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Workflow output definition #1227

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Workflow output definition #1227

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783ff86
Add output definition
bentsherman Feb 28, 2024
b572f52
Add complete output definition
bentsherman Feb 29, 2024
2a93c91
Add explicit inclusion of subworkflow outputs
bentsherman Mar 18, 2024
daf61c7
Apply updates from upstream
bentsherman Mar 30, 2024
69f258e
Move output definition to top-level workflow
bentsherman Apr 6, 2024
45ec2ef
Fix bugs
bentsherman Apr 6, 2024
9af6803
Disable processes not used by test profile (temporary)
bentsherman Apr 6, 2024
635203c
Move topic mappings to modules and subworkflows
bentsherman Apr 7, 2024
44af165
Update based on latest prototype
bentsherman Apr 10, 2024
3ee5753
Remove topic feature flag
bentsherman Apr 10, 2024
6719138
Rename output -> publish
bentsherman Apr 24, 2024
434024e
Redirect to null to disable publishing
bentsherman Apr 24, 2024
bd3d6ed
Move path renames from publish block to workflow publish section
bentsherman Apr 29, 2024
54b1f6f
Revert target renaming, re-map channels instead
bentsherman May 1, 2024
a8248d3
Rename publish -> output
bentsherman May 2, 2024
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Disable processes not used by test profile (temporary) 
Signed-off-by: Ben Sherman <[email protected]>
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@bentsherman
bentsherman committed Apr 6, 2024
commit 9af680340766aa847e9e71d7d98e61d09c2825a4
121 changes: 66 additions & 55 deletions workflows/rnaseq/main.nf
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Expand Up @@ -797,41 +797,46 @@ workflow RNASEQ {
QUANTIFY_STAR_SALMON.out.merged_gene_rds_scaled >> 'align'
QUANTIFY_STAR_SALMON.out.merged_transcript_rds >> 'align'

BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_TRANSCRIPTOME.out.bam >> 'align-intermeds'
BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_TRANSCRIPTOME.out.bai >> 'align-intermeds'
BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_TRANSCRIPTOME.out.stats >> 'align-samtools-stats'
BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_TRANSCRIPTOME.out.flagstat >> 'align-samtools-stats'
BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_TRANSCRIPTOME.out.idxstats >> 'align-samtools-stats'
BAM_SORT_STATS_SAMTOOLS.out.bam >> 'align-intermeds'
BAM_SORT_STATS_SAMTOOLS.out.bai >> 'align-intermeds'
BAM_SORT_STATS_SAMTOOLS.out.stats >> 'align-intermeds-samtools-stats'
BAM_SORT_STATS_SAMTOOLS.out.flagstat >> 'align-intermeds-samtools-stats'
BAM_SORT_STATS_SAMTOOLS.out.idxstats >> 'align-intermeds-samtools-stats'
SAMTOOLS_SORT.out.bam >> 'align-intermeds'
UMITOOLS_PREPAREFORSALMON.out.bam >> 'align-intermeds'
UMITOOLS_PREPAREFORSALMON.out.log >> 'align-intermeds-umitools-log'

BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME.out.bam >> 'align-intermeds'
BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME.out.bai >> 'align-intermeds'
BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME.out.stats >> 'align-samtools-stats'
BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME.out.flagstat >> 'align-samtools-stats'
BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME.out.idxstats >> 'align-samtools-stats'
// TODO: !params.skip_alignment && params.aligner == 'star_salmon' && params.with_umi
// BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_TRANSCRIPTOME.out.bam >> 'align-intermeds'
// BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_TRANSCRIPTOME.out.bai >> 'align-intermeds'
// BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_TRANSCRIPTOME.out.stats >> 'align-samtools-stats'
// BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_TRANSCRIPTOME.out.flagstat >> 'align-samtools-stats'
// BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_TRANSCRIPTOME.out.idxstats >> 'align-samtools-stats'
// BAM_SORT_STATS_SAMTOOLS.out.bam >> 'align-intermeds'
// BAM_SORT_STATS_SAMTOOLS.out.bai >> 'align-intermeds'
// BAM_SORT_STATS_SAMTOOLS.out.stats >> 'align-intermeds-samtools-stats'
// BAM_SORT_STATS_SAMTOOLS.out.flagstat >> 'align-intermeds-samtools-stats'
// BAM_SORT_STATS_SAMTOOLS.out.idxstats >> 'align-intermeds-samtools-stats'
// SAMTOOLS_SORT.out.bam >> 'align-intermeds'
// UMITOOLS_PREPAREFORSALMON.out.bam >> 'align-intermeds'
// UMITOOLS_PREPAREFORSALMON.out.log >> 'align-intermeds-umitools-log'

// TODO: !params.skip_alignment && params.aligner in ['star_salmon', 'hisat2']
// BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME.out.bam >> 'align-intermeds'
// BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME.out.bai >> 'align-intermeds'
// BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME.out.stats >> 'align-samtools-stats'
// BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME.out.flagstat >> 'align-samtools-stats'
// BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME.out.idxstats >> 'align-samtools-stats'

BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD.out.bigwig >> 'align-bigwig'
BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE.out.bigwig >> 'align-bigwig'

// TODO: !params.skip_alignment && params.aligner == 'star_salmon'
DESEQ2_QC_STAR_SALMON.out.rdata >> 'align-deseq2'
DESEQ2_QC_STAR_SALMON.out.pca_txt >> 'align-deseq2'
DESEQ2_QC_STAR_SALMON.out.pdf >> 'align-deseq2'
DESEQ2_QC_STAR_SALMON.out.dists_txt >> 'align-deseq2'
DESEQ2_QC_STAR_SALMON.out.size_factors >> 'align-deseq2'
DESEQ2_QC_STAR_SALMON.out.log >> 'align-deseq2'
DESEQ2_QC_RSEM.out.rdata >> 'align-deseq2'
DESEQ2_QC_RSEM.out.pca_txt >> 'align-deseq2'
DESEQ2_QC_RSEM.out.pdf >> 'align-deseq2'
DESEQ2_QC_RSEM.out.dists_txt >> 'align-deseq2'
DESEQ2_QC_RSEM.out.size_factors >> 'align-deseq2'
DESEQ2_QC_RSEM.out.log >> 'align-deseq2'

// TODO: !params.skip_alignment && params.aligner == 'star_rsem'
// DESEQ2_QC_RSEM.out.rdata >> 'align-deseq2'
// DESEQ2_QC_RSEM.out.pca_txt >> 'align-deseq2'
// DESEQ2_QC_RSEM.out.pdf >> 'align-deseq2'
// DESEQ2_QC_RSEM.out.dists_txt >> 'align-deseq2'
// DESEQ2_QC_RSEM.out.size_factors >> 'align-deseq2'
// DESEQ2_QC_RSEM.out.log >> 'align-deseq2'

QUANTIFY_PSEUDO_ALIGNMENT.out.tpm_gene >> 'pseudo-align'
QUANTIFY_PSEUDO_ALIGNMENT.out.counts_gene >> 'pseudo-align'
Expand Down Expand Up @@ -865,13 +870,15 @@ workflow RNASEQ {
MULTIQC.out.data >> 'multiqc'
MULTIQC.out.plots >> 'multiqc'

PRESEQ_LCEXTRAP.out.lc_extrap >> 'align-preseq'
PRESEQ_LCEXTRAP.out.log >> 'align-preseq-log'
// TODO: !params.skip_alignment && !params.skip_qc && !params.skip_preseq
// PRESEQ_LCEXTRAP.out.lc_extrap >> 'align-preseq'
// PRESEQ_LCEXTRAP.out.log >> 'align-preseq-log'

QUALIMAP_RNASEQ.out.results >> 'align-qualimap'

SORTMERNA.out.log >> 'sortmerna'
SORTMERNA.out.reads >> 'sortmerna-intermeds'
// TODO: params.remove_ribo_rna
// SORTMERNA.out.log >> 'sortmerna'
// SORTMERNA.out.reads >> 'sortmerna-intermeds'

STRINGTIE_STRINGTIE.out.transcript_gtf >> 'align-stringtie'
STRINGTIE_STRINGTIE.out.abundance >> 'align-stringtie'
Expand All @@ -891,17 +898,18 @@ workflow RNASEQ {
ALIGN_STAR.out.bam_transcript >> 'align-star-intermeds'
ALIGN_STAR.out.fastq >> 'align-star-unaligned'

QUANTIFY_RSEM.out.counts_gene >> 'quantify-rsem'
QUANTIFY_RSEM.out.counts_transcript >> 'quantify-rsem'
QUANTIFY_RSEM.out.stat >> 'quantify-rsem'
QUANTIFY_RSEM.out.logs >> 'quantify-rsem-log'
QUANTIFY_RSEM.out.bam_star >> 'quantify-rsem-intermeds'
QUANTIFY_RSEM.out.bam_genome >> 'quantify-rsem-intermeds'
QUANTIFY_RSEM.out.bam_transcript >> 'quantify-rsem-intermeds'
QUANTIFY_RSEM.out.merged_counts_gene >> 'quantify-rsem'
QUANTIFY_RSEM.out.merged_tpm_gene >> 'quantify-rsem'
QUANTIFY_RSEM.out.merged_counts_transcript >> 'quantify-rsem'
QUANTIFY_RSEM.out.merged_tpm_transcript >> 'quantify-rsem'
// TODO: !params.skip_alignment && params.aligner == 'star_rsem'
// QUANTIFY_RSEM.out.counts_gene >> 'quantify-rsem'
// QUANTIFY_RSEM.out.counts_transcript >> 'quantify-rsem'
// QUANTIFY_RSEM.out.stat >> 'quantify-rsem'
// QUANTIFY_RSEM.out.logs >> 'quantify-rsem-log'
// QUANTIFY_RSEM.out.bam_star >> 'quantify-rsem-intermeds'
// QUANTIFY_RSEM.out.bam_genome >> 'quantify-rsem-intermeds'
// QUANTIFY_RSEM.out.bam_transcript >> 'quantify-rsem-intermeds'
// QUANTIFY_RSEM.out.merged_counts_gene >> 'quantify-rsem'
// QUANTIFY_RSEM.out.merged_tpm_gene >> 'quantify-rsem'
// QUANTIFY_RSEM.out.merged_counts_transcript >> 'quantify-rsem'
// QUANTIFY_RSEM.out.merged_tpm_transcript >> 'quantify-rsem'

BAM_MARKDUPLICATES_PICARD.out.bam >> 'align-picard'
BAM_MARKDUPLICATES_PICARD.out.bai >> 'align-picard'
Expand Down Expand Up @@ -934,21 +942,24 @@ workflow RNASEQ {
BAM_RSEQC.out.innerdistance_rscript >> 'align-rseqc-innerdistance'
BAM_RSEQC.out.tin_txt >> 'align-rseqc-tin'

FASTQ_ALIGN_HISAT2.out.summary >> 'align-hisat2-log'
FASTQ_ALIGN_HISAT2.out.orig_bam >> 'align-hisat2-intermeds'
FASTQ_ALIGN_HISAT2.out.fastq >> 'align-hisat2-unaligned'

FASTQ_FASTQC_UMITOOLS_FASTP.out.fastqc_trim_html >> 'trim-fastqc'
FASTQ_FASTQC_UMITOOLS_FASTP.out.fastqc_trim_zip >> 'trim-fastqc'
FASTQ_FASTQC_UMITOOLS_FASTP.out.trim_json >> 'trim'
FASTQ_FASTQC_UMITOOLS_FASTP.out.trim_html >> 'trim'
FASTQ_FASTQC_UMITOOLS_FASTP.out.trim_log >> 'trim-log'
// FASTQ_FASTQC_UMITOOLS_FASTP.out.trim_reads >> 'trim-intermeds'
FASTQ_FASTQC_UMITOOLS_FASTP.out.trim_reads_fail >> 'trim-intermeds'
FASTQ_FASTQC_UMITOOLS_FASTP.out.trim_reads_merged >> 'trim-intermeds'
FASTQ_FASTQC_UMITOOLS_FASTP.out.umi_log >> 'umitools'
// FASTQ_FASTQC_UMITOOLS_FASTP.out.umi_reads >> 'umitools-intermeds'

// TODO: !params.skip_alignment && params.aligner == 'hisat2'
// FASTQ_ALIGN_HISAT2.out.summary >> 'align-hisat2-log'
// FASTQ_ALIGN_HISAT2.out.orig_bam >> 'align-hisat2-intermeds'
// FASTQ_ALIGN_HISAT2.out.fastq >> 'align-hisat2-unaligned'

// TODO: params.trimmer == 'fastp'
// FASTQ_FASTQC_UMITOOLS_FASTP.out.fastqc_trim_html >> 'trim-fastqc'
// FASTQ_FASTQC_UMITOOLS_FASTP.out.fastqc_trim_zip >> 'trim-fastqc'
// FASTQ_FASTQC_UMITOOLS_FASTP.out.trim_json >> 'trim'
// FASTQ_FASTQC_UMITOOLS_FASTP.out.trim_html >> 'trim'
// FASTQ_FASTQC_UMITOOLS_FASTP.out.trim_log >> 'trim-log'
// // FASTQ_FASTQC_UMITOOLS_FASTP.out.trim_reads >> 'trim-intermeds'
// FASTQ_FASTQC_UMITOOLS_FASTP.out.trim_reads_fail >> 'trim-intermeds'
// FASTQ_FASTQC_UMITOOLS_FASTP.out.trim_reads_merged >> 'trim-intermeds'
// FASTQ_FASTQC_UMITOOLS_FASTP.out.umi_log >> 'umitools'
// // FASTQ_FASTQC_UMITOOLS_FASTP.out.umi_reads >> 'umitools-intermeds'

// TODO: params.trimmer == 'trimgalore'
FASTQ_FASTQC_UMITOOLS_TRIMGALORE.out.trim_html >> 'trim-fastqc'
FASTQ_FASTQC_UMITOOLS_TRIMGALORE.out.trim_zip >> 'trim-fastqc'
FASTQ_FASTQC_UMITOOLS_TRIMGALORE.out.trim_log >> 'trim'
Expand Down