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Merged
merged 2 commits into from
Nov 28, 2024
Merged

Address review comments for Patch release v1.2.1 #556

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05e4f2e
Move the modules.config line below the base.config line
LilyAnderssonLee Nov 28, 2024
2a64aed
update configs
LilyAnderssonLee Nov 28, 2024
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2 changes: 1 addition & 1 deletion CHANGELOG.md
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Expand Up @@ -3,7 +3,7 @@
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).

## v1.2.1 - Bouncy Basenji Patch [2024-11-27]
## v1.2.1 - Bouncy Basenji Patch [2024-11-28]

### `Added`

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26 changes: 25 additions & 1 deletion conf/test.config
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Expand Up @@ -55,16 +55,40 @@ params {

process {
withName: MALT_RUN {
tag = {"${meta.db_name}|${meta.id}"}
maxForks = 1
ext.args = { "-m ${params.malt_mode} -J-Xmx12G" }
ext.args = { "${meta.db_params} -m ${params.malt_mode} -J-Xmx12G" }
ext.prefix = { "${meta.db_name}" }
publishDir = [
path: { "${params.outdir}/malt/${meta.db_name}/" },
mode: params.publish_dir_mode,
pattern: '*.{rma6,log,sam}'
]
}
withName: MEGAN_RMA2INFO_TSV {
tag = {"${meta.db_name}|${meta.id}"}
maxForks = 1
ext.args = "-c2c Taxonomy"
ext.prefix = { "${meta.id}" }
publishDir = [
path: { "${params.outdir}/malt/${meta.db_name}/" },
mode: params.publish_dir_mode,
pattern: '*.{txt.gz,megan}'
]
}
withName: MEGAN_RMA2INFO_KRONA {
tag = {"${meta.db_name}|${meta.id}"}
maxForks = 1
ext.args = { "--read2class Taxonomy" }
ext.prefix = { "${meta.id}_${meta.db_name}" }
}
withName: NONPAREIL_NONPAREIL {
ext.args = { "-k 5" }
ext.prefix = { "${meta.id}_${meta.run_accession}" }
publishDir = [
path: { "${params.outdir}/nonpareil/" },
mode: params.publish_dir_mode,
pattern: '*.np{a,c,l,o}'
]
}
}
15 changes: 14 additions & 1 deletion conf/test_alternativepreprocessing.config
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Expand Up @@ -51,10 +51,23 @@ params {

process {
withName: MALT_RUN {
tag = {"${meta.db_name}|${meta.id}"}
maxForks = 1
ext.args = { "-m ${params.malt_mode} -J-Xmx12G" }
ext.args = { "${meta.db_params} -m ${params.malt_mode} -J-Xmx12G" }
ext.prefix = { "${meta.db_name}" }
publishDir = [
path: { "${params.outdir}/malt/${meta.db_name}/" },
mode: params.publish_dir_mode,
pattern: '*.{rma6,log,sam}'
]
}
withName: NONPAREIL_NONPAREIL {
ext.args = { "-k 5" }
ext.prefix = { "${meta.id}_${meta.run_accession}" }
publishDir = [
path: { "${params.outdir}/nonpareil/" },
mode: params.publish_dir_mode,
pattern: '*.np{a,c,l,o}'
]
}
}
15 changes: 14 additions & 1 deletion conf/test_bbduk.config
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Expand Up @@ -49,10 +49,23 @@ params {

process {
withName: MALT_RUN {
tag = {"${meta.db_name}|${meta.id}"}
maxForks = 1
ext.args = { "-m ${params.malt_mode} -J-Xmx12G" }
ext.args = { "${meta.db_params} -m ${params.malt_mode} -J-Xmx12G" }
ext.prefix = { "${meta.db_name}" }
publishDir = [
path: { "${params.outdir}/malt/${meta.db_name}/" },
mode: params.publish_dir_mode,
pattern: '*.{rma6,log,sam}'
]
}
withName: NONPAREIL_NONPAREIL {
ext.args = { "-k 5" }
ext.prefix = { "${meta.id}_${meta.run_accession}" }
publishDir = [
path: { "${params.outdir}/nonpareil/" },
mode: params.publish_dir_mode,
pattern: '*.np{a,c,l,o}'
]
}
}
15 changes: 14 additions & 1 deletion conf/test_falco.config
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Expand Up @@ -49,10 +49,23 @@ params {

process {
withName: MALT_RUN {
tag = {"${meta.db_name}|${meta.id}"}
maxForks = 1
ext.args = { "-m ${params.malt_mode} -J-Xmx12G" }
ext.args = { "${meta.db_params} -m ${params.malt_mode} -J-Xmx12G" }
ext.prefix = { "${meta.db_name}" }
publishDir = [
path: { "${params.outdir}/malt/${meta.db_name}/" },
mode: params.publish_dir_mode,
pattern: '*.{rma6,log,sam}'
]
}
withName: NONPAREIL_NONPAREIL {
ext.args = { "-k 5" }
ext.prefix = { "${meta.id}_${meta.run_accession}" }
publishDir = [
path: { "${params.outdir}/nonpareil/" },
mode: params.publish_dir_mode,
pattern: '*.np{a,c,l,o}'
]
}
}
15 changes: 14 additions & 1 deletion conf/test_fastp.config
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Expand Up @@ -51,10 +51,23 @@ params {

process {
withName: MALT_RUN {
tag = {"${meta.db_name}|${meta.id}"}
maxForks = 1
ext.args = { "-m ${params.malt_mode} -J-Xmx12G" }
ext.args = { "${meta.db_params} -m ${params.malt_mode} -J-Xmx12G" }
ext.prefix = { "${meta.db_name}" }
publishDir = [
path: { "${params.outdir}/malt/${meta.db_name}/" },
mode: params.publish_dir_mode,
pattern: '*.{rma6,log,sam}'
]
}
withName: NONPAREIL_NONPAREIL {
ext.args = { "-k 5" }
ext.prefix = { "${meta.id}_${meta.run_accession}" }
publishDir = [
path: { "${params.outdir}/nonpareil/" },
mode: params.publish_dir_mode,
pattern: '*.np{a,c,l,o}'
]
}
}
25 changes: 25 additions & 0 deletions conf/test_krakenuniq.config
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Expand Up @@ -61,15 +61,40 @@ params {

process {
withName: MALT_RUN {
tag = {"${meta.db_name}|${meta.id}"}
maxForks = 1
ext.args = { "${meta.db_params} -m ${params.malt_mode} -J-Xmx12G" }
ext.prefix = { "${meta.db_name}" }
publishDir = [
path: { "${params.outdir}/malt/${meta.db_name}/" },
mode: params.publish_dir_mode,
pattern: '*.{rma6,log,sam}'
]
}
withName: MEGAN_RMA2INFO_TSV {
tag = {"${meta.db_name}|${meta.id}"}
maxForks = 1
ext.args = "-c2c Taxonomy"
ext.prefix = { "${meta.id}" }
publishDir = [
path: { "${params.outdir}/malt/${meta.db_name}/" },
mode: params.publish_dir_mode,
pattern: '*.{txt.gz,megan}'
]
}
withName: MEGAN_RMA2INFO_KRONA {
tag = {"${meta.db_name}|${meta.id}"}
maxForks = 1
ext.args = { "--read2class Taxonomy" }
ext.prefix = { "${meta.id}_${meta.db_name}" }
}
withName: NONPAREIL_NONPAREIL {
ext.args = { "-k 5" }
ext.prefix = { "${meta.id}_${meta.run_accession}" }
publishDir = [
path: { "${params.outdir}/nonpareil/" },
mode: params.publish_dir_mode,
pattern: '*.np{a,c,l,o}'
]
}
}
14 changes: 14 additions & 0 deletions conf/test_malt.config
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Expand Up @@ -53,9 +53,23 @@ params {

process {
withName: MALT_RUN {
tag = {"${meta.db_name}|${meta.id}"}
maxForks = 1
ext.args = { "${meta.db_params} -m ${params.malt_mode} -J-Xmx12G" }
ext.prefix = { "${meta.db_name}" }
publishDir = [
path: { "${params.outdir}/malt/${meta.db_name}/" },
mode: params.publish_dir_mode,
pattern: '*.{rma6,log,sam}'
]
}
withName: NONPAREIL_NONPAREIL {
ext.args = { "-k 5" }
ext.prefix = { "${meta.id}_${meta.run_accession}" }
publishDir = [
path: { "${params.outdir}/nonpareil/" },
mode: params.publish_dir_mode,
pattern: '*.np{a,c,l,o}'
]
}
}
14 changes: 14 additions & 0 deletions conf/test_motus.config
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Expand Up @@ -57,9 +57,23 @@ params {

process {
withName: MALT_RUN {
tag = {"${meta.db_name}|${meta.id}"}
maxForks = 1
ext.args = { "${meta.db_params} -m ${params.malt_mode} -J-Xmx12G" }
ext.prefix = { "${meta.db_name}" }
publishDir = [
path: { "${params.outdir}/malt/${meta.db_name}/" },
mode: params.publish_dir_mode,
pattern: '*.{rma6,log,sam}'
]
}
withName: NONPAREIL_NONPAREIL {
ext.args = { "-k 5" }
ext.prefix = { "${meta.id}_${meta.run_accession}" }
publishDir = [
path: { "${params.outdir}/nonpareil/" },
mode: params.publish_dir_mode,
pattern: '*.np{a,c,l,o}'
]
}
}
15 changes: 14 additions & 1 deletion conf/test_nopreprocessing.config
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Expand Up @@ -51,10 +51,23 @@ params {

process {
withName: MALT_RUN {
tag = {"${meta.db_name}|${meta.id}"}
maxForks = 1
ext.args = { "-m ${params.malt_mode} -J-Xmx12G" }
ext.args = { "${meta.db_params} -m ${params.malt_mode} -J-Xmx12G" }
ext.prefix = { "${meta.db_name}" }
publishDir = [
path: { "${params.outdir}/malt/${meta.db_name}/" },
mode: params.publish_dir_mode,
pattern: '*.{rma6,log,sam}'
]
}
withName: NONPAREIL_NONPAREIL {
ext.args = { "-k 5" }
ext.prefix = { "${meta.id}_${meta.run_accession}" }
publishDir = [
path: { "${params.outdir}/nonpareil/" },
mode: params.publish_dir_mode,
pattern: '*.np{a,c,l,o}'
]
}
}
14 changes: 14 additions & 0 deletions conf/test_noprofiling.config
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Expand Up @@ -50,9 +50,23 @@ params {

process {
withName: MALT_RUN {
tag = {"${meta.db_name}|${meta.id}"}
maxForks = 1
ext.args = { "${meta.db_params} -m ${params.malt_mode} -J-Xmx12G" }
ext.prefix = { "${meta.db_name}" }
publishDir = [
path: { "${params.outdir}/malt/${meta.db_name}/" },
mode: params.publish_dir_mode,
pattern: '*.{rma6,log,sam}'
]
}
withName: NONPAREIL_NONPAREIL {
ext.args = { "-k 5" }
ext.prefix = { "${meta.id}_${meta.run_accession}" }
publishDir = [
path: { "${params.outdir}/nonpareil/" },
mode: params.publish_dir_mode,
pattern: '*.np{a,c,l,o}'
]
}
}
15 changes: 14 additions & 1 deletion conf/test_nothing.config
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Expand Up @@ -49,10 +49,23 @@ params {

process {
withName: MALT_RUN {
tag = {"${meta.db_name}|${meta.id}"}
maxForks = 1
ext.args = { "-m ${params.malt_mode} -J-Xmx12G" }
ext.args = { "${meta.db_params} -m ${params.malt_mode} -J-Xmx12G" }
ext.prefix = { "${meta.db_name}" }
publishDir = [
path: { "${params.outdir}/malt/${meta.db_name}/" },
mode: params.publish_dir_mode,
pattern: '*.{rma6,log,sam}'
]
}
withName: NONPAREIL_NONPAREIL {
ext.args = { "-k 5" }
ext.prefix = { "${meta.id}_${meta.run_accession}" }
publishDir = [
path: { "${params.outdir}/nonpareil/" },
mode: params.publish_dir_mode,
pattern: '*.np{a,c,l,o}'
]
}
}
15 changes: 14 additions & 1 deletion conf/test_prinseqplusplus.config
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Expand Up @@ -50,10 +50,23 @@ params {

process {
withName: MALT_RUN {
tag = {"${meta.db_name}|${meta.id}"}
maxForks = 1
ext.args = { "-m ${params.malt_mode} -J-Xmx12G" }
ext.args = { "${meta.db_params} -m ${params.malt_mode} -J-Xmx12G" }
ext.prefix = { "${meta.db_name}" }
publishDir = [
path: { "${params.outdir}/malt/${meta.db_name}/" },
mode: params.publish_dir_mode,
pattern: '*.{rma6,log,sam}'
]
}
withName: NONPAREIL_NONPAREIL {
ext.args = { "-k 5" }
ext.prefix = { "${meta.id}_${meta.run_accession}" }
publishDir = [
path: { "${params.outdir}/nonpareil/" },
mode: params.publish_dir_mode,
pattern: '*.np{a,c,l,o}'
]
}
}
5 changes: 2 additions & 3 deletions nextflow.config
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Expand Up @@ -193,6 +193,8 @@ params {

// Load base.config by default for all pipelines
includeConfig 'conf/base.config'
// Load modules.config for DSL2 module specific options
includeConfig 'conf/modules.config'

profiles {
debug {
Expand Down Expand Up @@ -414,6 +416,3 @@ validation {
afterText = validation.help.afterText
}
}

// Load modules.config for DSL2 module specific options
includeConfig 'conf/modules.config'