Merge pull request #26 from karinlag/master

Solving issue 25 re work directory

run_track.sh

@@ -1,4 +1,4 @@
-#!/bin/bash -x
+#!/bin/bash
 
 # Wrapper script for running nextflow pipelines more reproducibly
 
@@ -12,14 +12,12 @@ track_script=$1
 template=$2
 profile=$3
 out_directory=$4
+workdir=${5:-$USERWORK/bifrost_work}
 
 mkdir -p ${out_directory}/config_files
 git --git-dir ${script_directory}/.git branch -v |grep "\*" | awk '{print $2, $3}' > ${out_directory}/config_files/pipeline_version.log
 cp ${script_directory}/${track_script} ${out_directory}/config_files
 cp ${template} ${out_directory}/config_files
-cp ${script_directory}/conf/${profile}.config ${out_directory}/config_files
 
-nextflow -c ${template} run -resume ${script_directory}/${track_script} -profile ${profile} --out_dir=${out_directory}
-# spades sometimes gets weird permissions. Doing this to help removal
-chmod -R 755 work 2> /dev/null
-chmod -R -x+X work 2> /dev/null
+echo "TEMPORARY WORKING DIRECTORY IS ${workdir}"
+nextflow -c ${template} run -resume ${script_directory}/${track_script} -profile ${profile} --out_dir=${out_directory} -work-dir ${workdir}