feat: speed up chr21 test

mskilab-org · Oct 8, 2024 · fce9996 · fce9996
1 parent aa16b06
commit fce9996
Show file tree

Hide file tree

Showing 4 changed files with 38 additions and 3 deletions.
diff --git a/nextflow.config b/nextflow.config
@@ -269,6 +269,40 @@ try {
 // }
 
 profiles {
+    chr21_test {
+        process {
+            withName: 'GRIDSS_GRIDSS' {
+                cpus            = { check_max( 4 * task.attempt, 'cpus' ) }
+                memory          = { check_max( 32.GB * task.attempt, 'memory' ) }
+                time            = { check_max( 2.h  * task.attempt, 'time'    ) }
+            }
+            withName: 'GRIDSS_SOMATIC' {
+                cpus            = { check_max( 2 * task.attempt, 'cpus' ) }
+                memory          = { check_max( 8.GB * task.attempt, 'memory' ) }
+                time            = { check_max( 1.h  * task.attempt, 'time'    ) }
+            }
+            withName: 'SAGE_SOMATIC' {
+                cpus            = { check_max( 20 * task.attempt, 'cpus' ) }
+                memory          = { check_max( 16.GB * task.attempt, 'memory' ) }
+                time            = { check_max( 1.h  * task.attempt, 'time'    ) }
+            }
+            withName: 'SAGE_GERMLINE' {
+                cpus            = { check_max( 8 * task.attempt, 'cpus' ) }
+                memory          = { check_max( 16.GB * task.attempt, 'memory' ) }
+                time            = { check_max( 1.h  * task.attempt, 'time'    ) }
+            }
+            withName: 'JABBA' {
+                cpus            = { check_max( 4 * task.attempt, 'cpus' ) }
+                memory          = { check_max( 16.GB * task.attempt, 'memory' ) }
+                time            = { check_max( 1.h  * task.attempt, 'time'    ) }
+            }
+            withName: 'FUSIONS' {
+                cpus            = { check_max( 4 * task.attempt, 'cpus' ) }
+                memory          = { check_max( 16.GB * task.attempt, 'memory' ) }
+                time            = { check_max( 1.h  * task.attempt, 'time'    ) }
+            }
+        }
+    }
 	debug {
 		dumpHashes             = true
 		process.beforeScript   = 'echo $HOSTNAME'

diff --git a/tests/test_runs/chr21_test/chr21_integration_test.sh b/tests/test_runs/chr21_test/chr21_integration_test.sh
@@ -33,7 +33,7 @@ nextflow run "$pipeline_dir" \
     -c $nygc_config \
     -dump-channels \
     -params-file ./params.json \
-	-profile singularity	\
+	-profile singularity,chr21_test	\
 	-with-report "report_$(date +'%Y%m%d_%H%M%S').html"	\
 	-with-trace	\
 	-resume
diff --git a/tests/test_runs/chr21_test/params.json b/tests/test_runs/chr21_test/params.json
@@ -1,9 +1,10 @@
 {
     "input": "./samplesheet.csv",
+    "mski_base": "/gpfs/commons/home/sdider/DB/nf_casereports",
     "fasta": "/gpfs/commons/home/sdider/DB/GATK/human_g1k_v37_decoy.fasta",
     "fasta_fai": "/gpfs/commons/home/sdider/DB/GATK/human_g1k_v37_decoy.fasta.fai",
     "bwa": "/gpfs/commons/home/sdider/DB/GATK/bwa/",
-    "tools": "hrdetect",
+    "tools": "all",
     "outdir": "./results",
     "pon_dryclean": "/gpfs/commons/home/sdider/Projects/nf-casereports/tests/test_data/chr21_pon.rds",
     "field_dryclean": "reads",

diff --git a/tests/test_runs/nygc.config b/tests/test_runs/nygc.config
@@ -44,5 +44,5 @@ executor {
 
 singularity {
     enabled = true
-    cacheDir = "/gpfs/commons/groups/imielinski_lab/singularity_files/nextflow_singularity_cache"
+    cacheDir = "/gpfs/commons/groups/imielinski_lab/data/pipeline/container_images_cache"
 }