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Workflow output DSL (channel selectors) #302

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Workflow output DSL (channel selectors) #302

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2a7a29f
Add workflow output DSL based on emits
bentsherman Mar 14, 2024
564f65d
Update publishing for multiqc versions yml
bentsherman Mar 14, 2024
6045321
Add common changes from other PR
bentsherman Mar 14, 2024
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31 changes: 31 additions & 0 deletions main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -34,6 +34,15 @@ workflow NFCORE_FETCHNGS {
//
SRA ( ids )

emit:
runinfo_tsv = SRA.out.runinfo_tsv
fastq = SRA.out.fastq
fastq_md5 = SRA.out.fastq_md5
samplesheet = SRA.out.samplesheet
mappings = SRA.out.mappings
sample_mappings = SRA.out.sample_mappings
sra_metadata = SRA.out.sra_metadata

}

/*
Expand Down Expand Up @@ -81,6 +90,28 @@ workflow {
params.monochrome_logs,
params.hook_url
)

output:
path(params.outdir, mode: params.publish_dir_mode) {
path('fastq') {
select NFCORE_FETCHNGS.out.fastq
}

path('fastq/md5') {
select NFCORE_FETCHNGS.out.fastq_md5
}

path('metadata') {
select NFCORE_FETCHNGS.out.runinfo_tsv
}

path('samplesheet') {
select NFCORE_FETCHNGS.out.samplesheet, schema: 'assets/schema_samplesheet.yml'
select NFCORE_FETCHNGS.out.mappings, schema: 'assets/schema_mappings.yml'
select NFCORE_FETCHNGS.out.sample_mappings
}
}

}

/*
Expand Down
27 changes: 25 additions & 2 deletions workflows/sra/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -54,6 +54,7 @@ workflow SRA {
SRA_RUNINFO_TO_FTP
.out
.tsv
.tap { ch_runinfo_tsv }
.splitCsv(header:true, sep:'\t')
.map {
meta ->
Expand Down Expand Up @@ -123,6 +124,13 @@ workflow SRA {
.fastq
.mix(SRA_FASTQ_FTP.out.fastq)
.mix(FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS.out.reads)
.set { ch_fastq_records }

ch_fastq_records
.flatMap { meta, fastq -> fastq }
.set { ch_fastq }

ch_fastq_records
.map {
meta, fastq ->
def reads = fastq instanceof List ? fastq.flatten() : [ fastq ]
Expand All @@ -134,6 +142,18 @@ workflow SRA {
return meta_clone
}
.set { ch_sra_metadata }

// Isolate MD5 channel which will be added to emit block
ASPERA_CLI
.out
.md5
.mix(SRA_FASTQ_FTP.out.md5)
.flatMap { meta, md5 -> md5 }
.set { ch_fastq_md5 }
}
else {
ch_fastq = Channel.empty()
ch_fastq_md5 = Channel.empty()
}

//
Expand All @@ -153,7 +173,7 @@ workflow SRA {
.map { it[1] }
.collectFile(name:'tmp_samplesheet.csv', newLine: true, keepHeader: true, sort: { it.baseName })
.map { it.text.tokenize('\n').join('\n') }
.collectFile(name:'samplesheet.csv', storeDir: "${params.outdir}/samplesheet")
.collectFile(name:'samplesheet.csv')
.set { ch_samplesheet }

SRA_TO_SAMPLESHEET
Expand All @@ -162,7 +182,7 @@ workflow SRA {
.map { it[1] }
.collectFile(name:'tmp_id_mappings.csv', newLine: true, keepHeader: true, sort: { it.baseName })
.map { it.text.tokenize('\n').join('\n') }
.collectFile(name:'id_mappings.csv', storeDir: "${params.outdir}/samplesheet")
.collectFile(name:'id_mappings.csv')
.set { ch_mappings }

//
Expand All @@ -184,6 +204,9 @@ workflow SRA {
.collectFile(storeDir: "${params.outdir}/pipeline_info", name: 'nf_core_fetchngs_software_mqc_versions.yml', sort: true, newLine: true)

emit:
runinfo_tsv = ch_runinfo_tsv
fastq = ch_fastq
fastq_md5 = ch_fastq_md5
samplesheet = ch_samplesheet
mappings = ch_mappings
sample_mappings = ch_sample_mappings_yml
Expand Down
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