390 fix threads parameter in medaka (#391)

* Update nextflow.base.config * Update nextflow.ci.config * Update nextflow.dev.config * Update nextflow.hopper.config * Update nextflow.ngp.config * fix medaka threads option
genomic-medicine-sweden · Jan 31, 2025 · 841a067 · 841a067
1 parent 23d3560
commit 841a067
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Showing 6 changed files with 6 additions and 5 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -41,6 +41,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Removed serotypefinder from saureus workflow
 - Fixed jasen running only on the first row/sample in csv
 - Fixed channel problem by changing `Channel.of([])` to `Channel.value([])`
+- Fixed medaka by changing `--threads` to `-t` in all the configs
 
 ### Changed
 

diff --git a/configs/nextflow.base.config b/configs/nextflow.base.config
@@ -260,7 +260,7 @@ process {
 		memory = '32.GB'
 		time=2.h
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/medaka", mode: 'copy', overwrite: true ]
-		ext.args = "--threads 40 -m r941_min_sup_g507"
+		ext.args = "-t 40 -m r941_min_sup_g507"
 	}
 	withName: mlst {
 		container = "${params.containerDir}/mlst.sif"

diff --git a/configs/nextflow.ci.config b/configs/nextflow.ci.config
@@ -239,7 +239,7 @@ process {
 		memory = '32.GB'
 		time=2.h
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/medaka", mode: 'copy', overwrite: true ]
-		ext.args = "--threads 40 -m r941_min_sup_g507"
+		ext.args = "-t 40 -m r941_min_sup_g507"
 	}
 	withName: mlst {
 		container = "${params.containerDir}/mlst.sif"

diff --git a/configs/nextflow.dev.config b/configs/nextflow.dev.config
@@ -262,7 +262,7 @@ process {
 		memory = '32.GB'
 		time=2.h
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/medaka", mode: 'copy', overwrite: true ]
-		ext.args = "--threads 40 -m r941_min_sup_g507"
+		ext.args = "-t 40 -m r941_min_sup_g507"
 	}
 	withName: mlst {
 		container = "https://depot.galaxyproject.org/singularity/mlst:2.23.0--hdfd78af_1"

diff --git a/configs/nextflow.hopper.config b/configs/nextflow.hopper.config
@@ -261,7 +261,7 @@ process {
 		memory = '32.GB'
 		time=2.h
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/medaka", mode: 'copy', overwrite: true ]
-		ext.args = "--threads 40 -m r941_min_sup_g507"
+		ext.args = "-t 40 -m r941_min_sup_g507"
 	}
 	withName: mlst {
 		container = "https://depot.galaxyproject.org/singularity/mlst:2.23.0--hdfd78af_1"

diff --git a/configs/nextflow.ngp.config b/configs/nextflow.ngp.config
@@ -266,7 +266,7 @@ process {
 		memory = '32.GB'
 		time=2.h
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/medaka", mode: 'copy', overwrite: true ]
-		ext.args = "--threads 40 -m r941_min_sup_g507"
+		ext.args = "-t 40 -m r941_min_sup_g507"
 	}
 	withName: mlst {
 		container = "${params.containerDir}/mlst.sif"