Merge pull request #19 from marieke-bijlsma/master

Updated parameters for release

generate_template.sh

@@ -1,6 +1,7 @@
 #!/bin/bash
 
 module load Molgenis-Compute/v16.11.1-Java-1.8.0_74
+module load Imputation/1.0.0
 module list
 
 PROJECT=XX
@@ -9,10 +10,8 @@ RUNID=XX
 TMPDIRECTORY=$(basename $(cd ../../ && pwd ))
 GROUP=$(basename $(cd ../../../ && pwd ))
 
-#TODO change GITHUBDIR in EBROOTMOLGENISMINIMPUTATION
 HOMEDIR=/groups/${GROUP}/${TMPDIRECTORY}/
 WORKDIR=${HOMEDIR}/generatedscripts/${PROJECT}/
-GITHUBDIR=/home/umcg-mbijlsma/github/Imputation/
 INTERMEDIATEDIR=${HOMEDIR}/tmp/${PROJECT}/
 RUNDIR=${HOMEDIR}/projects/${PROJECT}/run${RUNID}/jobs/
 
@@ -32,16 +31,16 @@ then
 fi
 
 
-perl ${GITHUBDIR}/convertParametersGitToMolgenis.pl ${GITHUBDIR}/parameters.csv > \
+perl ${EBROOTIMPUTATION}/convertParametersGitToMolgenis.pl ${EBROOTIMPUTATION}/parameters.csv > \
 ${WORKDIR}/parameters_converted.csv
 
 
-sh $EBROOTMOLGENISMINCOMPUTE/molgenis_compute.sh \
+sh ${EBROOTMOLGENISMINCOMPUTE}/molgenis_compute.sh \
 -p ${WORKDIR}/parameters_converted.csv \
 -p ${WORKDIR}/datasheet.csv \
--p ${GITHUBDIR}/chromosomes.csv \
--p ${GITHUBDIR}/chunks_b37.csv \
--w ${GITHUBDIR}/workflow.csv \
+-p ${EBROOTIMPUTATION}/chromosomes.csv \
+-p ${EBROOTIMPUTATION}/chunks_b37.csv \
+-w ${EBROOTIMPUTATION}/workflow.csv \
 -rundir ${RUNDIR} \
 -b slurm \
 --weave \

parameters.csv

@@ -1,7 +1,6 @@
 ##DEFAULT DIRECTORY PARAMETERS
 gafTmp,/groups/umcg-gaf/tmp04/
 workDir,${gafTmp}/generatedscripts/
-githubDir,/home/umcg-mbijlsma/github/Imputation/
 dataDir,/apps/data/
 tempDir,${gafTmp}/temp
 projectDir,${gafTmp}/projects/${studyData}/${run}/
@@ -45,6 +44,7 @@ outputPerChunk,${intermediateDir}/chr${chrom}_${fromChrPos}-${toChrPos}
 
 
 ##MODULE VERSIONS
+pipelineVersion,Imputation/1.0.0
 plinkVersion,plink/1.9-foss-2015b
 liftOverUcscVersion,liftOverUcsc/20161011
 shapeItVersion,shapeit/v2.r837-static

protocols/CopyToResultsDir.sh

@@ -5,13 +5,13 @@
 #string finalResultsDir
 #list chr
 #string intermediateDir
-#string githubDir
 #string projectDir
 #string studyData
 #string pigzVersion
 
 
 #Load modules and list currently loaded modules
+module load ${pipelineVersion}
 module load ${pigzVersion}
 module list
 
@@ -87,7 +87,7 @@ printf " finished (2/5)\n"
 
 
 #Create new file with chunks, based on parameter file with chunk notation: chr_pos-pos
-awk '{if (NR!=1){print "chr"$1"_"$2"-"$3}}' FS="," ${githubDir}/chunks_b37.csv > ${intermediateDir}/chunks.txt
+awk '{if (NR!=1){print "chr"$1"_"$2"-"$3}}' FS="," ${EBROOTIMPUTATION}/chunks_b37.csv > ${intermediateDir}/chunks.txt
 
 
 #Copy chunk file statistics to results directory