From fce99963e3993a528b69b5602823a31b4c22b617 Mon Sep 17 00:00:00 2001
From: Shihab Dider <shihabdider@gmail.com>
Date: Tue, 8 Oct 2024 11:45:15 -0400
Subject: [PATCH] feat: speed up chr21 test

---
 nextflow.config                               | 34 +++++++++++++++++++
 .../chr21_test/chr21_integration_test.sh      |  2 +-
 tests/test_runs/chr21_test/params.json        |  3 +-
 tests/test_runs/nygc.config                   |  2 +-
 4 files changed, 38 insertions(+), 3 deletions(-)

diff --git a/nextflow.config b/nextflow.config
index b6deb5f..2ddb755 100644
--- 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 $HOSTNAME'
diff --git a/tests/test_runs/chr21_test/chr21_integration_test.sh b/tests/test_runs/chr21_test/chr21_integration_test.sh
index f6f5ebb..a4252fd 100644
--- a/tests/test_runs/chr21_test/chr21_integration_test.sh
+++ b/tests/test_runs/chr21_test/chr21_integration_test.sh
@@ -33,7 +33,7 @@ nextflow run "$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
index 90fee22..ccf7554 100644
--- 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
index de17ced..11f4ad5 100644
--- 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"
 }