sarek test

.gitignore

@@ -1,2 +1,4 @@
 cleanup-volume-claim.sh
 build.sh
+*.tar.gz
+Dockerfile

sarek/nextflow-k8s.config

@@ -0,0 +1,24 @@
+workDir = '/workspace'
+
+process {
+	executor = 'k8s'
+	//container = 'ubuntu:22.04'
+
+	pod = [
+		imagePullPolicy: 'IfNotPresent'
+	]
+}
+
+k8s {
+	namespace = 'trogantk'
+
+	storageClaimName = 'cephfs-trogantk'
+	storageMountPath = '/workspace'
+	launchDir = '/workspace/launch'
+	projectDir = '/workspace/projects'
+	cleanup = true
+
+	pod = [
+		nodeSelector: [usedby: 'trogantk']
+	]
+}

sarek/run-k8s.sh

@@ -0,0 +1,9 @@
+#!/bin/sh
+SIZE=1
+if [ "$#" -eq 1 ]; then
+  SIZE=$1
+fi
+
+cp samplesheet${SIZE}.csv /workspace/launch/samplesheet.csv
+cp *.fastq.gz /workspace/launch/.
+time nextflow run -c nextflow-k8s.config  nf-core/sarek -r 3.9.0 -profile docker --genome GRCm38 --input samplesheet.csv --outdir out --skip_tools multiqc

sarek/run.sh

@@ -1,5 +1,10 @@
 #!/bin/sh
 
-cp samplesheet.csv /workspace/launch/samplesheet.csv
+SIZE=1
+if [ "$#" -eq 1 ]; then
+  SIZE=$1
+fi
+
+cp samplesheet${SIZE}.csv /workspace/launch/samplesheet.csv
 cp *.fastq.gz /workspace/launch/.
-time nextflow run -c nextflow.config  nf-core/sarek -r 3.9.0 -profile docker --genome GRCm38 --input samplesheet.csv --outdir out --skip-tools multiqc
+time nextflow run -c nextflow.config  nf-core/sarek -r 3.9.0 -profile docker --genome GRCm38 --input samplesheet.csv --outdir out --skip_tools multiqc

sarek/samplesheet3.csv

@@ -0,0 +1,4 @@
+patient,sample,lane,fastq_1,fastq_2
+ID1,S1,L001,SRR27016609_1.fastq.gz,SRR27016609_2.fastq.gz
+ID1,S2,L001,SRR27016607_1.fastq.gz,SRR27016607_2.fastq.gz
+ID1,S3,L001,SRR27016605_1.fastq.gz,SRR27016605_2.fastq.gz