Update to 0.3.0 - Githubissues

mikewolfe / ChIPseq_pipeline

A general ChIP-seq pipeline to reproducibly process many samples at once.

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Update to 0.3.0 #33

Closed mikewolfe closed 1 year ago

mikewolfe commented 1 year ago

0.3.0 - 2023-07-15

Added

A run_annotations rule to pull an annotation table for each genome specified in the config file
Ability to get relative coordinates out of postprocessing summaries
Spike-in quality control by reporting fragments per contig per sample
Ability to specify window sizes to traveling ratio as well as window A center for fixed traveling ratios
Ability to get raw read counts for a given set of windows and samples

Changes

Fixed traveling ratio which centers the promoter proximal window at the first coordinate of the given region.

Bug fixes

Fixed multiqc config file to report fastqc results both before and after trimming
Fixed issue with quality control where PE fragment size determination failed when sample sheets had both SE and PE samples

Changes

Relaxed size restriction on traveling ratios to be twice the window size. Down from 1000 bp

Bug fixes

Calculation of the center coordinate for traveling ratios was fixed