From 229c8c358d95fcb4652cba3f1db1cb9374fb86c1 Mon Sep 17 00:00:00 2001
From: Kevin Trogant <kevin_trog@proton.me>
Date: Wed, 16 Sep 2026 12:43:45 +0200
Subject: [PATCH] corrected sarek run

---
 sarek/run-k8s.sh | 33 +++++++++++++++++++++++++++------
 sarek/run.sh     | 30 +++++++++++++++++++++++++-----
 2 files changed, 52 insertions(+), 11 deletions(-)

diff --git a/sarek/run-k8s.sh b/sarek/run-k8s.sh
index fe4019b..7b61642 100644
--- a/sarek/run-k8s.sh
+++ b/sarek/run-k8s.sh
@@ -1,9 +1,30 @@
-#!/bin/sh
-SIZE=1
-if [ "$#" -eq 1 ]; then
-  SIZE=$1
-fi
+#!/bin/bash
 
+if [ "$#" -ne 2 ]; then
+  echo "Usage: $0 <size: 1 or 3> <logfile-outname>"
+  exit
+fi
+SIZE=$1
+LOGOUT=$2
+
+TESTDATA_ARCHIVE=/root/sarek-testdata.tar.gz
+
+MYDIR=$(pwd)
+
+mkdir -p /workspace/sarek
+mkdir -p /workspace/launch/work
+cp nextflow-k8s.config /workspace/sarek/nextflow-k8s.config
+cp runtimes.csv /workspace/launch/work/runtimes.csv
 cp samplesheet${SIZE}.csv /workspace/launch/samplesheet.csv
-cp *.fastq.gz /workspace/launch/.
+cp samplesheet${SIZE}.csv /workspace/sarek/samplesheet.csv
+
+cd /workspace/launch
+tar xzf ${TESTDATA_ARCHIVE}
+
+cd /workspace/sarek
 time nextflow run -c nextflow-k8s.config  nf-core/sarek -r 3.9.0 -profile docker --genome GRCm38 --input samplesheet.csv --outdir out --skip_tools multiqc
+rm -rf out
+cp .nextflow.log /${LOGOUT}
+
+cd ${MYDIR}
+rm -rf /workspace/*
diff --git a/sarek/run.sh b/sarek/run.sh
index 85c203f..2fe889a 100644
--- a/sarek/run.sh
+++ b/sarek/run.sh
@@ -1,10 +1,30 @@
-#!/bin/sh
+#!/bin/bash
 
-SIZE=1
-if [ "$#" -eq 1 ]; then
-  SIZE=$1
+if [ "$#" -ne 2 ]; then
+  echo "Usage: $0 <size: 1 or 3> <logfile-outname>"
+  exit
 fi
+SIZE=$1
+LOGOUT=$2
 
+TESTDATA_ARCHIVE=/root/sarek-testdata.tar.gz
+
+MYDIR=$(pwd)
+
+mkdir -p /workspace/sarek
+mkdir -p /workspace/launch/work
+cp nextflow.config /workspace/sarek/nextflow.config
+cp runtimes.csv /workspace/launch/work/runtimes.csv
 cp samplesheet${SIZE}.csv /workspace/launch/samplesheet.csv
-cp *.fastq.gz /workspace/launch/.
+cp samplesheet${SIZE}.csv /workspace/sarek/samplesheet.csv
+
+cd /workspace/launch
+tar xzf ${TESTDATA_ARCHIVE}
+
+cd /workspace/sarek
 time nextflow run -c nextflow.config  nf-core/sarek -r 3.9.0 -profile docker --genome GRCm38 --input samplesheet.csv --outdir out --skip_tools multiqc
+rm -rf out
+cp .nextflow.log /${LOGOUT}
+
+cd ${MYDIR}
+rm -rf /workspace/*