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demo: Record types for workflow outputs #1703

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236 changes: 93 additions & 143 deletions main.nf
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52 changes: 28 additions & 24 deletions modules/local/deseq2_qc/main.nf
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Original file line number Diff line number Diff line change
@@ -1,3 +1,16 @@
nextflow.preview.types = true

record DeSeq2Result {
pdf: Path?
rdata: Path?
pca_txt: Path?
pca_multiqc: Path?
dists_txt: Path?
dists_multiqc: Path?
log: Path?
size_factors: Path?
}
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@adamrtalbot adamrtalbot Feb 26, 2026

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When do you use this record?


process DESEQ2_QC {
label "process_medium"

Expand All @@ -9,20 +22,23 @@ process DESEQ2_QC {
'community.wave.seqera.io/library/r-base_r-optparse_r-ggplot2_r-rcolorbrewer_pruned:9e75394d0bc21987' }"

input:
path counts
path pca_header_multiqc
path clustering_header_multiqc
counts: Path
pca_header_multiqc: Path
clustering_header_multiqc: Path

output:
path "*.pdf" , optional:true, emit: pdf
path "*.RData" , optional:true, emit: rdata
path "*pca.vals.txt" , optional:true, emit: pca_txt
path "*pca.vals_mqc.tsv" , optional:true, emit: pca_multiqc
path "*sample.dists.txt" , optional:true, emit: dists_txt
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
record(
pdf: file("*.pdf", optional: true),
rdata: file("*.RData", optional: true),
pca_txt: file("*pca.vals.txt", optional: true),
pca_multiqc: file("*pca.vals_mqc.tsv", optional: true),
dists_txt: file("*sample.dists.txt", optional: true),
dists_multiqc: file("*sample.dists_mqc.tsv", optional: true),
log: file("*.log", optional: true),
size_factors: file("size_factors", optional: true)
)
tuple val("${task.process}"), val('r-base'), eval('echo $(R --version 2>&1) | sed "s/^.*R version //; s/ .*$//"'), topic: versions
tuple val("${task.process}"), val('bioconductor-deseq2'), eval('Rscript -e "library(DESeq2); cat(as.character(packageVersion(\'DESeq2\')))"'), topic: versions

when:
task.ext.when == null || task.ext.when
Expand Down Expand Up @@ -54,12 +70,6 @@ process DESEQ2_QC {
cat clustering_header.tmp *.sample.dists.txt > ${label_lower}.sample.dists_mqc.tsv
rm clustering_header.tmp
fi

cat <<-END_VERSIONS > versions.yml
"${task.process}":
r-base: \$(echo \$(R --version 2>&1) | sed 's/^.*R version //; s/ .*\$//')
bioconductor-deseq2: \$(Rscript -e "library(DESeq2); cat(as.character(packageVersion('DESeq2')))")
END_VERSIONS
"""

stub:
Expand All @@ -81,11 +91,5 @@ process DESEQ2_QC {
do
touch size_factors/\${i}.size_factors.RData
done

cat <<-END_VERSIONS >versions.yml
"${task.process}":
r-base: \$(echo \$(R --version 2>&1) | sed 's/^.*R version //; s/ .*\$//')
bioconductor-deseq2: \$(Rscript -e "library(DESeq2); cat(as.character(packageVersion('DESeq2')))")
END_VERSIONS
"""
}
41 changes: 22 additions & 19 deletions modules/local/rsem_merge_counts/main.nf
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Original file line number Diff line number Diff line change
@@ -1,3 +1,14 @@
nextflow.preview.types = true

record RsemMergedResult {
counts_gene: Path
tpm_gene: Path
counts_transcript: Path
tpm_transcript: Path
genes_long: Path
isoforms_long: Path
}

process RSEM_MERGE_COUNTS {
label "process_medium"

Expand All @@ -7,17 +18,19 @@ process RSEM_MERGE_COUNTS {
'nf-core/ubuntu:20.04' }"

input:
path ('genes/*')
path ('isoforms/*')
genes: Path // path ('genes/*')
isoforms: Path // path ('isoforms/*')

output:
path "rsem.merged.gene_counts.tsv" , emit: counts_gene
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 "rsem.merged.genes_long.tsv" , emit: genes_long
path "rsem.merged.isoforms_long.tsv" , emit: isoforms_long
path "versions.yml" , emit: versions
record(
counts_gene: file("rsem.merged.gene_counts.tsv"),
tpm_gene: file("rsem.merged.gene_tpm.tsv"),
counts_transcript: file("rsem.merged.transcript_counts.tsv"),
tpm_transcript: file("rsem.merged.transcript_tpm.tsv"),
genes_long: file("rsem.merged.genes_long.tsv"),
isoforms_long: file("rsem.merged.isoforms_long.tsv")
)
tuple val("${task.process}"), val('sed'), eval('echo $(sed --version 2>&1) | sed "s/^.*GNU sed) //; s/ .*$//"'), topic: versions

when:
task.ext.when == null || task.ext.when
Expand Down Expand Up @@ -62,11 +75,6 @@ process RSEM_MERGE_COUNTS {
samplename=`basename \$fileid | sed s/\\.isoforms.results\$//g`
tail -n+2 \$fileid | awk -v sample=\$samplename 'BEGIN{OFS="\t"}{print sample,\$1,\$2,\$3,\$4,\$5,\$6,\$7,\$8}' >> rsem.merged.isoforms_long.tsv
done

cat <<-END_VERSIONS > versions.yml
"${task.process}":
sed: \$(echo \$(sed --version 2>&1) | sed 's/^.*GNU sed) //; s/ .*\$//')
END_VERSIONS
"""

stub:
Expand All @@ -77,10 +85,5 @@ process RSEM_MERGE_COUNTS {
touch rsem.merged.transcript_tpm.tsv
touch rsem.merged.genes_long.tsv
touch rsem.merged.isoforms_long.tsv

cat <<-END_VERSIONS > versions.yml
"${task.process}":
sed: \$(echo \$(sed --version 2>&1) | sed 's/^.*GNU sed) //; s/ .*\$//')
END_VERSIONS
"""
}
87 changes: 54 additions & 33 deletions modules/local/star_align_igenomes/main.nf
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Original file line number Diff line number Diff line change
@@ -1,3 +1,26 @@
nextflow.preview.types = true

// Uses the same record type as STAR_ALIGN
record StarAlignResult {
meta: Map
bam: Path?
bam_sorted: Path?
bam_sorted_aligned: Path?
bam_transcript: Path?
bam_unsorted: Path?
log_final: Path
log_out: Path
log_progress: Path
fastq: Path?
tab: Path?
spl_junc_tab: Path?
read_per_gene_tab: Path?
junction: Path?
sam: Path?
wig: Path?
bedgraph: Path?
}

process STAR_ALIGN_IGENOMES {
tag "$meta.id"
label 'process_high'
Expand All @@ -8,27 +31,39 @@ process STAR_ALIGN_IGENOMES {
'community.wave.seqera.io/library/star_samtools_gawk:79ca42311e583cdc' }"

input:
tuple val(meta), path(reads, stageAs: "input*/*")
tuple val(meta2), path(index)
tuple val(meta3), path(gtf)
val star_ignore_sjdbgtf
val seq_platform
val seq_center
(meta: Map, reads: Path): Record
(meta2: Map, index: Path): Record

output:
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
stage:
stageAs(reads, 'input*/*')
(meta3: Map, gtf: Path): Record
star_ignore_sjdbgtf: String?
seq_platform: String?
seq_center: String?

tuple val(meta), path('*d.out.bam') , optional:true, emit: bam
tuple val(meta), path('*sortedByCoord.out.bam') , optional:true, emit: bam_sorted
tuple val(meta), path('*toTranscriptome.out.bam'), optional:true, emit: bam_transcript
tuple val(meta), path('*Aligned.unsort.out.bam') , optional:true, emit: bam_unsorted
tuple val(meta), path('*fastq.gz') , optional:true, emit: fastq
tuple val(meta), path('*.tab') , optional:true, emit: tab
tuple val(meta), path('*.out.junction') , optional:true, emit: junction
tuple val(meta), path('*.out.sam') , optional:true, emit: sam
output:
record(
meta: meta,
bam: file('*d.out.bam', optional: true),
bam_sorted: file('*sortedByCoord.out.bam', optional: true),
bam_sorted_aligned: file("*.Aligned.sortedByCoord.out.bam", optional: true),
bam_transcript: file('*toTranscriptome.out.bam', optional: true),
bam_unsorted: file('*Aligned.unsort.out.bam', optional: true),
log_final: file('*Log.final.out'),
log_out: file('*Log.out'),
log_progress: file('*Log.progress.out'),
fastq: file('*fastq.gz', optional: true),
tab: file('*.tab', optional: true),
spl_junc_tab: file('*.SJ.out.tab', optional: true),
read_per_gene_tab: file('*.ReadsPerGene.out.tab', optional: true),
junction: file('*.out.junction', optional: true),
sam: file('*.out.sam', optional: true),
wig: file('*.wig', optional: true),
bedgraph: file('*.bg', optional: true)
)
tuple val("${task.process}"), val('star'), eval('STAR --version | sed -e "s/STAR_//g"'), topic: versions
tuple val("${task.process}"), val('samtools'), eval('echo $(samtools --version 2>&1) | sed "s/^.*samtools //; s/Using.*$//"'), topic: versions
tuple val("${task.process}"), val('gawk'), eval('echo $(gawk --version 2>&1) | sed "s/^.*GNU Awk //; s/, .*$//"'), topic: versions

when:
task.ext.when == null || task.ext.when
Expand Down Expand Up @@ -65,13 +100,6 @@ process STAR_ALIGN_IGENOMES {
mv ${prefix}.Unmapped.out.mate2 ${prefix}.unmapped_2.fastq
gzip ${prefix}.unmapped_2.fastq
fi

cat <<-END_VERSIONS > versions.yml
"${task.process}":
star: \$(STAR --version | sed -e "s/STAR_//g")
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
gawk: \$(echo \$(gawk --version 2>&1) | sed 's/^.*GNU Awk //; s/, .*\$//')
END_VERSIONS
"""

stub:
Expand All @@ -94,12 +122,5 @@ process STAR_ALIGN_IGENOMES {
touch ${prefix}.out.sam
touch ${prefix}.Signal.UniqueMultiple.str1.out.wig
touch ${prefix}.Signal.UniqueMultiple.str1.out.bg

cat <<-END_VERSIONS > versions.yml
"${task.process}":
star: \$(STAR --version | sed -e "s/STAR_//g")
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
gawk: \$(echo \$(gawk --version 2>&1) | sed 's/^.*GNU Awk //; s/, .*\$//')
END_VERSIONS
"""
}
41 changes: 26 additions & 15 deletions modules/nf-core/dupradar/main.nf
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15 changes: 0 additions & 15 deletions modules/nf-core/dupradar/templates/dupradar.r
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