Looper/pipestat/issue update#102

Merged

nsheff merged 46 commits into

Mar 6, 2026

Commits on Feb 4, 2026

Commits on Feb 18, 2026

Fix smoothWig bugs. See #100
nsheff
committed
Merge pull request #101 from databio/wig-fix
jpsmith5
authored
update conda environment file
jpsmith5
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addresses #99; if 0 would be present, simply skip that row/gene
jpsmith5
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addresses #90; should capture prealignment information properly now; more testing to follow
jpsmith5
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closes #72; addresses the messaging concerns, but this function is deprecated now anyways so only will come up if we return it to usage
jpsmith5
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addresses #83; updates to looper masked this bug; should now fail the pipeline intentionally to ensure proper handling of protocol
jpsmith5
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addresses #93; can now check for a custom named environment or the activate environment. still need to manually edit the sample_pipeline_interface.yaml conda_env value.
jpsmith5
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fix issues with checking native when conda env is already active and vice versa
jpsmith5
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fix base checks
jpsmith5
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modify requirements
jpsmith5
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add customization for library strandedness; see #96. only current caveat is that it would apply to entire project run, not sample by sample. can add that at later date.
jpsmith5
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update instructions regarding UMI length parameters; closes #95
jpsmith5
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update bulker crate version
jpsmith5
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move cutadapt reporting to a little helper function to clean up multiple specifications; close #38
jpsmith5
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move pipeline name to top level
jpsmith5
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looper needs name as top-level but pipestat needs it in properties
jpsmith5
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fix issues with the cutadapt helper function calls
jpsmith5
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cutsToWigProcess now redirects its wig output to a temp file (_exact.wig / _smooth.wig) via shell redirection rather than piping
jpsmith5
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fix missing R2 reporting metrics
jpsmith5
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Commits on Feb 19, 2026

Commits on Feb 24, 2026

Commits on Feb 25, 2026

Commits on Mar 5, 2026

add bulker crate manifest and bump version to 1.0.12
nsheff
committed

Commits on Mar 6, 2026

update tests, changelog, final last fixes
nsheff
committed