sarek test

sarek/.gitignore

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+*.fastq.gz

sarek/clean.sh

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+#!/bin/sh
+
+rm -rf out work .nextflow .nextflow.log .nextflow.log.* measurements

sarek/nextflow-k8s.config

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+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/nextflow.config

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+plugins {
+	id 'k8s-dvfs@0.1.0'
+}
+
+workDir = '/workspace'
+
+process {
+	executor = 'k8s-dvfs'
+	//container = 'ubuntu:22.04'
+
+	pod = [
+		imagePullPolicy: 'IfNotPresent'
+	]
+}
+
+k8s {
+	namespace = 'trogantk'
+
+	storageClaimName = 'cephfs-trogantk'
+	storageMountPath = '/workspace'
+	launchDir = '/workspace/launch'
+	projectDir = '/workspace/projects'
+	cleanup = true
+
+	imagePullPolicy = 'IfNotPresent'
+	schedulerInterval = '1m'
+	recordTaskRuntimes = false
+	schedulingStrategy = 'DVFS'
+	runtimeComparisonEpsilon = '10s'
+	dvfsSchedulingNumTopRuntimes = 3
+	nodeLabel = 'usedby=trogantk'
+
+	nodeInit {
+		enabled = true
+		image = 'gitea.kleine.eulenhexe.de/kevin/ma/dvfs-agent:0.2.0'
+		command = ['/usr/local/bin/agent']
+		wait = 'Running'
+		cleanup = true
+	}
+	
+}

sarek/run-k8s.sh

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+#!/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

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+#!/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.config  nf-core/sarek -r 3.9.0 -profile docker --genome GRCm38 --input samplesheet.csv --outdir out --skip_tools multiqc

sarek/samplesheet1.csv

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+patient,sample,lane,fastq_1,fastq_2
+ID1,S1,L001,SRR27016609_1.fastq.gz,SRR27016609_2.fastq.gz

sarek/samplesheet3.csv

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+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