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Refer to mosdepth correctly like other tools #47

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hdashnow opened this issue Jan 8, 2019 · 2 comments
Open

Refer to mosdepth correctly like other tools #47

hdashnow opened this issue Jan 8, 2019 · 2 comments
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@hdashnow
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hdashnow commented Jan 8, 2019

Set mosdepth in pipeline_config (via install script) rather than referring to it in pipeline_stages as $STRETCH/tools/bin/mosdepth
@hdashnow hdashnow added the easy label Jan 8, 2019
@hdashnow hdashnow mentioned this issue Jan 8, 2019
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@wykswr
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wykswr commented Mar 15, 2021

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

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