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NYU-Molecular-Pathology / NGS580-nf

Target exome sequencing analysis for NYU NGS580 gene panel
GNU General Public License v3.0
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need bash trap for .nextflow.submitted #25

Closed stevekm closed 4 years ago

stevekm commented 4 years ago

Need to update the Makefile submit recipe to use a bash trap to catch kill commands and automatically remove the .nextflow.submitted lock file. Otherwise you have to always remember to delete .nextflow.submitted every time you use make kill which gets annoying

stevekm commented 4 years ago

example code to use for this is here: https://github.com/stevekm/fastq-bed-subset/blob/6f19f4e71c70776970b487bf673f54df6adae0f1/Makefile#L64

stevekm commented 4 years ago

implementing the desired bash trap in a SLURM submission wrapper conflicts with the tee left open by make run, preventing the trap from catching the signal correctly.