Merge branch 'master' of https://github.com/elixir-no-nels/Selma

Author: oskarvid

scripts/RunOnNode.sbatch

@@ -1,7 +1,7 @@
 #!/bin/bash
 #
 #SBATCH --job-name=Selma
-#SBATCH --account=p172
+#SBATCH --account=p11
 #SBATCH --time=00-25:00:00
 #SBATCH --mem-per-cpu=3750
 #SBATCH --cpus-per-task=16

scripts/start-workflow.sh

@@ -270,7 +270,7 @@ while true; do
 	fi
 
 	# Run squeue, store the current job state code and use it to give information to the user as well as act according to the status
-	STATUS=$(squeue -h -t all -j $SLURMID -o %t 2>&1)
+	STATUS=$(squeue -h -t all -j $SLURMID -o %t 2>&1) || true
 
 	# Begin checking the $STATUS variable by checking if the job has been canceled
 	if [[ $STATUS == CA ]]; then

settings/settings.conf

@@ -2,20 +2,25 @@
 
 #set -vo xtrace
 
+source scripts/functions.sh
 # Set the path to the directory containing the hg38 and b37 directories
-REFERENCES=/cluster/projects/p172
-
-if [[ ! -d ${REFERENCES%/}/hg38 || ! -d ${REFERENCES%/}/b37 ]]; then
-	echo "Neither the hg38 nor the b37 reference file directories can be found, make sure that the path ($REFERENCES) is correct and that at least one of the directories have been transferred there"
-	echo "You can use the ./utilities/Selma-setup.sh script to transfer one or both of the supported reference file directories"
+REFERENCES=/cluster/projects/p11/oskar
+
+if [[ -d ${REFERENCES%/}/hg38 ]]; then
+	true
+elif [[ -d ${REFERENCES%/}/b37 ]]; then
+	true
+else
+	err "Neither the hg38 nor the b37 reference file directories can be found, make sure that the path ($REFERENCES) is correct and that at least one of the directories have been transferred there"
+	inf "You can use the ./utilities/Selma-setup.sh script to transfer one or both of the supported reference file directories"
 	exit 1
 fi
 
 # Set the intermediary file storage location
-STAGINGDIR=/cluster/projects/p172/oskar/selma-staging
+STAGINGDIR=/cluster/projects/p11/oskar/selma-staging
 
 if [[ ! -d $STAGINGDIR ]]; then
-	echo "$STAGINGDIR does not exist, your need to create it with 'mkdir /and/the/path/to/your/stagingdir'"
+	err "$STAGINGDIR does not exist, your need to create it with 'mkdir /and/the/path/to/your/stagingdir'"
 	exit 1
 fi
 

utilities/Selma-setup.sh

@@ -95,6 +95,6 @@ fi
 if [[ $SDEST == false ]]; then
         :
 elif [[ $SDEST == "${s%/}" ]]; then
-        rprog /tsd/shared/bioinformatics/workflows/Selma/ $SDEST/Selma
+        rprog --exclude=.git /tsd/shared/bioinformatics/workflows/Selma/ $SDEST/Selma
 	rprog /tsd/shared/bioinformatics/containers/singularity/snakemake-germline-tools.simg $SDEST/Selma/singularity
 fi

workspace/samples.tsv

@@ -1,2 +1,2 @@
 flowcell	sample	library	lane	R1	R2
-FlowCellX	SAMPLE1	libZ	L001	Sample1.R1.fastq.gz	Sample1.R2.fastq.gz
+FlowCellX	test1	libZ	L001	Sample1.R1.fastq.gz	Sample1.R2.fastq.gz