Move output definition to top-level workflow

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

main.nf

@@ -164,6 +164,240 @@ workflow {
  )
 }
 
+output {
+ directory params.outdir, mode: params.publish_dir_mode
+
+ //
+ // Genome preparation
+ //
+ 'genome' {
+ enabled params.save_reference
+ from 'genome'
+ }
+
+ 'genome/index' {
+ enabled params.save_reference
+ from 'genome-index'
+ }
+
+ //
+ // Alignment
+ //
+ "${params.aligner}" {
+ from 'align'
+
+ 'samtools_stats' {
+ from 'align-samtools-stats'
+ }
+
+ 'umitools' {
+ from 'align-umitools'
+ }
+ }
+
+ "${params.aligner}" {
+ enabled params.save_align_intermeds || params.save_umi_intermeds
+ from 'align-intermeds'
+
+ 'samtools_stats' {
+ from 'align-intermeds-samtools-stats'
+ }
+ 'umitools/log' {
+ from 'align-intermeds-umitools-log'
+ }
+ }
+
+ //
+ // bigWig coverage
+ //
+ "${params.aligner}/bigwig" {
+ from 'align-bigwig'
+ }
+
+ //
+ // DESeq2 QC
+ //
+ "${params.aligner}/deseq2_qc" {
+ from 'align-deseq2'
+ }
+
+ //
+ // Pseudo-alignment
+ //
+ "${params.pseudo_aligner}" {
+ from 'pseudo-align'
+ // TODO: process 'QUANTIFY_PSEUDO_ALIGNMENT:CUSTOM_TX2GENE'
+
+ 'deseq2_qc' {
+ from 'pseudo-align-deseq2'
+ }
+ }
+
+ // modules/local/dupradar
+ "${params.aligner}/dupradar" {
+ 'scatter_plot' {
+ from 'align-dupradar', pattern: "*Dens.pdf"
+ }
+ 'box_plot' {
+ from 'align-dupradar', pattern: "*Boxplot.pdf"
+ }
+ 'histogram' {
+ from 'align-dupradar', pattern: "*Hist.pdf"
+ }
+ 'gene_data' {
+ from 'align-dupradar', pattern: "*Matrix.txt"
+ }
+ 'intercepts_slope' {
+ from 'align-dupradar', pattern: "*slope.txt"
+ }
+ }
+
+ // modules/nf-core/bbmap/bbsplit
+ 'bbsplit' {
+ from 'bbsplit'
+ from 'bbsplit-intermeds', enabled: params.save_bbsplit_reads
+ }
+
+ // modules/nf-core/cat/fastq
+ 'fastq' {
+ enabled params.save_merged_fastq
+ from 'merged-fastq'
+ }
+
+ // modules/nf-core/multiqc
+ def multiqc_path = params.skip_alignment
+ ? 'multiqc'
+ : "multiqc/${params.aligner}"
+
+ "${multiqc_path}" {
+ from 'multiqc'
+ }
+
+ // modules/nf-core/preseq/lcextrap
+ "${params.aligner}" {
+ 'preseq' {
+ from 'preseq'
+ }
+ 'preseq/log' {
+ from 'preseq-log'
+ }
+ }
+
+ // modules/nf-core/qualimap/rnaseq
+ "${params.aligner}/qualimap" {
+ from 'qualimap'
+ }
+
+ // modules/nf-core/sortmerna
+ 'sortmerna' {
+ from 'sortmerna'
+ from 'sortmerna-intermeds', enabled: params.save_non_ribo_reads
+ }
+
+ // modules/nf-core/stringtie/stringtie
+ "${params.aligner}/stringtie" {
+ from 'align-stringtie'
+ }
+
+ // modules/nf-core/subread/featurecounts
+ "${params.aligner}/featurecounts" {
+ from 'align-featurecounts'
+ }
+
+ // subworkflows/local/align_star
+ "${params.aligner}" {
+ 'log' {
+ from 'align-star-log'
+ }
+
+ from 'align-star-intermeds'
+
+ 'unmapped' {
+ from 'align-star-unaligned'
+ }
+ }
+
+ // subworkflows/local/quantify_rsem
+ "${params.aligner}" {
+ from 'quantify-rsem'
+ from 'quantify-rsem-intermeds', enabled: params.save_align_intermeds
+
+ 'log' {
+ from 'quantify-rsem-log'
+ }
+ }
+
+ // subworkflows/nf-core/bam_markduplicates_picard
+ "${params.aligner}" {
+ from 'align-picard'
+ 'picard_metrics' {
+ from 'align-picard-metrics'
+ }
+ 'samtools_stats' {
+ from 'align-picard-stats'
+ }
+ }
+
+ // subworkflows/nf-core/bam_rseqc
+ "${params.aligner}/rseqc" {
+ 'bam_stat' {
+ from 'align-rseqc-bamstat'
+ }
+ 'infer_experiment' {
+ from 'align-rseqc-inferexperiment'
+ }
+ 'junction_annotation' {
+ from 'align-rseqc-junctionannotation'
+ }
+ 'junction_saturation' {
+ from 'align-rseqc-junctionsaturation'
+ }
+ 'read_duplication' {
+ from 'align-rseqc-readduplication'
+ }
+ 'read_distribution' {
+ from 'align-rseqc-readdistribution'
+ }
+ 'inner_distance' {
+ from 'align-rseqc-innerdistance'
+ }
+ 'tin' {
+ from 'align-rseqc-tin'
+ }
+ }
+
+ // subworkflows/nf-core/fastq_align_hisat2
+ "${params.aligner}" {
+ 'log' {
+ from 'align-hisat2-log'
+ }
+
+ from 'align-hisat2-intermeds', enabled: params.save_align_intermeds
+
+ 'unmapped' {
+ from 'align-hisat2-unaligned', enabled: params.save_unaligned
+ }
+ }
+
+ // subworkflows/nf-core/fastq_fastqc_umitools_fastp
+ // subworkflows/nf-core/fastq_fastqc_umitools_trimgalore
+ "${params.trimmer}" {
+ 'fastqc' {
+ from 'trim-fastqc'
+ }
+ from 'trim'
+ 'log' {
+ from 'trim-log'
+ }
+ from 'trim-intermeds', enabled: params.save_trimmed
+ }
+
+ 'umitools' {
+ from 'umitools'
+ from 'umitools-intermeds', enabled: params.save_umi_intermeds
+ }
+}
+
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  THE END

subworkflows/local/prepare_genome/main.nf

@@ -327,6 +327,23 @@ workflow PREPARE_GENOME {
  }
  }
 
+ topic:
+ ch_fasta >> 'genome'
+ ch_gtf >> 'genome'
+ ch_gff >> 'genome'
+ ch_add_fasta >> 'genome'
+ ch_gene_bed >> 'genome'
+ ch_transcript_fasta >> 'genome'
+ ch_fai >> 'genome'
+ ch_sizes >> 'genome'
+ ch_splicesites >> 'genome-index'
+ ch_bbsplit_index >> 'genome-index'
+ ch_star_index >> 'genome-index'
+ ch_rsem_index >> 'genome-index'
+ ch_hisat2_index >> 'genome-index'
+ ch_salmon_index >> 'genome-index'
+ ch_kallisto_index >> 'genome-index'
+
  emit:
  fasta = ch_fasta // channel: path(genome.fasta)
  gtf = ch_gtf // channel: path(genome.gtf)
@@ -343,28 +360,3 @@ workflow PREPARE_GENOME {
  kallisto_index = ch_kallisto_index // channel: [ meta, path(kallisto/index/) ]
  versions = ch_versions.ifEmpty(null) // channel: [ versions.yml ]
 }
-
-output {
- directory params.outdir, mode: params.publish_dir_mode, enabled: params.save_reference
-
- 'genome' {
- from PREPARE_GENOME.out.fasta
- from PREPARE_GENOME.out.gtf
- // from PREPARE_GENOME.out.gff
- // from PREPARE_GENOME.out.add_fasta
- from PREPARE_GENOME.out.gene_bed
- from PREPARE_GENOME.out.transcript_fasta
- from PREPARE_GENOME.out.fai
- // from PREPARE_GENOME.out.sizes
- }
-
- 'genome/index' {
- from PREPARE_GENOME.out.splicesites
- from PREPARE_GENOME.out.bbsplit_index
- from PREPARE_GENOME.out.star_index
- from PREPARE_GENOME.out.rsem_index
- from PREPARE_GENOME.out.hisat2_index
- from PREPARE_GENOME.out.salmon_index
- from PREPARE_GENOME.out.kallisto_index
- }
-}