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Skyline transfer #36

Merged
merged 31 commits into from
Feb 8, 2024
Merged

Skyline transfer #36

merged 31 commits into from
Feb 8, 2024

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rroutsong
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This branch was intended for transfer to skyline hpc, however a few additional updates have been wrapped up in this as well:

  • Skyline HPC testing and verification
  • FastQC bug fix related to lscratch + filesystem bug
  • Bug fixing thanks to @ewalt98 's testing

Ryan Routsong and others added 22 commits February 1, 2024 16:31
fix: align mg assembly rules to expected outputs
725f091
@rroutsong
fix: sample sheet processing and run id searching fixes from bigsky t…
d1d46e1 
…esting
@rroutsong
fix: update resource config for bcl2fastq
74c84e8
@rroutsong
feat: add execution context documentation
27c1e5e
@rroutsong
feat: add execution docs to nav
020d289
@rroutsong
fix: update execution docs for sbatch execution on biowulf
9f8dd83
@rroutsong
fix: temporarily use branch version of profiles
56736e8
@rroutsong
feat: update execution documentation
4d39d40
@rroutsong
fix: update regex for miseq run id compatibility
4c21fd1
@rroutsong
fix: update miseq regex use . instead of \N
1183c31
@rroutsong
fix: don't error if progressbar is not installed
c3d2d20
@rroutsong
fix: process different read indicators in the sample sheet
8e3e736
@rroutsong
fix: clean up requirements
83cbb1d
@rroutsong
fix: update profiles
60095f6
@rroutsong
fix: fix cpu allocation bug, make it only possible to get 2 cpus per …
eaa0b8f 
…task
@rroutsong
fix: close sample sheet endedness bug
5932bd7
@rroutsong
fix: rework resources for demuxing and qc of certain rules
15c6620
@rroutsong
fix: correct overindentation
7985866
@rroutsong
fix: correct bugs with lscratch usage for fastqc rule
7166ad1
@rroutsong
fix: formatting
ad0258a
@rroutsong
fix: update biowulf scheduler interactions for lscratch
bb1ac3b
@rroutsong
feat: switch to main branch on submodule
e6d7ab6
ewalt98
ewalt98 approved these changes Feb 7, 2024
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@ewalt98 ewalt98 left a comment

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I tested the relevant changes, and everything looks good so far.

skchronicles
skchronicles requested changes Feb 8, 2024
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workflow/qc.smk Outdated Show resolved Hide resolved
@rroutsong
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@skchronicles changes sent

skchronicles
skchronicles reviewed Feb 8, 2024
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Thank you for the updates!

@skchronicles skchronicles merged commit a936fd6 into main Feb 8, 2024
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@skchronicles skchronicles skchronicles approved these changes

@ewalt98 ewalt98 ewalt98 approved these changes

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4 participants
@rroutsong @skchronicles @ewalt98 @jlac