Refer to mosdepth correctly like other tools

Oshlack / STRetch

Method for detecting STR expansions from short-read sequencing data

MIT License

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Refer to mosdepth correctly like other tools #47

Open hdashnow opened 5 years ago

hdashnow commented 5 years ago

Set mosdepth in pipeline_config (via install script) rather than referring to it in pipeline_stages as $STRETCH/tools/bin/mosdepth

wykswr commented 3 years ago

I guess there is a bug in ./STRetch_exome_bam_pipeline.groovy with $STRETCH/tools/bin/mosdepth but not $mosdepth, making it crash when dealing with cram inputs.

hdashnow commented 3 years ago

You're seeing a specific version of mosdepth crash on crams? Which version?