Commit c4df83bc authored by Thomas Van Parys's avatar Thomas Van Parys
Browse files

Add resume option to launch script (#19)

parent e22b9645
...@@ -305,8 +305,18 @@ def prompt(species_file): ...@@ -305,8 +305,18 @@ def prompt(species_file):
scriptLines = [] scriptLines = []
scriptLines.append("#!/bin/bash") scriptLines.append("#!/bin/bash")
scriptLines.append("module load nextflow") scriptLines.append("module load nextflow")
scriptLines.append(
'''
resume=""
if [ "$1" == "--resume" ]
then
resume="-resume"
fi
'''
)
scriptLines.append("export NXF_WORK={}".format(workDir)) 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 {} $resume".format(main_nf_path, runName, inputDir, outputDir))
with open(launchScript, 'w') as scriptFile: with open(launchScript, 'w') as scriptFile:
for line in scriptLines: for line in scriptLines:
......
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