Use topic channel for tool versions

Signed-off-by: Ben Sherman <[email protected]>

Author: bentsherman

main.nf

@@ -10,6 +10,7 @@
 */
 
 nextflow.enable.dsl = 2
+nextflow.preview.topic = true
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

modules/local/bedtools_genomecov.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
+    path "versions.yml"                        , topic: versions
 
     when:
     task.ext.when == null || task.ext.when

modules/local/cat_additional_fasta.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
+    path "versions.yml" , topic: versions
 
     when:
     task.ext.when == null || task.ext.when

modules/local/deseq2_qc.nf

@@ -22,7 +22,7 @@ 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
+    path "versions.yml"         , topic: versions
 
     when:
     task.ext.when == null || task.ext.when

modules/local/dupradar.nf

@@ -15,7 +15,7 @@ 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
+    path "versions.yml"               , topic: versions
 
     when:
     task.ext.when == null || task.ext.when

modules/local/gtf2bed.nf

@@ -12,7 +12,7 @@ process GTF2BED {
 
     output:
     path '*.bed'       , emit: bed
-    path "versions.yml", emit: versions
+    path "versions.yml", topic: versions
 
     when:
     task.ext.when == null || task.ext.when

modules/local/gtf_gene_filter.nf

@@ -12,7 +12,7 @@ process GTF_GENE_FILTER {
 
     output:
     path "*.gtf"       , emit: gtf
-    path "versions.yml", emit: versions
+    path "versions.yml", topic: versions
 
     when:
     task.ext.when == null || task.ext.when

modules/local/multiqc_custom_biotype.nf

@@ -12,7 +12,7 @@ process MULTIQC_CUSTOM_BIOTYPE {
 
     output:
     tuple val(meta), path("*.tsv"), emit: tsv
-    path "versions.yml"           , emit: versions
+    path "versions.yml"           , topic: versions
 
     when:
     task.ext.when == null || task.ext.when

modules/local/preprocess_transcripts_fasta_gencode.nf

@@ -11,7 +11,7 @@ process PREPROCESS_TRANSCRIPTS_FASTA_GENCODE {
 
     output:
     path "*.fa"        , emit: fasta
-    path "versions.yml", emit: versions
+    path "versions.yml", topic: versions
 
     when:
     task.ext.when == null || task.ext.when

modules/local/rsem_merge_counts.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
+    path "versions.yml"                     , topic: versions
 
     when:
     task.ext.when == null || task.ext.when

modules/local/salmon_summarizedexperiment.nf

@@ -14,7 +14,7 @@ process SALMON_SUMMARIZEDEXPERIMENT {
 
     output:
     path "*.rds"       , emit: rds
-    path "versions.yml", emit: versions
+    path "versions.yml", topic: versions
 
     when:
     task.ext.when == null || task.ext.when

modules/local/salmon_tx2gene.nf

@@ -13,7 +13,7 @@ process SALMON_TX2GENE {
 
     output:
     path "*.tsv"       , emit: tsv
-    path "versions.yml", emit: versions
+    path "versions.yml", topic: versions
 
     when:
     task.ext.when == null || task.ext.when

modules/local/salmon_tximport.nf

@@ -17,7 +17,7 @@ process SALMON_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
+    path "versions.yml"                  , topic: versions
 
     when:
     task.ext.when == null || task.ext.when

modules/local/samplesheet_check.nf

@@ -12,7 +12,7 @@ process SAMPLESHEET_CHECK {
 
     output:
     path '*.csv'       , emit: csv
-    path "versions.yml", emit: versions
+    path "versions.yml", topic: versions
 
     when:
     task.ext.when == null || task.ext.when

modules/local/star_align_igenomes.nf

@@ -20,7 +20,7 @@ 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
+    path  "versions.yml"                      , topic: versions
 
     tuple val(meta), path('*sortedByCoord.out.bam')  , optional:true, emit: bam_sorted
     tuple val(meta), path('*toTranscriptome.out.bam'), optional:true, emit: bam_transcript

modules/local/star_genomegenerate_igenomes.nf

@@ -13,7 +13,7 @@ process STAR_GENOMEGENERATE_IGENOMES {
 
     output:
     path "star"        , emit: index
-    path "versions.yml", emit: versions
+    path "versions.yml", topic: versions
 
     when:
     task.ext.when == null || task.ext.when

modules/local/umitools_prepareforrsem.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
+    path  "versions.yml"          , topic: versions
 
     when:
     task.ext.when == null || task.ext.when