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Fix path strings $STRetch reference #46

Merged
merged 3 commits into from
Jan 8, 2019
Merged

Fix path strings $STRetch reference #46

merged 3 commits into from
Jan 8, 2019

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bw2
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@bw2 bw2 commented Jan 5, 2019

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@hdashnow
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hdashnow commented Jan 8, 2019

Yep, this example setup is certainly out of date. It's also missing:

mosdepth="$STRETCH/tools/bin/mosdepth"
picard="$STRETCH/tools/bin/picard.jar"

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bw2 commented Jan 8, 2019

I think mosdepth is just referenced as $STRETCH/tools/bin/mosdepth in the pipeline

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hdashnow commented Jan 8, 2019

I've put an issue in to remind me to fix mosdepth so it's defined the same way as the others #47

@hdashnow hdashnow merged commit 38aee1f into Oshlack:master Jan 8, 2019
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hdashnow commented Jan 8, 2019

Thanks for the PR @bw2!

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