Workflow output definition

main.nf

@@ -164,6 +164,172 @@ workflow {
     )
 }
 
+output {
+    directory params.outdir
+    mode params.publish_dir_mode
+
+    'genome' {
+        enabled params.save_reference
+    }
+
+    'genome/index' {
+        enabled params.save_reference
+    }
+
+    'star_salmon/intermeds/' {
+        path 'star_salmon'
+        enabled params.save_align_intermeds || params.save_umi_intermeds
+    }
+
+    'star_salmon/samtools_stats/intermeds/' {
+        path 'star_salmon/samtools_stats'
+        enabled params.save_align_intermeds || params.save_umi_intermeds
+    }
+
+    'star_salmon/umitools/log/intermeds/' {
+        path 'star_salmon/umitools/log'
+        enabled params.save_align_intermeds || params.save_umi_intermeds
+    }
+
+    'bigwig' {
+        path "${params.aligner}/bigwig"
+    }
+
+    // modules/local/dupradar
+    'dupradar' {
+        path "${params.aligner}/dupradar"
+    }
+
+    // modules/nf-core/bbmap/bbsplit
+    'bbsplit/intermeds/' {
+        path 'bbsplit'
+        enabled params.save_bbsplit_reads
+    }
+
+    // modules/nf-core/cat/fastq
+    'cat/fastq' {
+        path 'fastq'
+        enabled params.save_merged_fastq
+    }
+
+    // modules/nf-core/multiqc
+    'multiqc' {
+        path params.skip_alignment ? 'multiqc' : "multiqc/${params.aligner}"
+    }
+
+    // modules/nf-core/preseq/lcextrap
+    'preseq' {
+        path "${params.aligner}/preseq"
+    }
+
+    'preseq/log' {
+        path "${params.aligner}/preseq/log"
+    }
+
+    // modules/nf-core/qualimap/rnaseq
+    'qualimap' {
+        path "${params.aligner}/qualimap"
+    }
+
+    // modules/nf-core/sortmerna
+    'sortmerna/intermeds/' {
+        path 'sortmerna'
+        enabled params.save_non_ribo_reads
+    }
+
+    // modules/nf-core/stringtie/stringtie
+    'stringtie' {
+        path "${params.aligner}/stringtie"
+    }
+
+    // modules/nf-core/subread/featurecounts
+    'featurecounts' {
+        path "${params.aligner}/featurecounts"
+    }
+
+    // subworkflows/local/align_star
+    // 'star_salmon/intermeds/' {
+    //     path 'star_salmon'
+    //     enabled params.save_align_intermeds
+    // }
+
+    'star_salmon/unmapped/' {
+        enabled params.save_unaligned
+    }
+
+    // subworkflows/local/quantify_rsem
+    'star_rsem/intermeds/' {
+        path 'star_rsem'
+        enabled params.save_align_intermeds
+    }
+
+    // subworkflows/nf-core/bam_markduplicates_picard
+    'picard/' {
+        path params.aligner
+    }
+
+    'picard/metrics/' {
+        path "${params.aligner}/picard_metrics"
+    }
+
+    'picard/samtools_stats/' {
+        path "${params.aligner}/samtools_stats"
+    }
+
+    // subworkflows/nf-core/bam_rseqc
+    'rseqc/bam_stat/' {
+        path "${params.aligner}/rseqc/bam_stat"
+    }
+    'rseqc/infer_experiment/' {
+        path "${params.aligner}/rseqc/infer_experiment"
+    }
+    'rseqc/junction_annotation/' {
+        path "${params.aligner}/rseqc/junction_annotation"
+    }
+    'rseqc/junction_saturation/' {
+        path "${params.aligner}/rseqc/junction_saturation"
+    }
+    'rseqc/read_duplication/' {
+        path "${params.aligner}/rseqc/read_duplication"
+    }
+    'rseqc/read_distribution/' {
+        path "${params.aligner}/rseqc/read_distribution"
+    }
+    'rseqc/inner_distance/' {
+        path "${params.aligner}/rseqc/inner_distance"
+    }
+    'rseqc/tin/' {
+        path "${params.aligner}/rseqc/tin"
+    }
+
+    // subworkflows/nf-core/fastq_align_hisat2
+    'hisat2/intermeds/' {
+        path 'hisat2'
+        enabled params.save_align_intermeds
+    }
+
+    'hisat2/unmapped/' {
+        enabled params.save_unaligned
+    }
+
+    // subworkflows/nf-core/fastq_fastqc_umitools_fastp
+    // subworkflows/nf-core/fastq_fastqc_umitools_trimgalore
+    'fastp/intermeds/' {
+        path 'fastp'
+        enabled params.save_trimmed
+    }
+
+    'trimgalore/intermeds/' {
+        path 'trimgalore'
+        enabled params.save_trimmed
+    }
+
+    'umitools/intermeds/' {
+        path 'umitools'
+        enabled params.save_umi_intermeds
+    }
+}
+
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     THE END

modules/local/bedtools_genomecov/nextflow.config

@@ -3,9 +3,6 @@ if (!params.skip_alignment && !params.skip_bigwig) {
     process {
         withName: 'BEDTOOLS_GENOMECOV' {
             ext.args   = '-split -du'
-            publishDir = [
-                enabled: false
-            ]
         }
     }
 }

modules/local/deseq2_qc/main.nf

@@ -24,6 +24,16 @@ process DESEQ2_QC {
     path "size_factors"         , optional:true, emit: size_factors
     path "versions.yml"         , emit: versions
 
+    publish:
+    pdf             >> 'deseq2'
+    rdata           >> 'deseq2'
+    pca_txt         >> 'deseq2'
+    pca_multiqc     >> 'deseq2'
+    dists_txt       >> 'deseq2'
+    dists_multiqc   >> 'deseq2'
+    log             >> 'deseq2'
+    size_factors    >> 'deseq2'
+
     when:
     task.ext.when == null || task.ext.when
 

modules/local/dupradar/main.nf

@@ -17,6 +17,10 @@ process DUPRADAR {
     tuple val(meta), path("*_mqc.txt"), emit: multiqc
     path "versions.yml"               , emit: versions
 
+    publish:
+    pdf >> 'dupradar'
+    txt >> 'dupradar'
+
     when:
     task.ext.when == null || task.ext.when
 

modules/local/multiqc_custom_biotype/main.nf

@@ -14,6 +14,9 @@ process MULTIQC_CUSTOM_BIOTYPE {
     tuple val(meta), path("*.tsv"), emit: tsv
     path "versions.yml"           , emit: versions
 
+    publish:
+    tsv >> 'featurecounts'
+
     when:
     task.ext.when == null || task.ext.when