Commit 02f9348c authored by Thomas Van Parys's avatar Thomas Van Parys
Browse files

Let launch script export working directory (fixes #49)

parent f5e729b6
...@@ -301,9 +301,15 @@ def prompt(species_file): ...@@ -301,9 +301,15 @@ def prompt(species_file):
outputDirEntered = input("Output folder (default: ./output)> ") outputDirEntered = input("Output folder (default: ./output)> ")
if outputDirEntered: if outputDirEntered:
outputDir = outputDirEntered outputDir = outputDirEntered
workDir = os.path.join(os.getcwd(),'work')
workDirEntered = input("Working and cache folder (default: ./work)> ")
if workDirEntered:
workDir = workDirEntered
scriptLines = [] scriptLines = []
scriptLines.append("module load nextflow") scriptLines.append("module load nextflow")
scriptLines.append("export NXF_WORK={}".format(workDir))
scriptLines.append("nextflow run {} --name {} --input {} --output {}".format(main_nf_path, runName, inputDir, outputDir)) scriptLines.append("nextflow run {} --name {} --input {} --output {}".format(main_nf_path, runName, inputDir, outputDir))
with open(launchScript, 'w') as scriptFile: with open(launchScript, 'w') as scriptFile:
......
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