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migrating from publishDir to output #654

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ccd700c
migrating from publishDir to output
LilyAnderssonLee Oct 9, 2025
f59e4f3
update module.config and main.nf
LilyAnderssonLee Oct 16, 2025
9371420
Merge branch 'dev' into metaval_samplesheet
LilyAnderssonLee Oct 16, 2025
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150 changes: 94 additions & 56 deletions conf/modules.config
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Original file line number Diff line number Diff line change
Expand Up @@ -538,9 +538,17 @@ process {
}

withName: KRAKEN2_KRAKEN2 {
tag = { "${meta.db_name}|${meta.tool}|${meta.id}" }
ext.args = params.kraken2_save_minimizers ? { "${meta.db_params} --report-minimizer-data" } : { "${meta.db_params}" }
ext.prefix = params.perform_runmerging ? { meta.tool == "bracken" ? "${meta.id}_${meta.db_name}.bracken" : "${meta.id}_${meta.db_name}.kraken2" } : { meta.tool == "bracken" ? "${meta.id}_${meta.run_accession}_${meta.db_name}.bracken" : "${meta.id}_${meta.run_accession}_${meta.db_name}.kraken2" }
tag = { "${meta.db_name}|${meta.tool}|${meta.id}" }
ext.args = params.kraken2_save_minimizers ? { "${meta.db_params} --report-minimizer-data" } : { "${meta.db_params}" }
ext.prefix = params.perform_runmerging ?
{ meta.tool == "bracken" ?
(meta.single_end ? "${meta.id}_${meta.db_name}_se.bracken" : "${meta.id}_${meta.db_name}.bracken" ) :
(meta.single_end ? "${meta.id}_${meta.db_name}_se.kraken2" : "${meta.id}_${meta.db_name}.kraken2" )
} :
{ meta.tool == "bracken" ?
"${meta.id}_${meta.run_accession}_${meta.db_name}.bracken" :
"${meta.id}_${meta.run_accession}_${meta.db_name}.kraken2"
}
publishDir = [
path: { "${params.outdir}/kraken2/${meta.db_name}/" },
mode: params.publish_dir_mode,
Expand All @@ -550,8 +558,16 @@ process {
}

withName: KRAKEN2_STANDARD_REPORT {
tag = { "${meta.db_name}|${meta.tool}|${meta.id}" }
ext.prefix = params.perform_runmerging ? { meta.tool == "bracken" ? "${meta.id}_${meta.db_name}.bracken" : "${meta.id}_${meta.db_name}.kraken2" } : { meta.tool == "bracken" ? "${meta.id}_${meta.run_accession}_${meta.db_name}.bracken" : "${meta.id}_${meta.run_accession}_${meta.db_name}.kraken2" }
tag = { "${meta.db_name}|${meta.tool}|${meta.id}" }
ext.prefix = params.perform_runmerging ?
{ meta.tool == "bracken" ?
(meta.single_end ? "${meta.id}_${meta.db_name}_se.bracken" : "${meta.id}_${meta.db_name}.bracken") :
(meta.single_end ? "${meta.id}_${meta.db_name}_se.kraken2" : "${meta.id}_${meta.db_name}.kraken2")
} :
{ meta.tool == "bracken" ?
"${meta.id}_${meta.run_accession}_${meta.db_name}.bracken" :
"${meta.id}_${meta.run_accession}_${meta.db_name}.kraken2"
}
publishDir = [
path: { "${params.outdir}/kraken2/${meta.db_name}/" },
mode: params.publish_dir_mode,
Expand All @@ -560,9 +576,11 @@ process {
}

withName: BRACKEN_BRACKEN {
tag = { "${meta.db_name}|${meta.id}" }
ext.args = { "${meta.db_params}" }
ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}.bracken" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}.bracken" }
tag = {"${meta.db_name}|${meta.id}"}
ext.args = { "${meta.db_params}" }
ext.prefix = params.perform_runmerging ?
{ meta.single_end ? "${meta.id}_${meta.db_name}_se.bracken" : "${meta.id}_${meta.db_name}.bracken" } :
{ "${meta.id}_${meta.run_accession}_${meta.db_name}.bracken" }
publishDir = [
path: { "${params.outdir}/bracken/${meta.db_name}/" },
mode: params.publish_dir_mode,
Expand Down Expand Up @@ -613,7 +631,9 @@ process {
}

withName: KRONA_CLEANUP {
ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}" }
ext.prefix = params.perform_runmerging ?
{ meta.single_end ? "${meta.id}_${meta.db_name}_se" : "${meta.id}_${meta.db_name}" } :
{ "${meta.id}_${meta.run_accession}_${meta.db_name}" }
publishDir = [
path: { "${params.outdir}/krona/" },
mode: params.publish_dir_mode,
Expand Down Expand Up @@ -647,9 +667,11 @@ process {
}

withName: METAPHLAN_METAPHLAN {
tag = { "${meta.db_name}|${meta.id}" }
ext.args = { "${meta.db_params}" }
ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}.metaphlan" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}.metaphlan" }
tag = {"${meta.db_name}|${meta.id}"}
ext.args = { "${meta.db_params}" }
ext.prefix = params.perform_runmerging ?
{ meta.single_end ? "${meta.id}_${meta.db_name}_se.metaphlan" : "${meta.id}_${meta.db_name}.metaphlan" } :
{ "${meta.id}_${meta.run_accession}_${meta.db_name}.metaphlan" }
publishDir = [
path: { "${params.outdir}/metaphlan/${meta.db_name}/" },
mode: params.publish_dir_mode,
Expand All @@ -667,9 +689,11 @@ process {
}

withName: CENTRIFUGE_CENTRIFUGE {
tag = { "${meta.db_name}|${meta.id}" }
ext.args = { "${meta.db_params}" }
ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}.centrifuge" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}.centrifuge" }
tag = {"${meta.db_name}|${meta.id}"}
ext.args = { "${meta.db_params}" }
ext.prefix = params.perform_runmerging ?
{ meta.single_end ? "${meta.id}_${meta.db_name}_se.centrifuge" : "${meta.id}_${meta.db_name}.centrifuge" } :
{ "${meta.id}_${meta.run_accession}_${meta.db_name}.centrifuge" }
publishDir = [
path: { "${params.outdir}/centrifuge/${meta.db_name}/" },
mode: params.publish_dir_mode,
Expand All @@ -678,9 +702,11 @@ process {
}

withName: CENTRIFUGE_KREPORT {
tag = { "${meta.db_name}|${meta.id}" }
ext.args = { "${meta.db_params}" }
ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}.centrifuge" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}.centrifuge" }
tag = {"${meta.db_name}|${meta.id}"}
ext.args = { "${meta.db_params}" }
ext.prefix = params.perform_runmerging ?
{ meta.single_end ? "${meta.id}_${meta.db_name}_se.centrifuge" : "${meta.id}_${meta.db_name}.centrifuge" } :
{ "${meta.id}_${meta.run_accession}_${meta.db_name}.centrifuge" }
publishDir = [
path: { "${params.outdir}/centrifuge/${meta.db_name}/" },
mode: params.publish_dir_mode,
Expand All @@ -698,24 +724,26 @@ process {
}

withName: KAIJU_KAIJU {
tag = { "${meta.db_name}|${meta.id}" }
ext.args = { "${meta.db_params}" }
ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}.kaiju" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}.kaiju" }
tag = {"${meta.db_name}|${meta.id}"}
ext.args = { "${meta.db_params}" }
ext.prefix = params.perform_runmerging ?
{ meta.single_end ? "${meta.id}_${meta.db_name}_se.kaiju" : "${meta.id}_${meta.db_name}.kaiju" } :
{ "${meta.id}_${meta.run_accession}_${meta.db_name}.kaiju" }
publishDir = [
path: { "${params.outdir}/kaiju/${meta.db_name}/" },
mode: params.publish_dir_mode,
pattern: '*.tsv',
]
}

withName: KAIJU_KAIJU2TABLE_SINGLE {
tag = { "${meta.db_name}|${meta.id}" }
ext.args = {
[
params.kaiju_expand_viruses ? "-e" : ""
].join(' ').trim()
}
ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}.kaijutable" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}.kaijutable" }
withName: 'KAIJU_KAIJU2TABLE_SINGLE' {
tag = {"${meta.db_name}|${meta.id}"}
ext.args = {[
params.kaiju_expand_viruses ? "-e" : ""
].join(' ').trim() }
ext.prefix = params.perform_runmerging ?
{ meta.single_end ? "${meta.id}_${meta.db_name}_se.kaijutable" : "${meta.id}_${meta.db_name}.kaijutable" } :
{ "${meta.id}_${meta.run_accession}_${meta.db_name}.kaijutable" }
publishDir = [
path: { "${params.outdir}/kaiju/${meta.db_name}/" },
mode: params.publish_dir_mode,
Expand All @@ -742,9 +770,11 @@ process {
}

withName: DIAMOND_BLASTX {
tag = { "${meta.db_name}|${meta.id}" }
ext.args = { "${meta.db_params}" }
ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}.diamond" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}.diamond" }
tag = {"${meta.db_name}|${meta.id}"}
ext.args = { "${meta.db_params}" }
ext.prefix = params.perform_runmerging ?
{ meta.single_end ? "${meta.id}_${meta.db_name}_se.diamond" : "${meta.id}_${meta.db_name}.diamond" } :
{ "${meta.id}_${meta.run_accession}_${meta.db_name}.diamond" }
publishDir = [
path: { "${params.outdir}/diamond/${meta.db_name}/" },
mode: params.publish_dir_mode,
Expand All @@ -758,10 +788,12 @@ process {
[
params.motus_remove_ncbi_ids ? "" : "-p",
params.motus_use_relative_abundance ? "" : "-c",
params.motus_save_mgc_read_counts ? "-M ${task.ext.prefix}.mgc" : "",
].join(',').replaceAll(',', " ")
}
ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}" }
params.motus_save_mgc_read_counts ? "-M ${task.ext.prefix}.mgc" : ""
].join(',').replaceAll(','," ")
}
ext.prefix = params.perform_runmerging ?
{ meta.single_end ? "${meta.id}_${meta.db_name}_se" : "${meta.id}_${meta.db_name}" } :
{ "${meta.id}_${meta.run_accession}_${meta.db_name}" }
publishDir = [
path: { "${params.outdir}/motus/${meta.db_name}/" },
mode: params.publish_dir_mode,
Expand All @@ -778,9 +810,11 @@ process {
}

withName: KMCP_SEARCH {
tag = { "${meta.db_name}|${meta.id}" }
ext.args = { "${meta.db_params}" }
ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}.kmcp_search" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}.kmcp_search" }
tag = {"${meta.db_name}|${meta.id}"}
ext.args = { "${meta.db_params}" }
ext.prefix = params.perform_runmerging ?
{ meta.single_end ? "${meta.id}_${meta.db_name}_se.kmcp_search" : "${meta.id}_${meta.db_name}.kmcp_search" } :
{ "${meta.id}_${meta.run_accession}_${meta.db_name}.kmcp_search" }
publishDir = [
path: { "${params.outdir}/kmcp/${meta.db_name}/" },
mode: params.publish_dir_mode,
Expand All @@ -789,9 +823,11 @@ process {
}

withName: KMCP_PROFILE {
tag = { "${meta.db_name}|${meta.id}" }
ext.args = { "${meta.db_params}" }
ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}.kmcp" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}.kmcp" }
tag = {"${meta.db_name}|${meta.id}"}
ext.args = { "${meta.db_params}" }
ext.prefix = params.perform_runmerging ?
{ meta.single_end ? "${meta.id}_${meta.db_name}_se.kmcp" : "${meta.id}_${meta.db_name}.kmcp" } :
{ "${meta.id}_${meta.run_accession}_${meta.db_name}.kmcp" }
publishDir = [
path: { "${params.outdir}/kmcp/${meta.db_name}/" },
mode: params.publish_dir_mode,
Expand All @@ -800,9 +836,11 @@ process {
}

withName: GANON_CLASSIFY {
tag = { "${meta.db_name}|${meta.id}" }
ext.args = params.ganon_save_readclassifications ? { "${meta.db_params} --output-all --output-unclassified" } : { "${meta.db_params}" }
ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}.ganon" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}.ganon" }
tag = {"${meta.db_name}|${meta.id}"}
ext.args = params.ganon_save_readclassifications ? { "${meta.db_params} --output-all --output-unclassified" } : { "${meta.db_params}" }
ext.prefix = params.perform_runmerging ?
{ meta.single_end ? "${meta.id}_${meta.db_name}_se.ganon" : "${meta.id}_${meta.db_name}.ganon" } :
{ "${meta.id}_${meta.run_accession}_${meta.db_name}.ganon" }
publishDir = [
path: { "${params.outdir}/ganon/${meta.db_name}/" },
mode: params.publish_dir_mode,
Expand All @@ -811,17 +849,17 @@ process {
}

withName: GANON_REPORT {
tag = { "${meta.db_name}|${meta.id}" }
ext.args = {
[
"--report-type ${params.ganon_report_type}",
ganon_report_rank != 'default' ? "--ranks ${params.ganon_report_rank}" : "",
"--top-percentile ${params.ganon_report_toppercentile}",
"--min-count ${params.ganon_report_mincount}",
"--max-count ${params.ganon_report_maxcount}",
].join(' ').trim()
}
ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}.ganon_report" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}.ganon_report" }
tag = {"${meta.db_name}|${meta.id}"}
ext.args = {[
"--report-type ${params.ganon_report_type}",
ganon_report_rank != 'default' ? "--ranks ${params.ganon_report_rank}" : "",
"--top-percentile ${params.ganon_report_toppercentile}",
"--min-count ${params.ganon_report_mincount}",
"--max-count ${params.ganon_report_maxcount}"
].join(' ').trim() }
ext.prefix = params.perform_runmerging ?
{ meta.single_end ? "${meta.id}_${meta.db_name}_se.ganon_report" : "${meta.id}_${meta.db_name}.ganon_report" } :
{ "${meta.id}_${meta.run_accession}_${meta.db_name}.ganon_report" }
publishDir = [
path: { "${params.outdir}/ganon/${meta.db_name}/" },
mode: params.publish_dir_mode,
Expand Down
15 changes: 8 additions & 7 deletions conf/test.config
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -28,27 +28,28 @@ params {
perform_shortread_qc = true
perform_shortread_redundancyestimation = true
perform_longread_qc = true
shortread_qc_mergepairs = true
shortread_qc_mergepairs = false
perform_shortread_complexityfilter = true
perform_shortread_hostremoval = true
perform_longread_hostremoval = true
perform_runmerging = true
hostremoval_reference = params.pipelines_testdata_base_path + 'modules/data/genomics/homo_sapiens/genome/genome.fasta'
run_kaiju = true
run_kaiju = false
run_kraken2 = true
run_bracken = true
run_bracken = false
run_malt = false
run_metaphlan = true
run_metaphlan = false
run_centrifuge = true
run_diamond = true
run_krakenuniq = true
run_krakenuniq = false
run_motus = false
run_ganon = true
run_ganon = false
run_krona = true
run_kmcp = true
run_kmcp = false
krona_taxonomy_directory = params.pipelines_testdata_base_path + 'modules/data/genomics/sarscov2/metagenome/krona_taxonomy.tab'
malt_save_reads = true
kraken2_save_reads = true
kraken2_save_readclassifications = true
centrifuge_save_reads = true
metaphlan_save_samfiles = true
run_profile_standardisation = true
Expand Down
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