Merging feature strict syntax

modules/local/blaze/main.nf

@@ -14,11 +14,11 @@ process BLAZE {
     path in_whitelist
 
     output:
-    tuple val(meta), path("*.putative_bc.no_header.csv") , emit: putative_bc
-    tuple val(meta), path("*.whitelist.csv")             , emit: whitelist
-    tuple val(meta), path("*.bc_count.txt")              , emit: bc_count
-    tuple val(meta), path("*.knee_plot.png")             , emit: knee_plot
-    path "versions.yml"                                  , emit: versions
+    tuple val(meta), path("*.putative_bc.no_header.csv"), emit: putative_bc
+    tuple val(meta), path("*.whitelist.csv")            , emit: whitelist
+    tuple val(meta), path("*.bc_count.txt")             , emit: bc_count
+    tuple val(meta), path("*.knee_plot.png")            , emit: knee_plot
+    path "versions.yml"                                  , emit: versions_blaze, topic: versions
 
     when:
     task.ext.when == null || task.ext.when

modules/local/chopper/main.nf

@@ -12,7 +12,7 @@ process CHOPPER {
 
     output:
     tuple val(meta), path("*.filtered.fastq.gz"), emit: reads
-    path "versions.yml"                         , emit: versions
+    path "versions.yml"                         , emit: versions_chopper, topic: versions
 
     when:
     task.ext.when == null || task.ext.when

modules/local/combine_seurat_stats/main.nf

@@ -11,7 +11,7 @@ process COMBINE_SEURAT_STATS {
 
     output:
     path "*.tsv"        , emit: combined_stats
-    path "versions.yml" , emit: versions
+    path "versions.yml" , emit: versions_combine_seurat_stats, topic: versions
 
     when:
     task.ext.when == null || task.ext.when

modules/local/correct_barcodes/main.nf

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

modules/local/group_transcripts/main.nf

@@ -9,18 +9,17 @@ process GROUP_TRANSCRIPTS {
 
     input:
     tuple val(meta), path(fasta)
-    tuple val(meta), path(gtf)
+    tuple val(meta2), path(gtf)
     val delimiter
 
     output:
     path "*.transcripts.txt", emit: grouped_transcripts
-    path "versions.yml"     , emit: versions
+    path "versions.yml"     , emit: versions_group_transcripts, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
-    def args      = task.ext.args ?: ''
     def delim_arg = delimiter ? "-d '${delimiter}'" : ''
 
     """

modules/local/isoquant/main.nf

@@ -35,7 +35,7 @@ process ISOQUANT {
     tuple val(meta), path("*/*/*.extended_annotation.gtf"),             emit: extended_gtf,                    optional: true
     tuple val(meta), path("*/*/*.transcript_model_grouped_counts.tsv"), emit: grouped_transcript_model_counts, optional: true
     tuple val(meta), path("*/*/*.transcript_model_grouped_tpm.tsv"),    emit: grouped_transcript_model_tpm,    optional: true
-    path "versions.yml",                                                emit: versions
+    path "versions.yml",                                                emit: versions_isoquant, topic: versions
 
     when:
     task.ext.when == null || task.ext.when

modules/local/merge_mtx/main.nf

@@ -12,13 +12,12 @@ process MERGE_MTX {
 
     output:
     tuple val(meta), path("*.merged.tsv"), emit: merged_mtx
-    path "versions.yml"                  , emit: versions
+    path "versions.yml"                  , emit: versions_merge_mtx, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
-    def args   = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
 
     """

modules/local/oarfish/main.nf

@@ -15,7 +15,7 @@ process OARFISH {
     tuple val(meta), path("*barcodes.tsv.gz") , emit: barcodes
     tuple val(meta), path("*matrix.mtx.gz")   , emit: mtx
     tuple val(meta), path("*meta_info.json")  , emit: meta_info
-    path "versions.yml"                       , emit: versions
+    path "versions.yml"                       , emit: versions_oarfish, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -55,5 +55,10 @@ process OARFISH {
     touch ${prefix}.barcodes.tsv.gz
     touch ${prefix}.matrix.mtx.gz
     touch ${prefix}.meta_info.json
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        oarfish: \$(oarfish --version | sed 's#oarfish ##g')
+    END_VERSIONS
     """
 }

modules/local/preextract_fastq/main.nf

@@ -15,7 +15,7 @@ process PREEXTRACT_FASTQ {
     output:
     tuple val(meta), path("*.putative_bc_umi.tsv")  , emit: barcode_info
     tuple val(meta), path("*.extracted.fastq")      , emit: extracted_fastq
-    path "versions.yml"                             , emit: versions
+    path "versions.yml"                             , emit: versions_preextract_fastq, topic: versions
 
     when:
     task.ext.when == null || task.ext.when

modules/local/read_counts/main.nf

@@ -14,7 +14,7 @@ process READ_COUNTS {
 
     output:
     path "read_counts.csv" , emit: read_counts
-    path "versions.yml"    , emit: versions
+    path "versions.yml"    , emit: versions_read_counts, topic: versions
 
     when:
     task.ext.when == null || task.ext.when

modules/local/seurat/main.nf

@@ -15,7 +15,7 @@ process SEURAT {
     tuple val(meta), path("*.csv"), emit: seurat_stats
     tuple val(meta), path("*.png"), emit: seurat_qcs
     tuple val(meta), path("*.rds"), emit: seurat_rds
-    path "versions.yml"           , emit: versions
+    path "versions.yml"           , emit: versions_seurat, topic: versions
 
     when:
     task.ext.when == null || task.ext.when

modules/local/split_bam/main.nf

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

modules/local/split_fasta/main.nf

@@ -11,14 +11,12 @@ process SPLIT_FASTA {
 
     output:
     path "*.split.fa"   , emit: split_fasta
-    path "versions.yml" , emit: versions
+    path "versions.yml" , emit: versions_split_fasta, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args ?: ''
-
     """
     awk '/^>/{chrom=(split(substr(\$0,2), a, " ")); filename=( a[1] ".split.fa"); print > filename; next}{print >> filename}' $fasta
 

modules/local/split_file/main.nf

@@ -14,13 +14,12 @@ process SPLIT_FILE {
 
     output:
     tuple val(meta), path("*$file_ext"), emit: split_files
-    path "versions.yml"                , emit: versions
+    path "versions.yml"                , emit: versions_split_file, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
-    def args   = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
 
     """

modules/local/split_gtf/main.nf

@@ -11,14 +11,12 @@ process SPLIT_GTF {
 
     output:
     path "*.split.gtf"  , emit: split_gtf
-    path "versions.yml" , emit: versions
+    path "versions.yml" , emit: versions_split_gtf, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args ?: ''
-
     """
     grep -v '^#' $gtf | awk -F \$'\\t' '{print > \$1".split.gtf"}'
 

modules/local/split_seq/main.nf

@@ -14,7 +14,7 @@ process SPLIT_SEQ {
 
     output:
     tuple val(meta), path("output/*$file_ext"), emit: split_files
-    path "versions.yml"                       , emit: versions
+    path "versions.yml"                       , emit: versions_split_seq, topic: versions
 
     when:
     task.ext.when == null || task.ext.when

modules/local/tag_barcodes/main.nf

@@ -12,13 +12,12 @@ process TAG_BARCODES {
 
     output:
     tuple val(meta), path("*.tagged.bam"), emit: tagged_bam
-    path "versions.yml"                  , emit: versions
+    path "versions.yml"                  , emit: versions_tag_barcodes, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
-    def args   = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
 
     """

modules/local/ucsc_genepredtobed/main.nf

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

modules/local/ucsc_gtftogenepred/main.nf

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