nf-core · bentsherman · Nov 14, 2023 · Dec 12, 2023 · Dec 12, 2023
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -24,7 +24,7 @@ jobs:
     strategy:
       matrix:
         NXF_VER:
-          - "23.04.0"
+          - "23.11.0-edge"
           - "latest-everything"
     steps:
       - name: Check out pipeline code

diff --git a/main.nf b/main.nf
@@ -10,6 +10,7 @@
 */
 
 nextflow.enable.dsl = 2
+nextflow.preview.topic = true
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

diff --git 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
+    path "versions.yml"                        , topic: versions
 
     when:
     task.ext.when == null || task.ext.when

diff --git 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
+    path "versions.yml" , topic: versions
 
     when:
     task.ext.when == null || task.ext.when

diff --git a/modules/local/deseq2_qc/main.nf b/modules/local/deseq2_qc/main.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

diff --git a/modules/local/dupradar/main.nf b/modules/local/dupradar/main.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

diff --git 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
+    path "versions.yml", topic: versions
 
     when:
     task.ext.when == null || task.ext.when

diff --git 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
+    path "versions.yml"  , topic: versions
 
     when:
     task.ext.when == null || task.ext.when

diff --git 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
+    path "versions.yml"           , topic: versions
 
     when:
     task.ext.when == null || task.ext.when

diff --git 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
+    path "versions.yml", topic: versions
 
     when:
     task.ext.when == null || task.ext.when

diff --git 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
+    path "versions.yml"                     , topic: versions
 
     when:
     task.ext.when == null || task.ext.when

diff --git a/modules/local/star_align_igenomes/main.nf b/modules/local/star_align_igenomes/main.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

diff --git a/modules/local/star_genomegenerate_igenomes/main.nf b/modules/local/star_genomegenerate_igenomes/main.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

diff --git a/modules/local/summarizedexperiment/main.nf b/modules/local/summarizedexperiment/main.nf
@@ -14,7 +14,7 @@ process SUMMARIZEDEXPERIMENT {
 
     output:
     path "*.rds"       , emit: rds
-    path "versions.yml", emit: versions
+    path "versions.yml", topic: versions
 
     when:
     task.ext.when == null || task.ext.when

diff --git 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
+    path "versions.yml", topic: versions
 
     when:
     task.ext.when == null || task.ext.when

diff --git a/modules/local/tximport/main.nf b/modules/local/tximport/main.nf
@@ -20,7 +20,7 @@ process TXIMPORT {
     path "*transcript_tpm.tsv"           , emit: tpm_transcript
     path "*transcript_counts.tsv"        , emit: counts_transcript
     path "*transcript_lengths.tsv"       , emit: lengths_transcript
-    path "versions.yml"                  , emit: versions
+    path "versions.yml"                  , topic: versions
 
     when:
     task.ext.when == null || task.ext.when

diff --git 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
+    path  "versions.yml"          , topic: versions
 
     when:
     task.ext.when == null || task.ext.when

diff --git a/modules/nf-core/bbmap/bbsplit/main.nf b/modules/nf-core/bbmap/bbsplit/main.nf
diff --git a/modules/nf-core/cat/fastq/main.nf b/modules/nf-core/cat/fastq/main.nf
diff --git a/modules/nf-core/custom/getchromsizes/main.nf b/modules/nf-core/custom/getchromsizes/main.nf
diff --git a/modules/nf-core/fastp/main.nf b/modules/nf-core/fastp/main.nf
diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf
diff --git a/modules/nf-core/fq/subsample/main.nf b/modules/nf-core/fq/subsample/main.nf
diff --git a/modules/nf-core/gffread/main.nf b/modules/nf-core/gffread/main.nf
diff --git a/modules/nf-core/gunzip/main.nf b/modules/nf-core/gunzip/main.nf
diff --git a/modules/nf-core/hisat2/align/main.nf b/modules/nf-core/hisat2/align/main.nf
diff --git a/modules/nf-core/hisat2/build/main.nf b/modules/nf-core/hisat2/build/main.nf
diff --git a/modules/nf-core/hisat2/extractsplicesites/main.nf b/modules/nf-core/hisat2/extractsplicesites/main.nf
diff --git a/modules/nf-core/kallisto/index/main.nf b/modules/nf-core/kallisto/index/main.nf
diff --git a/modules/nf-core/kallisto/quant/main.nf b/modules/nf-core/kallisto/quant/main.nf
diff --git a/modules/nf-core/picard/markduplicates/main.nf b/modules/nf-core/picard/markduplicates/main.nf
diff --git a/modules/nf-core/preseq/lcextrap/main.nf b/modules/nf-core/preseq/lcextrap/main.nf
diff --git a/modules/nf-core/qualimap/rnaseq/main.nf b/modules/nf-core/qualimap/rnaseq/main.nf
diff --git a/modules/nf-core/rsem/calculateexpression/main.nf b/modules/nf-core/rsem/calculateexpression/main.nf
diff --git a/modules/nf-core/rsem/preparereference/main.nf b/modules/nf-core/rsem/preparereference/main.nf
diff --git a/modules/nf-core/rseqc/bamstat/main.nf b/modules/nf-core/rseqc/bamstat/main.nf
diff --git a/modules/nf-core/rseqc/inferexperiment/main.nf b/modules/nf-core/rseqc/inferexperiment/main.nf
diff --git a/modules/nf-core/rseqc/innerdistance/main.nf b/modules/nf-core/rseqc/innerdistance/main.nf
diff --git a/modules/nf-core/rseqc/junctionannotation/main.nf b/modules/nf-core/rseqc/junctionannotation/main.nf
diff --git a/modules/nf-core/rseqc/junctionsaturation/main.nf b/modules/nf-core/rseqc/junctionsaturation/main.nf
diff --git a/modules/nf-core/rseqc/readdistribution/main.nf b/modules/nf-core/rseqc/readdistribution/main.nf
diff --git a/modules/nf-core/rseqc/readduplication/main.nf b/modules/nf-core/rseqc/readduplication/main.nf
diff --git a/modules/nf-core/rseqc/tin/main.nf b/modules/nf-core/rseqc/tin/main.nf
diff --git a/modules/nf-core/salmon/index/main.nf b/modules/nf-core/salmon/index/main.nf