From 05e4f2edf215e42a827ed862fb361d33afe7e48d Mon Sep 17 00:00:00 2001 From: LilyAnderssonLee Date: Thu, 28 Nov 2024 09:25:12 +0100 Subject: [PATCH 1/2] Move the modules.config line below the base.config line --- CHANGELOG.md | 2 +- nextflow.config | 5 ++--- 2 files changed, 3 insertions(+), 4 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 51c72ff5..72b253e9 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -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` diff --git a/nextflow.config b/nextflow.config index 77739126..f37fa63f 100644 --- a/nextflow.config +++ b/nextflow.config @@ -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 { @@ -414,6 +416,3 @@ validation { afterText = validation.help.afterText } } - -// Load modules.config for DSL2 module specific options -includeConfig 'conf/modules.config' From 2a64aed6362f02a744c63332967aca3bfb1e1db3 Mon Sep 17 00:00:00 2001 From: LilyAnderssonLee Date: Thu, 28 Nov 2024 10:17:22 +0100 Subject: [PATCH 2/2] update configs --- conf/test.config | 26 ++++++++++++++++++++++- conf/test_alternativepreprocessing.config | 15 ++++++++++++- conf/test_bbduk.config | 15 ++++++++++++- conf/test_falco.config | 15 ++++++++++++- conf/test_fastp.config | 15 ++++++++++++- conf/test_krakenuniq.config | 25 ++++++++++++++++++++++ conf/test_malt.config | 14 ++++++++++++ conf/test_motus.config | 14 ++++++++++++ conf/test_nopreprocessing.config | 15 ++++++++++++- conf/test_noprofiling.config | 14 ++++++++++++ conf/test_nothing.config | 15 ++++++++++++- conf/test_prinseqplusplus.config | 15 ++++++++++++- 12 files changed, 190 insertions(+), 8 deletions(-) diff --git a/conf/test.config b/conf/test.config index 51d28553..610a1d01 100644 --- a/conf/test.config +++ b/conf/test.config @@ -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}' + ] } } diff --git a/conf/test_alternativepreprocessing.config b/conf/test_alternativepreprocessing.config index 813a9f83..b67c06e2 100644 --- a/conf/test_alternativepreprocessing.config +++ b/conf/test_alternativepreprocessing.config @@ -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: { "${params.outdir}/nonpareil/" }, + mode: params.publish_dir_mode, + pattern: '*.np{a,c,l,o}' + ] } } diff --git a/conf/test_bbduk.config b/conf/test_bbduk.config index 4de2e195..3dafb0ff 100644 --- a/conf/test_bbduk.config +++ b/conf/test_bbduk.config @@ -49,10 +49,23 @@ params { process { withName: MALT_RUN { + tag = {"${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: { "${params.outdir}/nonpareil/" }, + mode: params.publish_dir_mode, + pattern: '*.np{a,c,l,o}' + ] } } diff --git a/conf/test_falco.config b/conf/test_falco.config index 43f93aed..17e11f37 100644 --- a/conf/test_falco.config +++ b/conf/test_falco.config @@ -49,10 +49,23 @@ params { process { withName: MALT_RUN { + tag = {"${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: { "${params.outdir}/nonpareil/" }, + mode: params.publish_dir_mode, + pattern: '*.np{a,c,l,o}' + ] } } diff --git a/conf/test_fastp.config b/conf/test_fastp.config index 84e0782b..b59af972 100644 --- a/conf/test_fastp.config +++ b/conf/test_fastp.config @@ -51,10 +51,23 @@ params { process { withName: MALT_RUN { + tag = {"${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: { "${params.outdir}/nonpareil/" }, + mode: params.publish_dir_mode, + pattern: '*.np{a,c,l,o}' + ] } } diff --git a/conf/test_krakenuniq.config b/conf/test_krakenuniq.config index 9f1862b4..3fb2791d 100644 --- a/conf/test_krakenuniq.config +++ b/conf/test_krakenuniq.config @@ -61,15 +61,40 @@ params { process { withName: MALT_RUN { + tag = {"${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}' + ] } } diff --git a/conf/test_malt.config b/conf/test_malt.config index 4bb5b44b..9e144d3d 100644 --- a/conf/test_malt.config +++ b/conf/test_malt.config @@ -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: { "${params.outdir}/nonpareil/" }, + mode: params.publish_dir_mode, + pattern: '*.np{a,c,l,o}' + ] } } diff --git a/conf/test_motus.config b/conf/test_motus.config index f51e735c..fe9d3e0a 100644 --- a/conf/test_motus.config +++ b/conf/test_motus.config @@ -57,9 +57,23 @@ params { process { withName: MALT_RUN { + tag = {"${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: { "${params.outdir}/nonpareil/" }, + mode: params.publish_dir_mode, + pattern: '*.np{a,c,l,o}' + ] } } diff --git a/conf/test_nopreprocessing.config b/conf/test_nopreprocessing.config index 537676e3..c31281d8 100644 --- a/conf/test_nopreprocessing.config +++ b/conf/test_nopreprocessing.config @@ -51,10 +51,23 @@ params { process { withName: MALT_RUN { + tag = {"${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: { "${params.outdir}/nonpareil/" }, + mode: params.publish_dir_mode, + pattern: '*.np{a,c,l,o}' + ] } } diff --git a/conf/test_noprofiling.config b/conf/test_noprofiling.config index 39d52115..ea91f489 100644 --- a/conf/test_noprofiling.config +++ b/conf/test_noprofiling.config @@ -50,9 +50,23 @@ params { process { withName: MALT_RUN { + tag = {"${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: { "${params.outdir}/nonpareil/" }, + mode: params.publish_dir_mode, + pattern: '*.np{a,c,l,o}' + ] } } diff --git a/conf/test_nothing.config b/conf/test_nothing.config index 5160093b..5d22558a 100644 --- a/conf/test_nothing.config +++ b/conf/test_nothing.config @@ -49,10 +49,23 @@ params { process { withName: MALT_RUN { + tag = {"${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: { "${params.outdir}/nonpareil/" }, + mode: params.publish_dir_mode, + pattern: '*.np{a,c,l,o}' + ] } } diff --git a/conf/test_prinseqplusplus.config b/conf/test_prinseqplusplus.config index 9f4f4417..6abb95fa 100644 --- a/conf/test_prinseqplusplus.config +++ b/conf/test_prinseqplusplus.config @@ -50,10 +50,23 @@ params { process { withName: MALT_RUN { + tag = {"${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}' + ] } }