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feat: enable gzip output for bedtools wrappers #3642

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Merged
merged 26 commits into from
May 26, 2025
Merged

feat: enable gzip output for bedtools wrappers #3642

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9c5f406
updated for use of gzip
gtuckerkellogg Feb 7, 2025
2e0bfdc
gzip support for bedtools bamtobed and complement (with tests)
gtuckerkellogg Feb 8, 2025
4f493c0
updated test_wrappers and tests for all current bedtools wrappers for…
gtuckerkellogg Feb 8, 2025
e313300
Merge branch 'snakemake:master' into bedtools-gzip-output
gtuckerkellogg Feb 8, 2025
cd57a18
addressed CodeRabbit review
gtuckerkellogg Feb 8, 2025
4c1265b
from gzip to bgzip
gtuckerkellogg Feb 8, 2025
40fe0c9
merged to bgzip
gtuckerkellogg Feb 8, 2025
0665f1a
all bgzip, no gzip
gtuckerkellogg Feb 8, 2025
8056dc6
all bgzip, no gzip
gtuckerkellogg Feb 8, 2025
760a76f
Merge remote-tracking branch 'refs/remotes/origin/bedtools-gzip-outpu…
gtuckerkellogg Feb 8, 2025
d2028aa
Update bio/bedtools/complement/wrapper.py
gtuckerkellogg Feb 8, 2025
bf9a66b
added hstlib dependency for bgzip in environment.yaml across bedtools…
gtuckerkellogg Feb 9, 2025
10eebb0
black check
gtuckerkellogg Feb 18, 2025
7be0d52
removed vscode cruft
gtuckerkellogg Feb 18, 2025
b926c85
Merge branch 'master' into bedtools-gzip-output
gtuckerkellogg Feb 18, 2025
76245e7
nitpicking resolved
gtuckerkellogg Feb 18, 2025
dda0a28
When coderabbit says nitpick, it means nitpick!
gtuckerkellogg Feb 18, 2025
d891935
Update bio/bedtools/bamtobed/wrapper.py
gtuckerkellogg Feb 18, 2025
db85a32
Remove unused import
fgvieira Feb 18, 2025
2c98855
Merge branch 'snakemake:master' into bedtools-gzip-output
gtuckerkellogg Feb 19, 2025
33aaf57
pinned environments
gtuckerkellogg Feb 19, 2025
4e00419
fixed mistakenly compressed bed file
gtuckerkellogg Feb 19, 2025
1599f1c
also for complement
gtuckerkellogg Feb 19, 2025
c23d6e2
Merge branch 'master' into bedtools-gzip-output
fgvieira May 23, 2025
341d84e
Disable tests of bed.gzip
fgvieira May 26, 2025
502fe26
Code refactoring
fgvieira May 26, 2025
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merged to bgzip
  • Loading branch information
@gtuckerkellogg
gtuckerkellogg committed Feb 8, 2025
commit 40fe0c9667a385f9e92974b61b27f575cf1f0f88
1 change: 1 addition & 0 deletions .#test_wrappers.py
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[email protected]:1736749975
5 changes: 5 additions & 0 deletions bio/bedtools/.vscode/settings.json
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{
"cSpell.words": [
"snakemake"
]
}