"
                     ].join('') },
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+                mode: params.publish_dir_mode
             ]
         }
     }
@@ -1093,7 +1075,7 @@ if (!params.skip_pseudo_alignment && params.pseudo_aligner == 'salmon') {
             publishDir = [
                 path: { "${params.outdir}/${params.pseudo_aligner}" },
                 mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') || filename.endsWith('_meta_info.json') ? null : filename }
+                saveAs: { filename -> filename.endsWith('_meta_info.json') ? null : filename }
             ]
         }
     }
@@ -1106,7 +1088,7 @@ if (!params.skip_pseudo_alignment && params.pseudo_aligner == 'kallisto') {
             publishDir = [
                 path: { "${params.outdir}/${params.pseudo_aligner}" },
                 mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') || filename.endsWith('.run_info.json') || filename.endsWith('.log') ? null : filename }
+                saveAs: { filename -> filename.endsWith('.run_info.json') || filename.endsWith('.log') ? null : filename }
             ]
         }
     }
@@ -1117,8 +1099,7 @@ if (!params.skip_pseudo_alignment) {
         withName: '.*:QUANTIFY_PSEUDO_ALIGNMENT:TX2GENE' {
             publishDir = [
                 path: { "${params.outdir}/${params.pseudo_aligner}" },
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+                mode: params.publish_dir_mode
             ]
         }
 
@@ -1126,16 +1107,14 @@ if (!params.skip_pseudo_alignment) {
             ext.prefix = { "${quant_type}.merged" }
             publishDir = [
                 path: { "${params.outdir}/${params.pseudo_aligner}" },
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+                mode: params.publish_dir_mode
             ]
         }
 
         withName: '.*:QUANTIFY_PSEUDO_ALIGNMENT:SE_.*' {
             publishDir = [
                 path: { "${params.outdir}/${params.pseudo_aligner}" },
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+                mode: params.publish_dir_mode
             ]
         }
     }
diff --git a/modules/local/bedtools_genomecov/main.nf b/modules/local/bedtools_genomecov/main.nf
index 0a0fb3c8b..74c1b7599 100644
--- a/modules/local/bedtools_genomecov/main.nf
+++ b/modules/local/bedtools_genomecov/main.nf
@@ -13,7 +13,7 @@ process BEDTOOLS_GENOMECOV {
     output:
     tuple val(meta), path("*.forward.bedGraph"), emit: bedgraph_forward
     tuple val(meta), path("*.reverse.bedGraph"), emit: bedgraph_reverse
-    path "versions.yml"                        , emit: versions
+    tuple val("${task.process}"), val('bedtools'), cmd("bedtools --version | sed -e 's/bedtools v//g'"), emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -44,10 +44,5 @@ process BEDTOOLS_GENOMECOV {
         -strand - \\
         $args \\
         | bedtools sort > ${prefix_reverse}.bedGraph
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        bedtools: \$(bedtools --version | sed -e "s/bedtools v//g")
-    END_VERSIONS
     """
 }
diff --git a/modules/local/cat_additional_fasta/main.nf b/modules/local/cat_additional_fasta/main.nf
index 72af4bc54..0011f5dda 100644
--- a/modules/local/cat_additional_fasta/main.nf
+++ b/modules/local/cat_additional_fasta/main.nf
@@ -15,7 +15,7 @@ process CAT_ADDITIONAL_FASTA {
     output:
     path "${name}.fasta", emit: fasta
     path "${name}.gtf"  , emit: gtf
-    path "versions.yml" , emit: versions
+    tuple val("${task.process}"), val('python'), cmd("python --version | sed 's/Python //g'"), emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -33,10 +33,5 @@ process CAT_ADDITIONAL_FASTA {
 
     cat $fasta $add_fasta > ${name}.fasta
     cat $gtf ${add_fasta.baseName}.gtf > ${name}.gtf
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        python: \$(python --version | sed 's/Python //g')
-    END_VERSIONS
     """
 }
diff --git a/modules/local/deseq2_qc/main.nf b/modules/local/deseq2_qc/main.nf
index 466194934..726bb7d02 100644
--- a/modules/local/deseq2_qc/main.nf
+++ b/modules/local/deseq2_qc/main.nf
@@ -22,7 +22,8 @@ process DESEQ2_QC {
     path "*sample.dists_mqc.tsv", optional:true, emit: dists_multiqc
     path "*.log"                , optional:true, emit: log
     path "size_factors"         , optional:true, emit: size_factors
-    path "versions.yml"         , emit: versions
+    tuple val("${task.process}"), val('r-base'), cmd("echo \$(R --version 2>&1) | sed 's/^.*R version //; s/ .*\$//'"), emit: versions1
+    tuple val("${task.process}"), val('bioconductor-deseq2'), cmd("Rscript -e 'library(DESeq2); cat(as.character(packageVersion(\'DESeq2\')))'"), emit: versions2
 
     when:
     task.ext.when == null || task.ext.when
@@ -50,11 +51,5 @@ process DESEQ2_QC {
         sed -i -e "s/DESeq2 sample/${label_upper} DESeq2 sample/g" tmp.txt
         cat tmp.txt *.sample.dists.txt > ${label_lower}.sample.dists_mqc.tsv
     fi
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        r-base: \$(echo \$(R --version 2>&1) | sed 's/^.*R version //; s/ .*\$//')
-        bioconductor-deseq2: \$(Rscript -e "library(DESeq2); cat(as.character(packageVersion('DESeq2')))")
-    END_VERSIONS
     """
 }
diff --git a/modules/local/dupradar/main.nf b/modules/local/dupradar/main.nf
index 9f9152d1e..27743fe25 100644
--- a/modules/local/dupradar/main.nf
+++ b/modules/local/dupradar/main.nf
@@ -15,7 +15,8 @@ process DUPRADAR {
     tuple val(meta), path("*.pdf")    , emit: pdf
     tuple val(meta), path("*.txt")    , emit: txt
     tuple val(meta), path("*_mqc.txt"), emit: multiqc
-    path "versions.yml"               , emit: versions
+    tuple val("${task.process}"), val('r-base'), cmd("echo \$(R --version 2>&1) | sed 's/^.*R version //; s/ .*\$//'"), emit: versions1
+    tuple val("${task.process}"), val('bioconductor-dupradar'), cmd("Rscript -e 'library(dupRadar); cat(as.character(packageVersion(\'dupRadar\')))'"), emit: versions2
 
     when:
     task.ext.when == null || task.ext.when
@@ -38,11 +39,5 @@ process DUPRADAR {
         $strandedness \\
         $paired_end \\
         $task.cpus
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        r-base: \$(echo \$(R --version 2>&1) | sed 's/^.*R version //; s/ .*\$//')
-        bioconductor-dupradar: \$(Rscript -e "library(dupRadar); cat(as.character(packageVersion('dupRadar')))")
-    END_VERSIONS
     """
 }
diff --git a/modules/local/gtf2bed/main.nf b/modules/local/gtf2bed/main.nf
index 8a4bae8ff..b8614dd85 100644
--- a/modules/local/gtf2bed/main.nf
+++ b/modules/local/gtf2bed/main.nf
@@ -12,7 +12,7 @@ process GTF2BED {
 
     output:
     path '*.bed'       , emit: bed
-    path "versions.yml", emit: versions
+    tuple val("${task.process}"), val('perl'), cmd("echo \$(perl --version 2>&1) | sed 's/.*v\\(.*\\)) built.*/\\1/'"), emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -22,10 +22,5 @@ process GTF2BED {
     gtf2bed \\
         $gtf \\
         > ${gtf.baseName}.bed
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        perl: \$(echo \$(perl --version 2>&1) | sed 's/.*v\\(.*\\)) built.*/\\1/')
-    END_VERSIONS
     """
 }
diff --git a/modules/local/gtf_filter/main.nf b/modules/local/gtf_filter/main.nf
index d14e8ff42..64a0b78ce 100644
--- a/modules/local/gtf_filter/main.nf
+++ b/modules/local/gtf_filter/main.nf
@@ -12,7 +12,7 @@ process GTF_FILTER {
 
     output:
     path "*.filtered.gtf", emit: genome_gtf
-    path "versions.yml"  , emit: versions
+    tuple val("${task.process}"), val('python'), cmd("python --version | sed 's/Python //g'"), emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -23,10 +23,5 @@ process GTF_FILTER {
         --gtf $gtf \\
         --fasta $fasta \\
         --prefix ${fasta.baseName}
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        python: \$(python --version | sed 's/Python //g')
-    END_VERSIONS
     """
 }
diff --git a/modules/local/multiqc/main.nf b/modules/local/multiqc/main.nf
index a59d8a533..7f5473a7d 100644
--- a/modules/local/multiqc/main.nf
+++ b/modules/local/multiqc/main.nf
@@ -49,7 +49,7 @@ process MULTIQC {
     path "*multiqc_report.html", emit: report
     path "*_data"              , emit: data
     path "*_plots"             , optional:true, emit: plots
-    path "versions.yml"        , emit: versions
+    tuple val("${task.process}"), val('multiqc'), cmd("multiqc --version | sed -e 's/multiqc, version //g'"), emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -65,10 +65,5 @@ process MULTIQC {
         $args \\
         $custom_config \\
         .
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" )
-    END_VERSIONS
     """
 }
diff --git a/modules/local/multiqc_custom_biotype/main.nf b/modules/local/multiqc_custom_biotype/main.nf
index 9c0fe94eb..8cd02a6b0 100644
--- a/modules/local/multiqc_custom_biotype/main.nf
+++ b/modules/local/multiqc_custom_biotype/main.nf
@@ -12,7 +12,7 @@ process MULTIQC_CUSTOM_BIOTYPE {
 
     output:
     tuple val(meta), path("*.tsv"), emit: tsv
-    path "versions.yml"           , emit: versions
+    tuple val("${task.process}"), val('python'), cmd("python --version | sed 's/Python //g'"), emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -27,10 +27,5 @@ process MULTIQC_CUSTOM_BIOTYPE {
         -s $meta.id \\
         -f rRNA \\
         -o ${prefix}.biotype_counts_rrna_mqc.tsv
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        python: \$(python --version | sed 's/Python //g')
-    END_VERSIONS
     """
 }
diff --git a/modules/local/preprocess_transcripts_fasta_gencode/main.nf b/modules/local/preprocess_transcripts_fasta_gencode/main.nf
index 41f1d42f6..b5127378d 100644
--- a/modules/local/preprocess_transcripts_fasta_gencode/main.nf
+++ b/modules/local/preprocess_transcripts_fasta_gencode/main.nf
@@ -11,7 +11,7 @@ process PREPROCESS_TRANSCRIPTS_FASTA_GENCODE {
 
     output:
     path "*.fa"        , emit: fasta
-    path "versions.yml", emit: versions
+    tuple val("${task.process}"), val('sed'), cmd("echo \$(sed --version 2>&1) | sed 's/^.*GNU sed) //; s/ .*\$//'"), emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -22,10 +22,5 @@ process PREPROCESS_TRANSCRIPTS_FASTA_GENCODE {
     def command = gzipped ? 'zcat' : 'cat'
     """
     $command $fasta | cut -d "|" -f1 > ${outfile}.fixed.fa
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        sed: \$(echo \$(sed --version 2>&1) | sed 's/^.*GNU sed) //; s/ .*\$//')
-    END_VERSIONS
     """
 }
diff --git a/modules/local/rsem_merge_counts/main.nf b/modules/local/rsem_merge_counts/main.nf
index 3f226f54d..ce14fb146 100644
--- a/modules/local/rsem_merge_counts/main.nf
+++ b/modules/local/rsem_merge_counts/main.nf
@@ -15,7 +15,7 @@ process RSEM_MERGE_COUNTS {
     path "rsem.merged.gene_tpm.tsv"         , emit: tpm_gene
     path "rsem.merged.transcript_counts.tsv", emit: counts_transcript
     path "rsem.merged.transcript_tpm.tsv"   , emit: tpm_transcript
-    path "versions.yml"                     , emit: versions
+    tuple val("${task.process}"), val('sed'), cmd("echo \$(sed --version 2>&1) | sed 's/^.*GNU sed) //; s/ .*\$//'"), emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -46,10 +46,5 @@ process RSEM_MERGE_COUNTS {
     paste gene_ids.txt tmp/genes/*.tpm.txt > rsem.merged.gene_tpm.tsv
     paste transcript_ids.txt tmp/isoforms/*.counts.txt > rsem.merged.transcript_counts.tsv
     paste transcript_ids.txt tmp/isoforms/*.tpm.txt > rsem.merged.transcript_tpm.tsv
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        sed: \$(echo \$(sed --version 2>&1) | sed 's/^.*GNU sed) //; s/ .*\$//')
-    END_VERSIONS
     """
 }
diff --git a/modules/local/star_align_igenomes/main.nf b/modules/local/star_align_igenomes/main.nf
index 3e5a169d8..e48b329f2 100644
--- a/modules/local/star_align_igenomes/main.nf
+++ b/modules/local/star_align_igenomes/main.nf
@@ -20,7 +20,9 @@ process STAR_ALIGN_IGENOMES {
     tuple val(meta), path('*Log.final.out')   , emit: log_final
     tuple val(meta), path('*Log.out')         , emit: log_out
     tuple val(meta), path('*Log.progress.out'), emit: log_progress
-    path  "versions.yml"                      , emit: versions
+    tuple val("${task.process}"), val('star'), cmd("STAR --version | sed -e 's/STAR_//g'"), emit: versions1
+    tuple val("${task.process}"), val('samtools'), cmd("echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//'"), emit: versions2
+    tuple val("${task.process}"), val('gawk'), cmd("echo \$(gawk --version 2>&1) | sed 's/^.*GNU Awk //; s/, .*\$//'"), emit: versions3
 
     tuple val(meta), path('*sortedByCoord.out.bam')  , optional:true, emit: bam_sorted
     tuple val(meta), path('*toTranscriptome.out.bam'), optional:true, emit: bam_transcript
@@ -62,12 +64,5 @@ process STAR_ALIGN_IGENOMES {
         mv ${prefix}.Unmapped.out.mate2 ${prefix}.unmapped_2.fastq
         gzip ${prefix}.unmapped_2.fastq
     fi
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        star: \$(STAR --version | sed -e "s/STAR_//g")
-        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
-        gawk: \$(echo \$(gawk --version 2>&1) | sed 's/^.*GNU Awk //; s/, .*\$//')
-    END_VERSIONS
     """
 }
diff --git a/modules/local/star_genomegenerate_igenomes/main.nf b/modules/local/star_genomegenerate_igenomes/main.nf
index 7766faaaf..0d8792699 100644
--- a/modules/local/star_genomegenerate_igenomes/main.nf
+++ b/modules/local/star_genomegenerate_igenomes/main.nf
@@ -13,7 +13,9 @@ process STAR_GENOMEGENERATE_IGENOMES {
 
     output:
     path "star"        , emit: index
-    path "versions.yml", emit: versions
+    tuple val("${task.process}"), val('star'), cmd("STAR --version | sed -e 's/STAR_//g'"), emit: versions1
+    tuple val("${task.process}"), val('samtools'), cmd("echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//'"), emit: versions2
+    tuple val("${task.process}"), val('gawk'), cmd("echo \$(gawk --version 2>&1) | sed 's/^.*GNU Awk //; s/, .*\$//'"), emit: versions3
 
     when:
     task.ext.when == null || task.ext.when
@@ -33,13 +35,6 @@ process STAR_GENOMEGENERATE_IGENOMES {
             --runThreadN $task.cpus \\
             $memory \\
             $args
-
-        cat <<-END_VERSIONS > versions.yml
-        "${task.process}":
-            star: \$(STAR --version | sed -e "s/STAR_//g")
-            samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
-            gawk: \$(echo \$(gawk --version 2>&1) | sed 's/^.*GNU Awk //; s/, .*\$//')
-        END_VERSIONS
         """
     } else {
         """
@@ -56,13 +51,6 @@ process STAR_GENOMEGENERATE_IGENOMES {
             --genomeSAindexNbases \$NUM_BASES \\
             $memory \\
             $args
-
-        cat <<-END_VERSIONS > versions.yml
-        "${task.process}":
-            star: \$(STAR --version | sed -e "s/STAR_//g")
-            samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
-            gawk: \$(echo \$(gawk --version 2>&1) | sed 's/^.*GNU Awk //; s/, .*\$//')
-        END_VERSIONS
         """
     }
 }
diff --git a/modules/local/summarizedexperiment/main.nf b/modules/local/summarizedexperiment/main.nf
index f278e2301..f4af876de 100644
--- a/modules/local/summarizedexperiment/main.nf
+++ b/modules/local/summarizedexperiment/main.nf
@@ -14,7 +14,8 @@ process SUMMARIZEDEXPERIMENT {
 
     output:
     path "*.rds"       , emit: rds
-    path "versions.yml", emit: versions
+    tuple val("${task.process}"), val('r-base'), cmd("echo \$(R --version 2>&1) | sed 's/^.*R version //; s/ .*\$//'"), emit: versions1
+    tuple val("${task.process}"), val('bioconductor-summarizedexperiment'), cmd("Rscript -e 'library(SummarizedExperiment); cat(as.character(packageVersion(\'SummarizedExperiment\')))'"), emit: versions2
 
     when:
     task.ext.when == null || task.ext.when
@@ -26,11 +27,5 @@ process SUMMARIZEDEXPERIMENT {
         $counts \\
         $tpm \\
         $tx2gene
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        r-base: \$(echo \$(R --version 2>&1) | sed 's/^.*R version //; s/ .*\$//')
-        bioconductor-summarizedexperiment: \$(Rscript -e "library(SummarizedExperiment); cat(as.character(packageVersion('SummarizedExperiment')))")
-    END_VERSIONS
     """
 }
diff --git a/modules/local/tx2gene/main.nf b/modules/local/tx2gene/main.nf
index 150e74afb..1bf21400c 100644
--- a/modules/local/tx2gene/main.nf
+++ b/modules/local/tx2gene/main.nf
@@ -14,7 +14,7 @@ process TX2GENE {
 
     output:
     path "*.tsv"       , emit: tsv
-    path "versions.yml", emit: versions
+    tuple val("${task.process}"), val('python'), cmd("python --version | sed 's/Python //g'"), emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -28,10 +28,5 @@ process TX2GENE {
         --id $params.gtf_group_features \\
         --extra $params.gtf_extra_attributes \\
         -o tx2gene.tsv
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        python: \$(python --version | sed 's/Python //g')
-    END_VERSIONS
     """
 }
diff --git a/modules/local/tximport/main.nf b/modules/local/tximport/main.nf
index 56d826a7d..243689cdf 100644
--- a/modules/local/tximport/main.nf
+++ b/modules/local/tximport/main.nf
@@ -18,7 +18,8 @@ process TXIMPORT {
     path "*gene_counts_scaled.tsv"       , emit: counts_gene_scaled
     path "*transcript_tpm.tsv"           , emit: tpm_transcript
     path "*transcript_counts.tsv"        , emit: counts_transcript
-    path "versions.yml"                  , emit: versions
+    tuple val("${task.process}"), val('r-base'), cmd("echo \$(R --version 2>&1) | sed 's/^.*R version //; s/ .*\$//'"), emit: versions1
+    tuple val("${task.process}"), val('bioconductor-tximeta'), cmd("Rscript -e 'library(tximeta); cat(as.character(packageVersion(\'tximeta\')))'"), emit: versions2
 
     when:
     task.ext.when == null || task.ext.when
@@ -32,11 +33,5 @@ process TXIMPORT {
         $prefix \\
         $quant_type \\
         $tx2gene
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        r-base: \$(echo \$(R --version 2>&1) | sed 's/^.*R version //; s/ .*\$//')
-        bioconductor-tximeta: \$(Rscript -e "library(tximeta); cat(as.character(packageVersion('tximeta')))")
-    END_VERSIONS
     """
 }
diff --git a/modules/local/umitools_prepareforrsem/main.nf b/modules/local/umitools_prepareforrsem/main.nf
index 9ee41737d..f197c2402 100644
--- a/modules/local/umitools_prepareforrsem/main.nf
+++ b/modules/local/umitools_prepareforrsem/main.nf
@@ -13,7 +13,7 @@ process UMITOOLS_PREPAREFORRSEM {
     output:
     tuple val(meta), path('*.bam'), emit: bam
     tuple val(meta), path('*.log'), emit: log
-    path  "versions.yml"          , emit: versions
+    tuple val("${task.process}"), val('umitools'), cmd("umi_tools --version 2>&1 | sed 's/^.*UMI-tools version://; s/ *\$//'"), emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -27,10 +27,5 @@ process UMITOOLS_PREPAREFORRSEM {
         --stdout=${prefix}.bam \\
         --log=${prefix}.prepare_for_rsem.log \\
         $args
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        umitools: \$(umi_tools --version 2>&1 | sed 's/^.*UMI-tools version://; s/ *\$//')
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/bbmap/bbsplit/main.nf b/modules/nf-core/bbmap/bbsplit/main.nf
index f82bb9e47..816d26650 100644
--- a/modules/nf-core/bbmap/bbsplit/main.nf
+++ b/modules/nf-core/bbmap/bbsplit/main.nf
@@ -20,7 +20,7 @@ process BBMAP_BBSPLIT {
     tuple val(meta), path('*primary*fastq.gz'), optional:true, emit: primary_fastq
     tuple val(meta), path('*fastq.gz')        , optional:true, emit: all_fastq
     tuple val(meta), path('*txt')             , optional:true, emit: stats
-    path "versions.yml"                       , emit: versions
+    tuple val("${task.process}"), val('bbmap'), cmd("bbversion.sh | grep -v 'Duplicate cpuset'"), emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -50,11 +50,6 @@ process BBMAP_BBSPLIT {
                 path=bbsplit \\
                 threads=$task.cpus \\
                 $args
-
-            cat <<-END_VERSIONS > versions.yml
-            "${task.process}":
-                bbmap: \$(bbversion.sh | grep -v "Duplicate cpuset")
-            END_VERSIONS
             """
         } else {
             log.error 'ERROR: Please specify as input a primary fasta file along with names and paths to non-primary fasta files.'
@@ -79,11 +74,6 @@ process BBMAP_BBSPLIT {
             $fastq_out \\
             refstats=${prefix}.stats.txt \\
             $args
-
-        cat <<-END_VERSIONS > versions.yml
-        "${task.process}":
-            bbmap: \$(bbversion.sh | grep -v "Duplicate cpuset")
-        END_VERSIONS
         """
     }
 }
diff --git a/modules/nf-core/cat/fastq/main.nf b/modules/nf-core/cat/fastq/main.nf
index 5021e6fcb..df99dd4dd 100644
--- a/modules/nf-core/cat/fastq/main.nf
+++ b/modules/nf-core/cat/fastq/main.nf
@@ -12,7 +12,7 @@ process CAT_FASTQ {
 
     output:
     tuple val(meta), path("*.merged.fastq.gz"), emit: reads
-    path "versions.yml"                       , emit: versions
+    tuple val("${task.process}"), val('cat'), cmd("echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//'"), emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -25,11 +25,6 @@ process CAT_FASTQ {
         if (readList.size >= 1) {
             """
             cat ${readList.join(' ')} > ${prefix}.merged.fastq.gz
-
-            cat <<-END_VERSIONS > versions.yml
-            "${task.process}":
-                cat: \$(echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//')
-            END_VERSIONS
             """
         }
     } else {
@@ -40,11 +35,6 @@ process CAT_FASTQ {
             """
             cat ${read1.join(' ')} > ${prefix}_1.merged.fastq.gz
             cat ${read2.join(' ')} > ${prefix}_2.merged.fastq.gz
-
-            cat <<-END_VERSIONS > versions.yml
-            "${task.process}":
-                cat: \$(echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//')
-            END_VERSIONS
             """
         }
     }
@@ -56,11 +46,6 @@ process CAT_FASTQ {
         if (readList.size > 1) {
             """
             touch ${prefix}.merged.fastq.gz
-
-            cat <<-END_VERSIONS > versions.yml
-            "${task.process}":
-                cat: \$(echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//')
-            END_VERSIONS
             """
         }
     } else {
@@ -68,11 +53,6 @@ process CAT_FASTQ {
             """
             touch ${prefix}_1.merged.fastq.gz
             touch ${prefix}_2.merged.fastq.gz
-
-            cat <<-END_VERSIONS > versions.yml
-            "${task.process}":
-                cat: \$(echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//')
-            END_VERSIONS
             """
         }
     }
diff --git a/modules/nf-core/custom/getchromsizes/main.nf b/modules/nf-core/custom/getchromsizes/main.nf
index 060a2e885..f537e55a5 100644
--- a/modules/nf-core/custom/getchromsizes/main.nf
+++ b/modules/nf-core/custom/getchromsizes/main.nf
@@ -14,7 +14,7 @@ process CUSTOM_GETCHROMSIZES {
     tuple val(meta), path ("*.sizes"), emit: sizes
     tuple val(meta), path ("*.fai")  , emit: fai
     tuple val(meta), path ("*.gzi")  , emit: gzi, optional: true
-    path  "versions.yml"             , emit: versions
+    tuple val("${task.process}"), val('getchromsizes'), cmd("echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//'"), emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -24,21 +24,11 @@ process CUSTOM_GETCHROMSIZES {
     """
     samtools faidx $fasta
     cut -f 1,2 ${fasta}.fai > ${fasta}.sizes
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        getchromsizes: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
-    END_VERSIONS
     """
 
     stub:
     """
     touch ${fasta}.fai
     touch ${fasta}.sizes
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        getchromsizes: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/fastp/main.nf b/modules/nf-core/fastp/main.nf
index 831b7f128..a5f07e542 100644
--- a/modules/nf-core/fastp/main.nf
+++ b/modules/nf-core/fastp/main.nf
@@ -18,7 +18,7 @@ process FASTP {
     tuple val(meta), path('*.json')           , emit: json
     tuple val(meta), path('*.html')           , emit: html
     tuple val(meta), path('*.log')            , emit: log
-    path "versions.yml"                       , emit: versions
+    tuple val("${task.process}"), val('fastp'), cmd("fastp --version 2>&1 | sed -e 's/fastp //g'"), emit: versions
     tuple val(meta), path('*.fail.fastq.gz')  , optional:true, emit: reads_fail
     tuple val(meta), path('*.merged.fastq.gz'), optional:true, emit: reads_merged
 
@@ -47,11 +47,6 @@ process FASTP {
             $args \\
             2> ${prefix}.fastp.log \\
         | gzip -c > ${prefix}.fastp.fastq.gz
-
-        cat <<-END_VERSIONS > versions.yml
-        "${task.process}":
-            fastp: \$(fastp --version 2>&1 | sed -e "s/fastp //g")
-        END_VERSIONS
         """
     } else if (meta.single_end) {
         """
@@ -67,11 +62,6 @@ process FASTP {
             $fail_fastq \\
             $args \\
             2> ${prefix}.fastp.log
-
-        cat <<-END_VERSIONS > versions.yml
-        "${task.process}":
-            fastp: \$(fastp --version 2>&1 | sed -e "s/fastp //g")
-        END_VERSIONS
         """
     } else {
         def merge_fastq = save_merged ? "-m --merged_out ${prefix}.merged.fastq.gz" : ''
@@ -92,11 +82,6 @@ process FASTP {
             --detect_adapter_for_pe \\
             $args \\
             2> ${prefix}.fastp.log
-
-        cat <<-END_VERSIONS > versions.yml
-        "${task.process}":
-            fastp: \$(fastp --version 2>&1 | sed -e "s/fastp //g")
-        END_VERSIONS
         """
     }
 }
diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf
index 67209f793..53dfa2786 100644
--- a/modules/nf-core/fastqc/main.nf
+++ b/modules/nf-core/fastqc/main.nf
@@ -13,7 +13,7 @@ process FASTQC {
     output:
     tuple val(meta), path("*.html"), emit: html
     tuple val(meta), path("*.zip") , emit: zip
-    path  "versions.yml"           , emit: versions
+    tuple val("${task.process}"), val('fastqc'), cmd("fastqc --version | sed -e 's/FastQC v//g'"), emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -34,11 +34,6 @@ process FASTQC {
         $args \\
         --threads $task.cpus \\
         $renamed_files
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" )
-    END_VERSIONS
     """
 
     stub:
@@ -46,10 +41,5 @@ process FASTQC {
     """
     touch ${prefix}.html
     touch ${prefix}.zip
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" )
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/fq/subsample/main.nf b/modules/nf-core/fq/subsample/main.nf
index 8b4ff5be0..1098fb599 100644
--- a/modules/nf-core/fq/subsample/main.nf
+++ b/modules/nf-core/fq/subsample/main.nf
@@ -12,7 +12,7 @@ process FQ_SUBSAMPLE {
 
     output:
     tuple val(meta), path("*.fastq.gz"), emit: fastq
-    path "versions.yml"                , emit: versions
+    tuple val("${task.process}"), val('fq'), cmd("echo \$(fq subsample --version | sed 's/fq-subsample //g')"), emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -46,10 +46,5 @@ process FQ_SUBSAMPLE {
         $fastq \\
         $fastq1_output \\
         $fastq2_output
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        fq: \$(echo \$(fq subsample --version | sed 's/fq-subsample //g'))
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/gffread/main.nf b/modules/nf-core/gffread/main.nf
index f4472b0e8..d033bb41c 100644
--- a/modules/nf-core/gffread/main.nf
+++ b/modules/nf-core/gffread/main.nf
@@ -12,7 +12,7 @@ process GFFREAD {
 
     output:
     path "*.gtf"        , emit: gtf
-    path "versions.yml" , emit: versions
+    tuple val("${task.process}"), val('gffread'), cmd("gffread --version 2>&1"), emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -25,9 +25,5 @@ process GFFREAD {
         $gff \\
         $args \\
         -o ${prefix}.gtf
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        gffread: \$(gffread --version 2>&1)
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/gunzip/main.nf b/modules/nf-core/gunzip/main.nf
index 73bf08cde..4a0c6151b 100644
--- a/modules/nf-core/gunzip/main.nf
+++ b/modules/nf-core/gunzip/main.nf
@@ -12,7 +12,7 @@ process GUNZIP {
 
     output:
     tuple val(meta), path("$gunzip"), emit: gunzip
-    path "versions.yml"             , emit: versions
+    tuple val("${task.process}"), val('gunzip'), cmd("echo \$(gunzip --version 2>&1) | sed 's/^.*(gzip) //; s/ Copyright.*\$//'"), emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -29,20 +29,11 @@ process GUNZIP {
         $args \\
         $archive \\
         > $gunzip
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        gunzip: \$(echo \$(gunzip --version 2>&1) | sed 's/^.*(gzip) //; s/ Copyright.*\$//')
-    END_VERSIONS
     """
 
     stub:
     gunzip = archive.toString() - '.gz'
     """
     touch $gunzip
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        gunzip: \$(echo \$(gunzip --version 2>&1) | sed 's/^.*(gzip) //; s/ Copyright.*\$//')
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/hisat2/align/main.nf b/modules/nf-core/hisat2/align/main.nf
index db8e8bb6d..ae9603122 100644
--- a/modules/nf-core/hisat2/align/main.nf
+++ b/modules/nf-core/hisat2/align/main.nf
@@ -17,7 +17,8 @@ process HISAT2_ALIGN {
     tuple val(meta), path("*.bam")                   , emit: bam
     tuple val(meta), path("*.log")                   , emit: summary
     tuple val(meta), path("*fastq.gz"), optional:true, emit: fastq
-    path  "versions.yml"                             , emit: versions
+    tuple val("${task.process}"), val('hisat2'), val('2.2.1'), emit: versions1
+    tuple val("${task.process}"), val('samtools'), cmd("echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//'"), emit: versions2
 
     when:
     task.ext.when == null || task.ext.when
@@ -25,7 +26,6 @@ process HISAT2_ALIGN {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def VERSION = '2.2.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
 
     def strandedness = ''
     if (meta.strandedness == 'forward') {
@@ -50,12 +50,6 @@ process HISAT2_ALIGN {
             $unaligned \\
             $args \\
             | samtools view -bS -F 4 -F 256 - > ${prefix}.bam
-
-        cat <<-END_VERSIONS > versions.yml
-        "${task.process}":
-            hisat2: $VERSION
-            samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
-        END_VERSIONS
         """
     } else {
         def unaligned = params.save_unaligned ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : ''
@@ -82,12 +76,6 @@ process HISAT2_ALIGN {
         if [ -f ${prefix}.unmapped.fastq.2.gz ]; then
             mv ${prefix}.unmapped.fastq.2.gz ${prefix}.unmapped_2.fastq.gz
         fi
-
-        cat <<-END_VERSIONS > versions.yml
-        "${task.process}":
-            hisat2: $VERSION
-            samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
-        END_VERSIONS
         """
     }
 }
diff --git a/modules/nf-core/hisat2/build/main.nf b/modules/nf-core/hisat2/build/main.nf
index 90f8efcc6..e5aa09271 100644
--- a/modules/nf-core/hisat2/build/main.nf
+++ b/modules/nf-core/hisat2/build/main.nf
@@ -16,7 +16,7 @@ process HISAT2_BUILD {
 
     output:
     tuple val(meta), path("hisat2") , emit: index
-    path "versions.yml"             , emit: versions
+    tuple val("${task.process}"), val('hisat2'), val('2.2.1'), emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -44,7 +44,6 @@ process HISAT2_BUILD {
         log.info "[HISAT2 index build] Less than ${hisat2_build_memory} GB available, so NOT using splice sites and exons to build HISAT2 index."
         log.info "[HISAT2 index build] Use --hisat2_build_memory [small number] to skip this check."
     }
-    def VERSION = '2.2.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     mkdir hisat2
     $extract_exons
@@ -55,10 +54,5 @@ process HISAT2_BUILD {
         $args \\
         $fasta \\
         hisat2/${fasta.baseName}
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        hisat2: $VERSION
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/hisat2/extractsplicesites/main.nf b/modules/nf-core/hisat2/extractsplicesites/main.nf
index a6e59e202..ed690f992 100644
--- a/modules/nf-core/hisat2/extractsplicesites/main.nf
+++ b/modules/nf-core/hisat2/extractsplicesites/main.nf
@@ -13,19 +13,14 @@ process HISAT2_EXTRACTSPLICESITES {
 
     output:
     tuple val(meta), path("*.splice_sites.txt"), emit: txt
-    path "versions.yml"                        , emit: versions
+    tuple val("${task.process}"), val('hisat2'), val('2.2.1'), emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
     def args = task.ext.args ?: ''
-    def VERSION = '2.2.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     hisat2_extract_splice_sites.py $gtf > ${gtf.baseName}.splice_sites.txt
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        hisat2: $VERSION
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/kallisto/index/main.nf b/modules/nf-core/kallisto/index/main.nf
index 28a47dbeb..4f8a66b41 100644
--- a/modules/nf-core/kallisto/index/main.nf
+++ b/modules/nf-core/kallisto/index/main.nf
@@ -12,7 +12,7 @@ process KALLISTO_INDEX {
 
     output:
     tuple val(meta), path("kallisto")  , emit: index
-    path "versions.yml"                , emit: versions
+    tuple val("${task.process}"), val('kallisto'), cmd("echo \$(kallisto 2>&1) | sed 's/^kallisto //; s/Usage.*\$//'"), emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -25,20 +25,10 @@ process KALLISTO_INDEX {
         $args \\
         -i kallisto \\
         $fasta
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        kallisto: \$(echo \$(kallisto 2>&1) | sed 's/^kallisto //; s/Usage.*\$//')
-    END_VERSIONS
     """
 
     stub:
     """
     touch kallisto
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        kallisto: \$(echo \$(kallisto 2>&1) | sed 's/^kallisto //; s/Usage.*\$//')
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/kallisto/quant/main.nf b/modules/nf-core/kallisto/quant/main.nf
index f5444d791..04a602ef3 100644
--- a/modules/nf-core/kallisto/quant/main.nf
+++ b/modules/nf-core/kallisto/quant/main.nf
@@ -19,7 +19,7 @@ process KALLISTO_QUANT {
     tuple val(meta), path("${prefix}")        , emit: results
     tuple val(meta), path("*.run_info.json")  , emit: json_info
     tuple val(meta), path("*.log")            , emit: log
-    path "versions.yml"                       , emit: versions
+    tuple val("${task.process}"), val('kallisto'), cmd("echo \$(kallisto version) | sed 's/kallisto, version //g'"), emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -61,18 +61,9 @@ process KALLISTO_QUANT {
 
     cp ${prefix}/kallisto_quant.log ${prefix}.log
     cp ${prefix}/run_info.json ${prefix}.run_info.json
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        kallisto: \$(echo \$(kallisto version) | sed "s/kallisto, version //g" )
-    END_VERSIONS
     """
 
     stub:
     """
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        kallisto: \$(echo \$(kallisto version) | sed "s/kallisto, version //g" )
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/picard/markduplicates/main.nf b/modules/nf-core/picard/markduplicates/main.nf
index ebfa0864d..28702bb64 100644
--- a/modules/nf-core/picard/markduplicates/main.nf
+++ b/modules/nf-core/picard/markduplicates/main.nf
@@ -16,7 +16,7 @@ process PICARD_MARKDUPLICATES {
     tuple val(meta), path("*.bam")        , emit: bam
     tuple val(meta), path("*.bai")        , optional:true, emit: bai
     tuple val(meta), path("*.metrics.txt"), emit: metrics
-    path  "versions.yml"                  , emit: versions
+    tuple val("${task.process}"), val('picard'), cmd("echo \$(picard MarkDuplicates --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:"), emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -42,11 +42,6 @@ process PICARD_MARKDUPLICATES {
         --OUTPUT ${prefix}.bam \\
         --REFERENCE_SEQUENCE $fasta \\
         --METRICS_FILE ${prefix}.MarkDuplicates.metrics.txt
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        picard: \$(echo \$(picard MarkDuplicates --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:)
-    END_VERSIONS
     """
 
     stub:
@@ -56,10 +51,5 @@ process PICARD_MARKDUPLICATES {
     touch ${prefix}.bam
     touch ${prefix}.bam.bai
     touch ${prefix}.MarkDuplicates.metrics.txt
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        picard: \$(echo \$(picard MarkDuplicates --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:)
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/preseq/lcextrap/main.nf b/modules/nf-core/preseq/lcextrap/main.nf
index 12546f0a2..bc1bf3c8f 100644
--- a/modules/nf-core/preseq/lcextrap/main.nf
+++ b/modules/nf-core/preseq/lcextrap/main.nf
@@ -14,7 +14,7 @@ process PRESEQ_LCEXTRAP {
     output:
     tuple val(meta), path("*.lc_extrap.txt"), emit: lc_extrap
     tuple val(meta), path("*.log")          , emit: log
-    path  "versions.yml"                    , emit: versions
+    tuple val("${task.process}"), val('preseq'), cmd("echo \$(preseq 2>&1) | sed 's/^.*Version: //; s/Usage:.*\$//'"), emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -31,10 +31,5 @@ process PRESEQ_LCEXTRAP {
         -output ${prefix}.lc_extrap.txt \\
         $bam
     cp .command.err ${prefix}.command.log
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        preseq: \$(echo \$(preseq 2>&1) | sed 's/^.*Version: //; s/Usage:.*\$//')
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/qualimap/rnaseq/main.nf b/modules/nf-core/qualimap/rnaseq/main.nf
index 044c983fc..18cbb07a9 100644
--- a/modules/nf-core/qualimap/rnaseq/main.nf
+++ b/modules/nf-core/qualimap/rnaseq/main.nf
@@ -13,7 +13,7 @@ process QUALIMAP_RNASEQ {
 
     output:
     tuple val(meta), path("${prefix}"), emit: results
-    path  "versions.yml"              , emit: versions
+    tuple val("${task.process}"), val('qualimap'), cmd("echo \$(qualimap 2>&1) | sed 's/^.*QualiMap v.//; s/Built.*\$//'"), emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -43,21 +43,11 @@ process QUALIMAP_RNASEQ {
         -p $strandedness \\
         $paired_end \\
         -outdir $prefix
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        qualimap: \$(echo \$(qualimap 2>&1) | sed 's/^.*QualiMap v.//; s/Built.*\$//')
-    END_VERSIONS
     """
 
     stub:
     prefix = task.ext.prefix ?: "${meta.id}"
     """
     mkdir ${prefix}
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        qualimap: \$(echo \$(qualimap 2>&1) | sed 's/^.*QualiMap v.//; s/Built.*\$//')
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/rsem/calculateexpression/main.nf b/modules/nf-core/rsem/calculateexpression/main.nf
index 54041aedb..5d2fe2277 100644
--- a/modules/nf-core/rsem/calculateexpression/main.nf
+++ b/modules/nf-core/rsem/calculateexpression/main.nf
@@ -16,7 +16,8 @@ process RSEM_CALCULATEEXPRESSION {
     tuple val(meta), path("*.isoforms.results"), emit: counts_transcript
     tuple val(meta), path("*.stat")            , emit: stat
     tuple val(meta), path("*.log")             , emit: logs
-    path  "versions.yml"                       , emit: versions
+    tuple val("${task.process}"), val('rsem'), cmd("rsem-calculate-expression --version | sed -e 's/Current version: RSEM v//g'"), emit: versions1
+    tuple val("${task.process}"), val('star'), cmd("STAR --version | sed -e 's/STAR_//g'"), emit: versions2
 
     tuple val(meta), path("*.STAR.genome.bam")       , optional:true, emit: bam_star
     tuple val(meta), path("${prefix}.genome.bam")    , optional:true, emit: bam_genome
@@ -47,11 +48,5 @@ process RSEM_CALCULATEEXPRESSION {
         $reads \\
         \$INDEX \\
         $prefix
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        rsem: \$(rsem-calculate-expression --version | sed -e "s/Current version: RSEM v//g")
-        star: \$(STAR --version | sed -e "s/STAR_//g")
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/rsem/preparereference/main.nf b/modules/nf-core/rsem/preparereference/main.nf
index 62b93d08a..31fc6881d 100644
--- a/modules/nf-core/rsem/preparereference/main.nf
+++ b/modules/nf-core/rsem/preparereference/main.nf
@@ -14,7 +14,8 @@ process RSEM_PREPAREREFERENCE {
     output:
     path "rsem"           , emit: index
     path "*transcripts.fa", emit: transcript_fasta
-    path "versions.yml"   , emit: versions
+    tuple val("${task.process}"), val('rsem'), cmd("rsem-calculate-expression --version | sed -e 's/Current version: RSEM v//g'"), emit: versions1
+    tuple val("${task.process}"), val('star'), cmd("STAR --version | sed -e 's/STAR_//g'"), emit: versions2
 
     when:
     task.ext.when == null || task.ext.when
@@ -44,12 +45,6 @@ process RSEM_PREPAREREFERENCE {
             rsem/genome
 
         cp rsem/genome.transcripts.fa .
-
-        cat <<-END_VERSIONS > versions.yml
-        "${task.process}":
-            rsem: \$(rsem-calculate-expression --version | sed -e "s/Current version: RSEM v//g")
-            star: \$(STAR --version | sed -e "s/STAR_//g")
-        END_VERSIONS
         """
     } else {
         """
@@ -61,12 +56,6 @@ process RSEM_PREPAREREFERENCE {
             rsem/genome
 
         cp rsem/genome.transcripts.fa .
-
-        cat <<-END_VERSIONS > versions.yml
-        "${task.process}":
-            rsem: \$(rsem-calculate-expression --version | sed -e "s/Current version: RSEM v//g")
-            star: \$(STAR --version | sed -e "s/STAR_//g")
-        END_VERSIONS
         """
     }
 }
diff --git a/modules/nf-core/rseqc/bamstat/main.nf b/modules/nf-core/rseqc/bamstat/main.nf
index 04c1eefd0..19fe2de25 100644
--- a/modules/nf-core/rseqc/bamstat/main.nf
+++ b/modules/nf-core/rseqc/bamstat/main.nf
@@ -12,7 +12,7 @@ process RSEQC_BAMSTAT {
 
     output:
     tuple val(meta), path("*.bam_stat.txt"), emit: txt
-    path  "versions.yml"                   , emit: versions
+    tuple val("${task.process}"), val('rseqc'), cmd("bam_stat.py --version | sed -e 's/bam_stat.py //g'"), emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -25,10 +25,5 @@ process RSEQC_BAMSTAT {
         -i $bam \\
         $args \\
         > ${prefix}.bam_stat.txt
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        rseqc: \$(bam_stat.py --version | sed -e "s/bam_stat.py //g")
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/rseqc/inferexperiment/main.nf b/modules/nf-core/rseqc/inferexperiment/main.nf
index 5f9f4b111..142a578c9 100644
--- a/modules/nf-core/rseqc/inferexperiment/main.nf
+++ b/modules/nf-core/rseqc/inferexperiment/main.nf
@@ -13,7 +13,7 @@ process RSEQC_INFEREXPERIMENT {
 
     output:
     tuple val(meta), path("*.infer_experiment.txt"), emit: txt
-    path  "versions.yml"                           , emit: versions
+    tuple val("${task.process}"), val('rseqc'), cmd("infer_experiment.py --version | sed -e 's/infer_experiment.py //g'"), emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -27,10 +27,5 @@ process RSEQC_INFEREXPERIMENT {
         -r $bed \\
         $args \\
         > ${prefix}.infer_experiment.txt
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        rseqc: \$(infer_experiment.py --version | sed -e "s/infer_experiment.py //g")
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/rseqc/innerdistance/main.nf b/modules/nf-core/rseqc/innerdistance/main.nf
index a63a2bf03..3aa79e073 100644
--- a/modules/nf-core/rseqc/innerdistance/main.nf
+++ b/modules/nf-core/rseqc/innerdistance/main.nf
@@ -17,7 +17,7 @@ process RSEQC_INNERDISTANCE {
     tuple val(meta), path("*mean.txt")    , optional:true, emit: mean
     tuple val(meta), path("*.pdf")        , optional:true, emit: pdf
     tuple val(meta), path("*.r")          , optional:true, emit: rscript
-    path  "versions.yml"                  , emit: versions
+    tuple val("${task.process}"), val('rseqc'), cmd("inner_distance.py --version | sed -e 's/inner_distance.py //g'"), emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -34,18 +34,9 @@ process RSEQC_INNERDISTANCE {
             $args \\
             > stdout.txt
         head -n 2 stdout.txt > ${prefix}.inner_distance_mean.txt
-
-        cat <<-END_VERSIONS > versions.yml
-        "${task.process}":
-            rseqc: \$(inner_distance.py --version | sed -e "s/inner_distance.py //g")
-        END_VERSIONS
         """
     } else {
         """
-        cat <<-END_VERSIONS > versions.yml
-        "${task.process}":
-            rseqc: \$(inner_distance.py --version | sed -e "s/inner_distance.py //g")
-        END_VERSIONS
         """
     }
 }
diff --git a/modules/nf-core/rseqc/junctionannotation/main.nf b/modules/nf-core/rseqc/junctionannotation/main.nf
index 4029ac765..33f367dae 100644
--- a/modules/nf-core/rseqc/junctionannotation/main.nf
+++ b/modules/nf-core/rseqc/junctionannotation/main.nf
@@ -19,7 +19,7 @@ process RSEQC_JUNCTIONANNOTATION {
     tuple val(meta), path("*.Interact.bed"), optional:true, emit: interact_bed
     tuple val(meta), path("*junction.pdf") , optional:true, emit: pdf
     tuple val(meta), path("*events.pdf")   , optional:true, emit: events_pdf
-    path  "versions.yml"                   , emit: versions
+    tuple val("${task.process}"), val('rseqc'), cmd("junction_annotation.py --version | sed -e 's/junction_annotation.py //g'"), emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -34,10 +34,5 @@ process RSEQC_JUNCTIONANNOTATION {
         -o $prefix \\
         $args \\
         2> ${prefix}.junction_annotation.log
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        rseqc: \$(junction_annotation.py --version | sed -e "s/junction_annotation.py //g")
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/rseqc/junctionsaturation/main.nf b/modules/nf-core/rseqc/junctionsaturation/main.nf
index 93cc61b23..84196d64e 100644
--- a/modules/nf-core/rseqc/junctionsaturation/main.nf
+++ b/modules/nf-core/rseqc/junctionsaturation/main.nf
@@ -14,7 +14,7 @@ process RSEQC_JUNCTIONSATURATION {
     output:
     tuple val(meta), path("*.pdf"), emit: pdf
     tuple val(meta), path("*.r")  , emit: rscript
-    path  "versions.yml"          , emit: versions
+    tuple val("${task.process}"), val('rseqc'), cmd("junction_saturation.py --version | sed -e 's/junction_saturation.py //g'"), emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -28,10 +28,5 @@ process RSEQC_JUNCTIONSATURATION {
         -r $bed \\
         -o $prefix \\
         $args
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        rseqc: \$(junction_saturation.py --version | sed -e "s/junction_saturation.py //g")
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/rseqc/readdistribution/main.nf b/modules/nf-core/rseqc/readdistribution/main.nf
index f3e588d69..33208ba8c 100644
--- a/modules/nf-core/rseqc/readdistribution/main.nf
+++ b/modules/nf-core/rseqc/readdistribution/main.nf
@@ -13,7 +13,7 @@ process RSEQC_READDISTRIBUTION {
 
     output:
     tuple val(meta), path("*.read_distribution.txt"), emit: txt
-    path  "versions.yml"                            , emit: versions
+    tuple val("${task.process}"), val('rseqc'), cmd("read_distribution.py --version | sed -e 's/read_distribution.py //g'"), emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -26,10 +26,5 @@ process RSEQC_READDISTRIBUTION {
         -i $bam \\
         -r $bed \\
         > ${prefix}.read_distribution.txt
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        rseqc: \$(read_distribution.py --version | sed -e "s/read_distribution.py //g")
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/rseqc/readduplication/main.nf b/modules/nf-core/rseqc/readduplication/main.nf
index 023118536..bc9dd19dd 100644
--- a/modules/nf-core/rseqc/readduplication/main.nf
+++ b/modules/nf-core/rseqc/readduplication/main.nf
@@ -15,7 +15,7 @@ process RSEQC_READDUPLICATION {
     tuple val(meta), path("*pos.DupRate.xls"), emit: pos_xls
     tuple val(meta), path("*.pdf")           , emit: pdf
     tuple val(meta), path("*.r")             , emit: rscript
-    path  "versions.yml"                     , emit: versions
+    tuple val("${task.process}"), val('rseqc'), cmd("read_duplication.py --version | sed -e 's/read_duplication.py //g'"), emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -28,10 +28,5 @@ process RSEQC_READDUPLICATION {
         -i $bam \\
         -o $prefix \\
         $args
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        rseqc: \$(read_duplication.py --version | sed -e "s/read_duplication.py //g")
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/rseqc/tin/main.nf b/modules/nf-core/rseqc/tin/main.nf
index 872938b62..4f422839a 100644
--- a/modules/nf-core/rseqc/tin/main.nf
+++ b/modules/nf-core/rseqc/tin/main.nf
@@ -14,7 +14,7 @@ process RSEQC_TIN {
     output:
     tuple val(meta), path("*.txt"), emit: txt
     tuple val(meta), path("*.xls"), emit: xls
-    path "versions.yml"           , emit: versions
+    tuple val("${task.process}"), val('rseqc'), cmd("tin.py --version | sed -e 's/tin.py //g'"), emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -27,10 +27,5 @@ process RSEQC_TIN {
         -i $bam \\
         -r $bed \\
         $args
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        rseqc: \$(tin.py --version | sed -e "s/tin.py //g")
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/salmon/index/main.nf b/modules/nf-core/salmon/index/main.nf
index 118ee6704..f5822cd37 100644
--- a/modules/nf-core/salmon/index/main.nf
+++ b/modules/nf-core/salmon/index/main.nf
@@ -13,7 +13,7 @@ process SALMON_INDEX {
 
     output:
     path "salmon"      , emit: index
-    path "versions.yml", emit: versions
+    tuple val("${task.process}"), val('salmon'), cmd("echo \$(salmon --version) | sed -e 's/salmon //g'"), emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -38,10 +38,5 @@ process SALMON_INDEX {
         -d decoys.txt \\
         $args \\
         -i salmon
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        salmon: \$(echo \$(salmon --version) | sed -e "s/salmon //g")
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/salmon/quant/main.nf b/modules/nf-core/salmon/quant/main.nf
index f11b6c2e2..23a2690ee 100644
--- a/modules/nf-core/salmon/quant/main.nf
+++ b/modules/nf-core/salmon/quant/main.nf
@@ -18,7 +18,7 @@ process SALMON_QUANT {
     output:
     tuple val(meta), path("${prefix}") , emit: results
     tuple val(meta), path("*info.json"), emit: json_info, optional: true
-    path  "versions.yml"               , emit: versions
+    tuple val("${task.process}"), val('salmon'), cmd("echo \$(salmon --version) | sed -e 's/salmon //g'"), emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -70,10 +70,5 @@ process SALMON_QUANT {
     if [ -f $prefix/aux_info/meta_info.json ]; then
         cp $prefix/aux_info/meta_info.json "${prefix}_meta_info.json"
     fi
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        salmon: \$(echo \$(salmon --version) | sed -e "s/salmon //g")
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/samtools/flagstat/main.nf b/modules/nf-core/samtools/flagstat/main.nf
index b75707eca..3d237bbba 100644
--- a/modules/nf-core/samtools/flagstat/main.nf
+++ b/modules/nf-core/samtools/flagstat/main.nf
@@ -12,7 +12,7 @@ process SAMTOOLS_FLAGSTAT {
 
     output:
     tuple val(meta), path("*.flagstat"), emit: flagstat
-    path  "versions.yml"               , emit: versions
+    tuple val("${task.process}"), val('samtools'), cmd("echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//'"), emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -26,21 +26,11 @@ process SAMTOOLS_FLAGSTAT {
         --threads ${task.cpus} \\
         $bam \\
         > ${prefix}.flagstat
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
-    END_VERSIONS
     """
 
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     touch ${prefix}.flagstat
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/samtools/idxstats/main.nf b/modules/nf-core/samtools/idxstats/main.nf
index 83c7c34b9..03df0929b 100644
--- a/modules/nf-core/samtools/idxstats/main.nf
+++ b/modules/nf-core/samtools/idxstats/main.nf
@@ -12,7 +12,7 @@ process SAMTOOLS_IDXSTATS {
 
     output:
     tuple val(meta), path("*.idxstats"), emit: idxstats
-    path  "versions.yml"               , emit: versions
+    tuple val("${task.process}"), val('samtools'), cmd("echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//'"), emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -27,11 +27,6 @@ process SAMTOOLS_IDXSTATS {
         --threads ${task.cpus-1} \\
         $bam \\
         > ${prefix}.idxstats
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
-    END_VERSIONS
     """
 
     stub:
@@ -39,10 +34,5 @@ process SAMTOOLS_IDXSTATS {
 
     """
     touch ${prefix}.idxstats
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/samtools/index/main.nf b/modules/nf-core/samtools/index/main.nf
index 0b20aa4bb..9b60f9596 100644
--- a/modules/nf-core/samtools/index/main.nf
+++ b/modules/nf-core/samtools/index/main.nf
@@ -14,7 +14,7 @@ process SAMTOOLS_INDEX {
     tuple val(meta), path("*.bai") , optional:true, emit: bai
     tuple val(meta), path("*.csi") , optional:true, emit: csi
     tuple val(meta), path("*.crai"), optional:true, emit: crai
-    path  "versions.yml"           , emit: versions
+    tuple val("${task.process}"), val('samtools'), cmd("echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//'"), emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -27,11 +27,6 @@ process SAMTOOLS_INDEX {
         -@ ${task.cpus-1} \\
         $args \\
         $input
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
-    END_VERSIONS
     """
 
     stub:
@@ -39,10 +34,5 @@ process SAMTOOLS_INDEX {
     touch ${input}.bai
     touch ${input}.crai
     touch ${input}.csi
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/samtools/sort/main.nf b/modules/nf-core/samtools/sort/main.nf
index 2b7753fd8..3d237dc81 100644
--- a/modules/nf-core/samtools/sort/main.nf
+++ b/modules/nf-core/samtools/sort/main.nf
@@ -13,7 +13,7 @@ process SAMTOOLS_SORT {
     output:
     tuple val(meta), path("*.bam"), emit: bam
     tuple val(meta), path("*.csi"), emit: csi, optional: true
-    path  "versions.yml"          , emit: versions
+    tuple val("${task.process}"), val('samtools'), cmd("echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//'"), emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -29,21 +29,11 @@ process SAMTOOLS_SORT {
         -o ${prefix}.bam \\
         -T $prefix \\
         $bam
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
-    END_VERSIONS
     """
 
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     touch ${prefix}.bam
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/samtools/stats/main.nf b/modules/nf-core/samtools/stats/main.nf
index 4a2607ded..78a8f9a30 100644
--- a/modules/nf-core/samtools/stats/main.nf
+++ b/modules/nf-core/samtools/stats/main.nf
@@ -13,7 +13,7 @@ process SAMTOOLS_STATS {
 
     output:
     tuple val(meta), path("*.stats"), emit: stats
-    path  "versions.yml"            , emit: versions
+    tuple val("${task.process}"), val('samtools'), cmd("echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//'"), emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -29,21 +29,11 @@ process SAMTOOLS_STATS {
         ${reference} \\
         ${input} \\
         > ${prefix}.stats
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
-    END_VERSIONS
     """
 
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     touch ${prefix}.stats
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/sortmerna/main.nf b/modules/nf-core/sortmerna/main.nf
index 7afae5a68..936a08af0 100644
--- a/modules/nf-core/sortmerna/main.nf
+++ b/modules/nf-core/sortmerna/main.nf
@@ -14,7 +14,7 @@ process SORTMERNA {
     output:
     tuple val(meta), path("*non_rRNA.fastq.gz"), emit: reads
     tuple val(meta), path("*.log")     , emit: log
-    path  "versions.yml"               , emit: versions
+    tuple val("${task.process}"), val('sortmerna'), cmd("echo \$(sortmerna --version 2>&1) | sed 's/^.*SortMeRNA version //; s/ Build Date.*\$//'"), emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -36,11 +36,6 @@ process SORTMERNA {
 
         mv non_rRNA_reads.f*q.gz ${prefix}.non_rRNA.fastq.gz
         mv rRNA_reads.log ${prefix}.sortmerna.log
-
-        cat <<-END_VERSIONS > versions.yml
-        "${task.process}":
-            sortmerna: \$(echo \$(sortmerna --version 2>&1) | sed 's/^.*SortMeRNA version //; s/ Build Date.*\$//')
-        END_VERSIONS
         """
     } else {
         """
@@ -60,11 +55,6 @@ process SORTMERNA {
         mv non_rRNA_reads_fwd.f*q.gz ${prefix}_1.non_rRNA.fastq.gz
         mv non_rRNA_reads_rev.f*q.gz ${prefix}_2.non_rRNA.fastq.gz
         mv rRNA_reads.log ${prefix}.sortmerna.log
-
-        cat <<-END_VERSIONS > versions.yml
-        "${task.process}":
-            sortmerna: \$(echo \$(sortmerna --version 2>&1) | sed 's/^.*SortMeRNA version //; s/ Build Date.*\$//')
-        END_VERSIONS
         """
     }
 }
diff --git a/modules/nf-core/star/align/main.nf b/modules/nf-core/star/align/main.nf
index d0e203848..6c24ac7eb 100644
--- a/modules/nf-core/star/align/main.nf
+++ b/modules/nf-core/star/align/main.nf
@@ -19,7 +19,9 @@ process STAR_ALIGN {
     tuple val(meta), path('*Log.final.out')   , emit: log_final
     tuple val(meta), path('*Log.out')         , emit: log_out
     tuple val(meta), path('*Log.progress.out'), emit: log_progress
-    path  "versions.yml"                      , emit: versions
+    tuple val("${task.process}"), val('star'), cmd("STAR --version | sed -e 's/STAR_//g'"), emit: versions1
+    tuple val("${task.process}"), val('samtools'), cmd("echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//'"), emit: versions2
+    tuple val("${task.process}"), val('gawk'), cmd("echo \$(gawk --version 2>&1) | sed 's/^.*GNU Awk //; s/, .*\$//'"), emit: versions3
 
     tuple val(meta), path('*d.out.bam')              , optional:true, emit: bam
     tuple val(meta), path('*sortedByCoord.out.bam')  , optional:true, emit: bam_sorted
@@ -69,13 +71,6 @@ process STAR_ALIGN {
         mv ${prefix}.Unmapped.out.mate2 ${prefix}.unmapped_2.fastq
         gzip ${prefix}.unmapped_2.fastq
     fi
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        star: \$(STAR --version | sed -e "s/STAR_//g")
-        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
-        gawk: \$(echo \$(gawk --version 2>&1) | sed 's/^.*GNU Awk //; s/, .*\$//')
-    END_VERSIONS
     """
 
     stub:
@@ -98,12 +93,5 @@ process STAR_ALIGN {
     touch ${prefix}.out.sam
     touch ${prefix}.Signal.UniqueMultiple.str1.out.wig
     touch ${prefix}.Signal.UniqueMultiple.str1.out.bg
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        star: \$(STAR --version | sed -e "s/STAR_//g")
-        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
-        gawk: \$(echo \$(gawk --version 2>&1) | sed 's/^.*GNU Awk //; s/, .*\$//')
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/star/genomegenerate/main.nf b/modules/nf-core/star/genomegenerate/main.nf
index 434240427..e5350280b 100644
--- a/modules/nf-core/star/genomegenerate/main.nf
+++ b/modules/nf-core/star/genomegenerate/main.nf
@@ -13,7 +13,9 @@ process STAR_GENOMEGENERATE {
 
     output:
     tuple val(meta), path("star")  , emit: index
-    path "versions.yml"            , emit: versions
+    tuple val("${task.process}"), val('star'), cmd("STAR --version | sed -e 's/STAR_//g'"), emit: versions1
+    tuple val("${task.process}"), val('samtools'), cmd("echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//'"), emit: versions2
+    tuple val("${task.process}"), val('gawk'), cmd("echo \$(gawk --version 2>&1) | sed 's/^.*GNU Awk //; s/, .*\$//'"), emit: versions3
 
     when:
     task.ext.when == null || task.ext.when
@@ -33,13 +35,6 @@ process STAR_GENOMEGENERATE {
             --runThreadN $task.cpus \\
             $memory \\
             $args
-
-        cat <<-END_VERSIONS > versions.yml
-        "${task.process}":
-            star: \$(STAR --version | sed -e "s/STAR_//g")
-            samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
-            gawk: \$(echo \$(gawk --version 2>&1) | sed 's/^.*GNU Awk //; s/, .*\$//')
-        END_VERSIONS
         """
     } else {
         """
@@ -56,13 +51,6 @@ process STAR_GENOMEGENERATE {
             --genomeSAindexNbases \$NUM_BASES \\
             $memory \\
             $args
-
-        cat <<-END_VERSIONS > versions.yml
-        "${task.process}":
-            star: \$(STAR --version | sed -e "s/STAR_//g")
-            samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
-            gawk: \$(echo \$(gawk --version 2>&1) | sed 's/^.*GNU Awk //; s/, .*\$//')
-        END_VERSIONS
         """
     }
 
@@ -85,12 +73,5 @@ process STAR_GENOMEGENERATE {
     touch star/sjdbList.fromGTF.out.tab
     touch star/sjdbList.out.tab
     touch star/transcriptInfo.tab
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        star: \$(STAR --version | sed -e "s/STAR_//g")
-        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
-        gawk: \$(echo \$(gawk --version 2>&1) | sed 's/^.*GNU Awk //; s/, .*\$//')
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/stringtie/stringtie/main.nf b/modules/nf-core/stringtie/stringtie/main.nf
index d0f8b563f..de59c7fa1 100644
--- a/modules/nf-core/stringtie/stringtie/main.nf
+++ b/modules/nf-core/stringtie/stringtie/main.nf
@@ -16,7 +16,7 @@ process STRINGTIE_STRINGTIE {
     tuple val(meta), path("*.abundance.txt")  , emit: abundance
     tuple val(meta), path("*.coverage.gtf")   , optional: true, emit: coverage_gtf
     tuple val(meta), path("*.ballgown")       , optional: true, emit: ballgown
-    path  "versions.yml"                      , emit: versions
+    tuple val("${task.process}"), val('stringtie'), cmd("stringtie --version 2>&1"), emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -45,11 +45,6 @@ process STRINGTIE_STRINGTIE {
         $ballgown \\
         -p $task.cpus \\
         $args
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        stringtie: \$(stringtie --version 2>&1)
-    END_VERSIONS
     """
 
     stub:
@@ -59,10 +54,5 @@ process STRINGTIE_STRINGTIE {
     touch ${prefix}.gene.abundance.txt
     touch ${prefix}.coverage.gtf
     touch ${prefix}.ballgown
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        stringtie: \$(stringtie --version 2>&1)
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/subread/featurecounts/main.nf b/modules/nf-core/subread/featurecounts/main.nf
index a524b92f1..fa844cd8c 100644
--- a/modules/nf-core/subread/featurecounts/main.nf
+++ b/modules/nf-core/subread/featurecounts/main.nf
@@ -13,7 +13,7 @@ process SUBREAD_FEATURECOUNTS {
     output:
     tuple val(meta), path("*featureCounts.txt")        , emit: counts
     tuple val(meta), path("*featureCounts.txt.summary"), emit: summary
-    path "versions.yml"                                , emit: versions
+    tuple val("${task.process}"), val('subread'), cmd("echo \$(featureCounts -v 2>&1) | sed -e 's/featureCounts v//g'"), emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -38,10 +38,5 @@ process SUBREAD_FEATURECOUNTS {
         -s $strandedness \\
         -o ${prefix}.featureCounts.txt \\
         ${bams.join(' ')}
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        subread: \$( echo \$(featureCounts -v 2>&1) | sed -e "s/featureCounts v//g")
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/trimgalore/main.nf b/modules/nf-core/trimgalore/main.nf
index dcb77ae7b..13e3e496b 100644
--- a/modules/nf-core/trimgalore/main.nf
+++ b/modules/nf-core/trimgalore/main.nf
@@ -16,7 +16,8 @@ process TRIMGALORE {
     tuple val(meta), path("*unpaired*.fq.gz")                   , emit: unpaired, optional: true
     tuple val(meta), path("*.html")                             , emit: html    , optional: true
     tuple val(meta), path("*.zip")                              , emit: zip     , optional: true
-    path "versions.yml"                                         , emit: versions
+    tuple val("${task.process}"), val('trimgalore'), cmd("echo \$(trim_galore --version 2>&1) | sed 's/^.*version //; s/Last.*\$//'"), emit: versions1
+    tuple val("${task.process}"), val('cutadapt'), cmd("cutadapt --version"), emit: versions2
 
     when:
     task.ext.when == null || task.ext.when
@@ -46,12 +47,6 @@ process TRIMGALORE {
             --cores $cores \\
             --gzip \\
             ${prefix}.fastq.gz
-
-        cat <<-END_VERSIONS > versions.yml
-        "${task.process}":
-            trimgalore: \$(echo \$(trim_galore --version 2>&1) | sed 's/^.*version //; s/Last.*\$//')
-            cutadapt: \$(cutadapt --version)
-        END_VERSIONS
         """
     } else {
         """
@@ -64,12 +59,6 @@ process TRIMGALORE {
             --gzip \\
             ${prefix}_1.fastq.gz \\
             ${prefix}_2.fastq.gz
-
-        cat <<-END_VERSIONS > versions.yml
-        "${task.process}":
-            trimgalore: \$(echo \$(trim_galore --version 2>&1) | sed 's/^.*version //; s/Last.*\$//')
-            cutadapt: \$(cutadapt --version)
-        END_VERSIONS
         """
     }
 }
diff --git a/modules/nf-core/ucsc/bedclip/main.nf b/modules/nf-core/ucsc/bedclip/main.nf
index 4bad9a399..7a85a4755 100755
--- a/modules/nf-core/ucsc/bedclip/main.nf
+++ b/modules/nf-core/ucsc/bedclip/main.nf
@@ -14,7 +14,7 @@ process UCSC_BEDCLIP {
 
     output:
     tuple val(meta), path("*.bedGraph"), emit: bedgraph
-    path "versions.yml"                , emit: versions
+    tuple val("${task.process}"), val('ucsc'), val('377'), emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -22,16 +22,10 @@ process UCSC_BEDCLIP {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def VERSION = '377' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     bedClip \\
         $bedgraph \\
         $sizes \\
         ${prefix}.bedGraph
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        ucsc: $VERSION
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/ucsc/bedgraphtobigwig/main.nf b/modules/nf-core/ucsc/bedgraphtobigwig/main.nf
index 06bb47099..d1628c082 100644
--- a/modules/nf-core/ucsc/bedgraphtobigwig/main.nf
+++ b/modules/nf-core/ucsc/bedgraphtobigwig/main.nf
@@ -14,7 +14,7 @@ process UCSC_BEDGRAPHTOBIGWIG {
 
     output:
     tuple val(meta), path("*.bigWig"), emit: bigwig
-    path "versions.yml"              , emit: versions
+    tuple val("${task.process}"), val('ucsc'), val('445'), emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -22,28 +22,16 @@ process UCSC_BEDGRAPHTOBIGWIG {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def VERSION = '445' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     bedGraphToBigWig \\
         $bedgraph \\
         $sizes \\
         ${prefix}.bigWig
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        ucsc: $VERSION
-    END_VERSIONS
     """
 
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def VERSION = '445' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     touch ${prefix}.bigWig
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        ucsc: $VERSION
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/umitools/dedup/main.nf b/modules/nf-core/umitools/dedup/main.nf
index 56ea04691..bb281c497 100644
--- a/modules/nf-core/umitools/dedup/main.nf
+++ b/modules/nf-core/umitools/dedup/main.nf
@@ -17,7 +17,7 @@ process UMITOOLS_DEDUP {
     tuple val(meta), path("*edit_distance.tsv"), optional:true, emit: tsv_edit_distance
     tuple val(meta), path("*per_umi.tsv")      , optional:true, emit: tsv_per_umi
     tuple val(meta), path("*per_position.tsv") , optional:true, emit: tsv_umi_per_position
-    path  "versions.yml"                       , emit: versions
+    tuple val("${task.process}"), val('umitools'), cmd("umi_tools --version 2>&1 | sed 's/^.*UMI-tools version://; s/ *\$//'"), emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -39,11 +39,6 @@ process UMITOOLS_DEDUP {
         $stats \\
         $paired \\
         $args
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        umitools: \$(umi_tools --version 2>&1 | sed 's/^.*UMI-tools version://; s/ *\$//')
-    END_VERSIONS
     """
 
     stub:
@@ -53,10 +48,5 @@ process UMITOOLS_DEDUP {
     touch ${prefix}_edit_distance.tsv
     touch ${prefix}_per_umi.tsv
     touch ${prefix}_per_position.tsv
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        umitools: \$(umi_tools --version 2>&1 | sed 's/^.*UMI-tools version://; s/ *\$//')
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/umitools/extract/main.nf b/modules/nf-core/umitools/extract/main.nf
index 2f94fa93e..cb2b09366 100644
--- a/modules/nf-core/umitools/extract/main.nf
+++ b/modules/nf-core/umitools/extract/main.nf
@@ -14,7 +14,7 @@ process UMITOOLS_EXTRACT {
     output:
     tuple val(meta), path("*.fastq.gz"), emit: reads
     tuple val(meta), path("*.log")     , emit: log
-    path  "versions.yml"               , emit: versions
+    tuple val("${task.process}"), val('umitools'), cmd("umi_tools --version 2>&1 | sed 's/^.*UMI-tools version://; s/ *\$//'"), emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -30,11 +30,6 @@ process UMITOOLS_EXTRACT {
             -S ${prefix}.umi_extract.fastq.gz \\
             $args \\
             > ${prefix}.umi_extract.log
-
-        cat <<-END_VERSIONS > versions.yml
-        "${task.process}":
-            umitools: \$(umi_tools --version 2>&1 | sed 's/^.*UMI-tools version://; s/ *\$//')
-        END_VERSIONS
         """
     }  else {
         """
@@ -46,11 +41,6 @@ process UMITOOLS_EXTRACT {
             --read2-out=${prefix}.umi_extract_2.fastq.gz \\
             $args \\
             > ${prefix}.umi_extract.log
-
-        cat <<-END_VERSIONS > versions.yml
-        "${task.process}":
-            umitools: \$(umi_tools --version 2>&1 | sed 's/^.*UMI-tools version://; s/ *\$//')
-        END_VERSIONS
         """
     }
 }
diff --git a/modules/nf-core/untar/main.nf b/modules/nf-core/untar/main.nf
index 61461c391..5c5096f4a 100644
--- a/modules/nf-core/untar/main.nf
+++ b/modules/nf-core/untar/main.nf
@@ -12,7 +12,7 @@ process UNTAR {
 
     output:
     tuple val(meta), path("$prefix"), emit: untar
-    path "versions.yml"             , emit: versions
+    tuple val("${task.process}"), val('untar'), cmd("echo \$(tar --version 2>&1) | sed 's/^.*(GNU tar) //; s/ Copyright.*\$//'"), emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -42,11 +42,6 @@ process UNTAR {
             $archive \\
             $args2
     fi
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        untar: \$(echo \$(tar --version 2>&1) | sed 's/^.*(GNU tar) //; s/ Copyright.*\$//')
-    END_VERSIONS
     """
 
     stub:
@@ -54,10 +49,5 @@ process UNTAR {
     """
     mkdir $prefix
     touch ${prefix}/file.txt
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        untar: \$(echo \$(tar --version 2>&1) | sed 's/^.*(GNU tar) //; s/ Copyright.*\$//')
-    END_VERSIONS
     """
 }
diff --git a/subworkflows/local/align_star/main.nf b/subworkflows/local/align_star/main.nf
index 1dba0c085..2184be05e 100644
--- a/subworkflows/local/align_star/main.nf
+++ b/subworkflows/local/align_star/main.nf
@@ -42,7 +42,7 @@ workflow ALIGN_STAR {
         ch_bam_transcript = STAR_ALIGN_IGENOMES.out.bam_transcript
         ch_fastq          = STAR_ALIGN_IGENOMES.out.fastq
         ch_tab            = STAR_ALIGN_IGENOMES.out.tab
-        ch_versions       = ch_versions.mix(STAR_ALIGN_IGENOMES.out.versions.first())
+        ch_versions       = ch_versions.mix(STAR_ALIGN_IGENOMES.out.versions1, STAR_ALIGN_IGENOMES.out.versions2, STAR_ALIGN_IGENOMES.out.versions3)
     } else {
         STAR_ALIGN ( reads, index, gtf, star_ignore_sjdbgtf, seq_platform, seq_center )
         ch_orig_bam       = STAR_ALIGN.out.bam
@@ -53,7 +53,7 @@ workflow ALIGN_STAR {
         ch_bam_transcript = STAR_ALIGN.out.bam_transcript
         ch_fastq          = STAR_ALIGN.out.fastq
         ch_tab            = STAR_ALIGN.out.tab
-        ch_versions       = ch_versions.mix(STAR_ALIGN.out.versions.first())
+        ch_versions       = ch_versions.mix(STAR_ALIGN.out.versions1, STAR_ALIGN.out.versions2, STAR_ALIGN.out.versions3)
     }
 
     //
@@ -79,5 +79,5 @@ workflow ALIGN_STAR {
     flagstat       = BAM_SORT_STATS_SAMTOOLS.out.flagstat // channel: [ val(meta), [ flagstat ] ]
     idxstats       = BAM_SORT_STATS_SAMTOOLS.out.idxstats // channel: [ val(meta), [ idxstats ] ]
 
-    versions       = ch_versions                    // channel: [ versions.yml ]
+    versions       = ch_versions                    // channel: [ process, tool, version ]
 }
diff --git a/subworkflows/local/prepare_genome/main.nf b/subworkflows/local/prepare_genome/main.nf
index 0be947954..4462cd1a7 100644
--- a/subworkflows/local/prepare_genome/main.nf
+++ b/subworkflows/local/prepare_genome/main.nf
@@ -147,7 +147,7 @@ workflow PREPARE_GENOME {
     } else {
         ch_transcript_fasta = MAKE_TRANSCRIPTS_FASTA ( ch_fasta, ch_gtf ).transcript_fasta
         ch_versions         = ch_versions.mix(GTF_FILTER.out.versions)
-        ch_versions         = ch_versions.mix(MAKE_TRANSCRIPTS_FASTA.out.versions)
+        ch_versions         = ch_versions.mix(MAKE_TRANSCRIPTS_FASTA.out.versions1, MAKE_TRANSCRIPTS_FASTA.out.versions2)
     }
 
     //
@@ -200,10 +200,10 @@ workflow PREPARE_GENOME {
         } else {
             if (is_aws_igenome) {
                 ch_star_index = STAR_GENOMEGENERATE_IGENOMES ( ch_fasta, ch_gtf ).index
-                ch_versions   = ch_versions.mix(STAR_GENOMEGENERATE_IGENOMES.out.versions)
+                ch_versions   = ch_versions.mix(STAR_GENOMEGENERATE_IGENOMES.out.versions1, STAR_GENOMEGENERATE_IGENOMES.out.versions2, STAR_GENOMEGENERATE_IGENOMES.out.versions3)
             } else {
                 ch_star_index = STAR_GENOMEGENERATE ( ch_fasta.map { [ [:], it ] }, ch_gtf.map { [ [:], it ] } ).index.map { it[1] }
-                ch_versions   = ch_versions.mix(STAR_GENOMEGENERATE.out.versions)
+                ch_versions   = ch_versions.mix(STAR_GENOMEGENERATE.out.versions1, STAR_GENOMEGENERATE.out.versions2, STAR_GENOMEGENERATE.out.versions3)
             }
         }
     }
@@ -222,7 +222,7 @@ workflow PREPARE_GENOME {
             }
         } else {
             ch_rsem_index = RSEM_PREPAREREFERENCE_GENOME ( ch_fasta, ch_gtf ).index
-            ch_versions   = ch_versions.mix(RSEM_PREPAREREFERENCE_GENOME.out.versions)
+            ch_versions   = ch_versions.mix(RSEM_PREPAREREFERENCE_GENOME.out.versions1, RSEM_PREPAREREFERENCE_GENOME.out.versions2)
         }
     }
 
@@ -301,5 +301,5 @@ workflow PREPARE_GENOME {
     hisat2_index     = ch_hisat2_index           // channel: path(hisat2/index/)
     salmon_index     = ch_salmon_index           // channel: path(salmon/index/)
     kallisto_index   = ch_kallisto_index         // channel: [ meta, path(kallisto/index/) ]
-    versions         = ch_versions.ifEmpty(null) // channel: [ versions.yml ]
+    versions         = ch_versions.ifEmpty(null) // channel: [ process, tool, version ]
 }
diff --git a/subworkflows/local/quantify_pseudo/main.nf b/subworkflows/local/quantify_pseudo/main.nf
index 886b45e7b..e825b8efa 100644
--- a/subworkflows/local/quantify_pseudo/main.nf
+++ b/subworkflows/local/quantify_pseudo/main.nf
@@ -48,14 +48,14 @@ workflow QUANTIFY_PSEUDO_ALIGNMENT {
     ch_versions = ch_versions.mix(TX2GENE.out.versions)
 
     TXIMPORT ( ch_pseudo_results.collect{it[1]}, TX2GENE.out.tsv.collect(), pseudo_aligner )
-    ch_versions = ch_versions.mix(TXIMPORT.out.versions)
+    ch_versions = ch_versions.mix(TXIMPORT.out.versions1, TXIMPORT.out.versions2)
 
     SE_GENE (
         TXIMPORT.out.counts_gene,
         TXIMPORT.out.tpm_gene,
         TX2GENE.out.tsv.collect()
     )
-    ch_versions = ch_versions.mix(SE_GENE.out.versions)
+    ch_versions = ch_versions.mix(SE_GENE.out.versions1, SE_GENE.out.versions2)
 
     SE_GENE_LENGTH_SCALED (
         TXIMPORT.out.counts_gene_length_scaled,
@@ -94,5 +94,5 @@ workflow QUANTIFY_PSEUDO_ALIGNMENT {
     merged_tpm_transcript         = TXIMPORT.out.tpm_transcript            //    path: *.transcript_tpm.tsv
     merged_transcript_rds         = SE_TRANSCRIPT.out.rds                  //    path: *.rds
 
-    versions                      = ch_versions                            // channel: [ versions.yml ]
+    versions                      = ch_versions                            // channel: [ process, tool, version ]
 }
diff --git a/subworkflows/local/quantify_rsem/main.nf b/subworkflows/local/quantify_rsem/main.nf
index 4b7473634..e1398325f 100644
--- a/subworkflows/local/quantify_rsem/main.nf
+++ b/subworkflows/local/quantify_rsem/main.nf
@@ -20,7 +20,7 @@ workflow QUANTIFY_RSEM {
     // Quantify reads with RSEM
     //
     RSEM_CALCULATEEXPRESSION ( reads, index )
-    ch_versions = ch_versions.mix(RSEM_CALCULATEEXPRESSION.out.versions.first())
+    ch_versions = ch_versions.mix(RSEM_CALCULATEEXPRESSION.out.versions1, RSEM_CALCULATEEXPRESSION.out.versions2)
 
     //
     // Sort, index BAM file and run samtools stats, flagstat and idxstats
@@ -58,5 +58,5 @@ workflow QUANTIFY_RSEM {
     merged_counts_transcript = RSEM_MERGE_COUNTS.out.counts_transcript        //    path: *.transcript_counts.tsv
     merged_tpm_transcript    = RSEM_MERGE_COUNTS.out.tpm_transcript           //    path: *.transcript_tpm.tsv
 
-    versions                 = ch_versions                                    // channel: [ versions.yml ]
+    versions                 = ch_versions                                    // channel: [ process, tool, version ]
 }
diff --git a/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/main.nf b/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/main.nf
index 7c07084ff..8676d00ff 100644
--- a/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/main.nf
+++ b/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/main.nf
@@ -51,5 +51,5 @@ workflow BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS {
     flagstat = BAM_STATS_SAMTOOLS.out.flagstat // channel: [ val(meta), path(flagstat) ]
     idxstats = BAM_STATS_SAMTOOLS.out.idxstats // channel: [ val(meta), path(idxstats) ]
 
-    versions = ch_versions                     // channel: [ path(versions.yml) ]
+    versions = ch_versions                     // channel: [ process, tool, version ]
 }
diff --git a/subworkflows/nf-core/bam_markduplicates_picard/main.nf b/subworkflows/nf-core/bam_markduplicates_picard/main.nf
index 6e3df3320..fbb6824df 100644
--- a/subworkflows/nf-core/bam_markduplicates_picard/main.nf
+++ b/subworkflows/nf-core/bam_markduplicates_picard/main.nf
@@ -48,5 +48,5 @@ workflow BAM_MARKDUPLICATES_PICARD {
     flagstat = BAM_STATS_SAMTOOLS.out.flagstat   // channel: [ val(meta), path(flagstat) ]
     idxstats = BAM_STATS_SAMTOOLS.out.idxstats   // channel: [ val(meta), path(idxstats) ]
 
-    versions = ch_versions                       // channel: [ versions.yml ]
+    versions = ch_versions                       // channel: [ process, tool, version ]
 }
diff --git a/subworkflows/nf-core/bam_rseqc/main.nf b/subworkflows/nf-core/bam_rseqc/main.nf
index a698b30ab..3f258958a 100644
--- a/subworkflows/nf-core/bam_rseqc/main.nf
+++ b/subworkflows/nf-core/bam_rseqc/main.nf
@@ -164,5 +164,5 @@ workflow BAM_RSEQC {
 
     tin_txt                         // channel: [ val(meta), txt ]
 
-    versions = ch_versions          // channel: [ versions.yml ]
+    versions = ch_versions          // channel: [ process, tool, version ]
 }
diff --git a/subworkflows/nf-core/bam_sort_stats_samtools/main.nf b/subworkflows/nf-core/bam_sort_stats_samtools/main.nf
index fc1c652b9..898ada0e1 100644
--- a/subworkflows/nf-core/bam_sort_stats_samtools/main.nf
+++ b/subworkflows/nf-core/bam_sort_stats_samtools/main.nf
@@ -46,5 +46,5 @@ workflow BAM_SORT_STATS_SAMTOOLS {
     flagstat = BAM_STATS_SAMTOOLS.out.flagstat // channel: [ val(meta), [ flagstat ] ]
     idxstats = BAM_STATS_SAMTOOLS.out.idxstats // channel: [ val(meta), [ idxstats ] ]
 
-    versions = ch_versions                     // channel: [ versions.yml ]
+    versions = ch_versions                     // channel: [ process, tool, version ]
 }
diff --git a/subworkflows/nf-core/bam_stats_samtools/main.nf b/subworkflows/nf-core/bam_stats_samtools/main.nf
index 44d4c010a..8405094d8 100644
--- a/subworkflows/nf-core/bam_stats_samtools/main.nf
+++ b/subworkflows/nf-core/bam_stats_samtools/main.nf
@@ -28,5 +28,5 @@ workflow BAM_STATS_SAMTOOLS {
     flagstat = SAMTOOLS_FLAGSTAT.out.flagstat // channel: [ val(meta), path(flagstat) ]
     idxstats = SAMTOOLS_IDXSTATS.out.idxstats // channel: [ val(meta), path(idxstats) ]
 
-    versions = ch_versions                    // channel: [ path(versions.yml) ]
+    versions = ch_versions                    // channel: [ process, tool, version ]
 }
diff --git a/subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/main.nf b/subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/main.nf
index 6c3b7b0cb..ced8ac854 100644
--- a/subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/main.nf
+++ b/subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/main.nf
@@ -30,5 +30,5 @@ workflow BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG {
     bigwig   = UCSC_BEDGRAPHTOBIGWIG.out.bigwig // channel: [ val(meta), [ bigwig ] ]
     bedgraph = UCSC_BEDCLIP.out.bedgraph        // channel: [ val(meta), [ bedgraph ] ]
 
-    versions = ch_versions                      // channel: [ versions.yml ]
+    versions = ch_versions                      // channel: [ process, tool, version ]
 }
diff --git a/subworkflows/nf-core/fastq_align_hisat2/main.nf b/subworkflows/nf-core/fastq_align_hisat2/main.nf
index a2ec1cf5e..bd48e9e05 100644
--- a/subworkflows/nf-core/fastq_align_hisat2/main.nf
+++ b/subworkflows/nf-core/fastq_align_hisat2/main.nf
@@ -18,7 +18,7 @@ workflow FASTQ_ALIGN_HISAT2 {
     // Map reads with HISAT2
     //
     HISAT2_ALIGN ( reads, index, splicesites )
-    ch_versions = ch_versions.mix(HISAT2_ALIGN.out.versions.first())
+    ch_versions = ch_versions.mix(HISAT2_ALIGN.out.versions1, HISAT2_ALIGN.out.versions2)
 
     //
     // Sort, index BAM file and run samtools stats, flagstat and idxstats
@@ -39,6 +39,6 @@ workflow FASTQ_ALIGN_HISAT2 {
     flagstat = BAM_SORT_STATS_SAMTOOLS.out.flagstat // channel: [ val(meta), [ flagstat ] ]
     idxstats = BAM_SORT_STATS_SAMTOOLS.out.idxstats // channel: [ val(meta), [ idxstats ] ]
 
-    versions = ch_versions                          // channel: [ versions.yml ]
+    versions = ch_versions                          // channel: [ process, tool, version ]
 }
 
diff --git a/subworkflows/nf-core/fastq_fastqc_umitools_fastp/main.nf b/subworkflows/nf-core/fastq_fastqc_umitools_fastp/main.nf
index 3dbb27eae..867f740be 100644
--- a/subworkflows/nf-core/fastq_fastqc_umitools_fastp/main.nf
+++ b/subworkflows/nf-core/fastq_fastqc_umitools_fastp/main.nf
@@ -136,5 +136,5 @@ workflow FASTQ_FASTQC_UMITOOLS_FASTP {
     fastqc_trim_html   // channel: [ val(meta), [ html ] ]
     fastqc_trim_zip    // channel: [ val(meta), [ zip ] ]
 
-    versions = ch_versions.ifEmpty(null) // channel: [ versions.yml ]
+    versions = ch_versions.ifEmpty(null) // channel: [ process, tool, version ]
 }
diff --git a/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/main.nf b/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/main.nf
index db2e5b329..7dced39f3 100644
--- a/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/main.nf
+++ b/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/main.nf
@@ -75,7 +75,7 @@ workflow FASTQ_FASTQC_UMITOOLS_TRIMGALORE {
         trim_html     = TRIMGALORE.out.html
         trim_zip      = TRIMGALORE.out.zip
         trim_log      = TRIMGALORE.out.log
-        ch_versions   = ch_versions.mix(TRIMGALORE.out.versions.first())
+        ch_versions   = ch_versions.mix(TRIMGALORE.out.versions1, TRIMGALORE.out.versions2)
 
         //
         // Filter FastQ files based on minimum trimmed read count after adapter trimming
@@ -119,5 +119,5 @@ workflow FASTQ_FASTQC_UMITOOLS_TRIMGALORE {
     trim_log           // channel: [ val(meta), [ txt ] ]
     trim_read_count    // channel: [ val(meta), val(count) ]
 
-    versions = ch_versions.ifEmpty(null) // channel: [ versions.yml ]
+    versions = ch_versions.ifEmpty(null) // channel: [ process, tool, version ]
 }
diff --git a/subworkflows/nf-core/fastq_subsample_fq_salmon/main.nf b/subworkflows/nf-core/fastq_subsample_fq_salmon/main.nf
index 0ac3e53a3..ee9e82bfc 100644
--- a/subworkflows/nf-core/fastq_subsample_fq_salmon/main.nf
+++ b/subworkflows/nf-core/fastq_subsample_fq_salmon/main.nf
@@ -50,5 +50,5 @@ workflow FASTQ_SUBSAMPLE_FQ_SALMON {
     results   = SALMON_QUANT.out.results   // channel: [ val(meta), results_dir ]
     json_info = SALMON_QUANT.out.json_info // channel: [ val(meta), json_info
 
-    versions  = ch_versions                // channel: [ versions.yml ]
+    versions  = ch_versions                // channel: [ process, tool, version ]
 }
diff --git a/workflows/rnaseq.nf b/workflows/rnaseq.nf
index 403194ac2..01d647c93 100755
--- a/workflows/rnaseq.nf
+++ b/workflows/rnaseq.nf
@@ -511,7 +511,7 @@ workflow RNASEQ {
             )
             ch_aligner_pca_multiqc        = DESEQ2_QC_STAR_SALMON.out.pca_multiqc
             ch_aligner_clustering_multiqc = DESEQ2_QC_STAR_SALMON.out.dists_multiqc
-            ch_versions = ch_versions.mix(DESEQ2_QC_STAR_SALMON.out.versions)
+            ch_versions = ch_versions.mix(DESEQ2_QC_STAR_SALMON.out.versions1, DESEQ2_QC_STAR_SALMON.out.versions2)
         }
     }
 
@@ -545,7 +545,7 @@ workflow RNASEQ {
             )
             ch_aligner_pca_multiqc        = DESEQ2_QC_RSEM.out.pca_multiqc
             ch_aligner_clustering_multiqc = DESEQ2_QC_RSEM.out.dists_multiqc
-            ch_versions = ch_versions.mix(DESEQ2_QC_RSEM.out.versions)
+            ch_versions = ch_versions.mix(DESEQ2_QC_RSEM.out.versions1, DESEQ2_QC_RSEM.out.versions2)
         }
     }
 
@@ -765,7 +765,7 @@ workflow RNASEQ {
                 PREPARE_GENOME.out.gtf
             )
             ch_dupradar_multiqc = DUPRADAR.out.multiqc
-            ch_versions = ch_versions.mix(DUPRADAR.out.versions.first())
+            ch_versions = ch_versions.mix(DUPRADAR.out.versions1, DUPRADAR.out.versions2)
         }
 
         if (!params.skip_rseqc && rseqc_modules.size() > 0) {
@@ -849,15 +849,24 @@ workflow RNASEQ {
             )
             ch_pseudoaligner_pca_multiqc        = DESEQ2_QC_PSEUDO.out.pca_multiqc
             ch_pseudoaligner_clustering_multiqc = DESEQ2_QC_PSEUDO.out.dists_multiqc
-            ch_versions = ch_versions.mix(DESEQ2_QC_PSEUDO.out.versions)
+            ch_versions = ch_versions.mix(DESEQ2_QC_PSEUDO.out.versions1, DESEQ2_QC_PSEUDO.out.versions2)
         }
     }
     
     //
     // MODULE: Pipeline reporting
     //
+    ch_versions = ch_versions
+        .unique()
+        .map { process, name, version ->
+            """
+            ${process}:
+              ${name}: ${version}
+            """.stripIndent()
+        }
+
     CUSTOM_DUMPSOFTWAREVERSIONS (
-        ch_versions.unique().collectFile(name: 'collated_versions.yml')
+        ch_versions.collectFile(name: 'collated_versions.yml')
     )
 
     //