Update ska resources in configs

genomic-medicine-sweden · Sep 25, 2024 · 7ee2df2 · 7ee2df2
1 parent 41e6b44
commit 7ee2df2
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Showing 5 changed files with 10 additions and 10 deletions.
diff --git a/configs/nextflow.base.config b/configs/nextflow.base.config
@@ -259,10 +259,10 @@ process {
 	}
 	withName: ska_build {
 		container = "${params.containerDir}/ska2.sif"
-		cpus = 8
+		cpus = 2
 		memory = '10 GB'
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/ska", mode: 'copy', overwrite: true ]
-		ext.args = "-k 31 --threads 8"
+		ext.args = "-k 31 --threads 1"
 	}
 	withName: skesa {
 		container = "${params.containerDir}/skesa.sif"

diff --git a/configs/nextflow.ci.config b/configs/nextflow.ci.config
@@ -231,10 +231,10 @@ process {
 	}
 	withName: ska_build {
 		container = "${params.containerDir}/ska2.sif"
-		cpus = 4
+		cpus = 2
 		memory = '10 GB'
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/ska", mode: 'copy', overwrite: true ]
-		ext.args = "-k 31 --threads 4"
+		ext.args = "-k 31 --threads 1"
 	}
 	withName: skesa {
 		container = "${params.containerDir}/skesa.sif"

diff --git a/configs/nextflow.dev.config b/configs/nextflow.dev.config
@@ -246,10 +246,10 @@ process {
 	}
 	withName: ska_build {
 		container = "https://depot.galaxyproject.org/singularity/ska2:0.3.10--h4349ce8_0"
-		cpus = 8
+		cpus = 2
 		memory = '10 GB'
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/ska", mode: 'copy', overwrite: true ]
-		ext.args = "-k 31 --threads 8"
+		ext.args = "-k 31 --threads 1"
 	}
 	withName: skesa {
 		container = "https://depot.galaxyproject.org/singularity/skesa:2.4.0--he1c1bb9_0"

diff --git a/configs/nextflow.hopper.config b/configs/nextflow.hopper.config
@@ -261,10 +261,10 @@ process {
 	}
 	withName: ska_build {
 		container = "https://depot.galaxyproject.org/singularity/ska2:0.3.10--h4349ce8_0"
-		cpus = 8
+		cpus = 2
 		memory = '10 GB'
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/ska", mode: 'copy', overwrite: true ]
-		ext.args = "-k 31 --threads 8"
+		ext.args = "-k 31 --threads 1"
 	}
 	withName: skesa {
 		container = "https://depot.galaxyproject.org/singularity/skesa:2.4.0--he1c1bb9_0"

diff --git a/configs/nextflow.ngp.config b/configs/nextflow.ngp.config
@@ -265,10 +265,10 @@ process {
 	}
 	withName: ska_build {
 		container = "${params.containerDir}/ska2.sif"
-		cpus = params.cpus_medium
+		cpus = params.cpus_small
 		memory = params.mem_small
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/ska", mode: 'copy', overwrite: true ]
-		ext.args = "-k 31 --threads 8"
+		ext.args = "-k 31 --threads 1"
 	}
 	withName: skesa {
 		container = "${params.containerDir}/skesa.sif"