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Prepare release v0.2.0 #112

Merged
merged 76 commits into from
Oct 27, 2023
Merged

Prepare release v0.2.0 #112

merged 76 commits into from
Oct 27, 2023

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kelly-sovacool
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@kelly-sovacool kelly-sovacool commented Oct 12, 2023 •
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Changes

  • Overhaul the README and docs to emphasize usage on biowulf.
    • Also removed placeholders from template/carlisle examples.
  • Refactor the CLI.
  • Various bug fixes.
  • use filter_blacklist subworkflow and other modules from CCBR/nf-modules.

Issues

PR Checklist

(Strikethrough any points that are not applicable.)

  • This comment contains a description of changes with justifications, with any relevant issues linked.
  • [ ] Write unit tests for any new features, bug fixes, or other code changes. testing framework not yet implemented
  • Update docs if there are any API changes.
  • [ ] If a new nextflow process is implemented, define the process container and stub.
  • Update CHANGELOG.md with a short description of any user-facing changes and reference the PR number. Guidelines: https://keepachangelog.com/en/1.1.0/

@kelly-sovacool
refactor: fully separate run & init (copy config) commands
bc618b9
@kelly-sovacool
fix: copy assets on init
184a577
@kelly-sovacool
refactor: run tests from tests/ dir
deacddb 
makes sure champagne init works
@kelly-sovacool
docs: document init command
3c02261
@kelly-sovacool
feat: support local or slurm execution
1d2bb82 
resolves #84
@kelly-sovacool
refactor!: require python 3.10 for itertools.pairwise()
0ebdad3
@kelly-sovacool
feat!: modify -profile depending on hpc if run mode is slurm
b985c0c
@kelly-sovacool
chore: remove nextflow dep
6682a81 
it's a python package that doesn't seem to do anything
@kelly-sovacool
docs: create release guide
d7079fc
@kelly-sovacool
fix: make sure profile gets set when mode=slurm
61966ae
@kelly-sovacool
docs: delete placeholders & start fresh
9aa5772
@kelly-sovacool
style: sort imports alphabetically
c5f6be8
@kelly-sovacool
feat: run local version or from github
be7358e 
resolves #111
@kelly-sovacool
chore: document CLI updates
1def175
@kelly-sovacool
docs: overhaul readme for biowulf
49703c9
@kelly-sovacool
fix(cli): main.nf path must be a flag, not positional
8b949d1 
otherwise it messes with the nextflow args
@kelly-sovacool
fix(cli): correctly pair up nextflow args
4bd9c27
@kelly-sovacool
docs: describe custom genome usage
8155aa6
@kelly-sovacool
docs: minor tweaks
0134e17
@kelly-sovacool
fix: remove baseDir from conf
540734d 
it's deprecated by nextflow
@kelly-sovacool
chore: assets don't need to be executable
0c93f75
@kelly-sovacool
ci: test gha pip paths
d84bb71
@kelly-sovacool
chore: update version for release candidate
b0a0569
@kelly-sovacool
docs: need conda py3.11 to install successfully
474ede0
@kelly-sovacool
fix: typo in config filename
cde5c94
@kelly-sovacool
feat: create install script for ccbrpipeliner module
95e9a0b
@kelly-sovacool
chore: Merge branch 'release-v0.2.0' of https://github.com/CCBR/CHAMP…
2228d54 
…AGNE into release-v0.2.0
@kelly-sovacool
docs: need to export path & pythonpath after installing
6958b4f
@kelly-sovacool
chore: Merge branch 'release-v0.2.0' of https://github.com/CCBR/CHAMP…
ed6cb1f 
…AGNE into release-v0.2.0
@kelly-sovacool
docs: use py311 conda env during installation
94bc9e2
@kelly-sovacool kelly-sovacool self-assigned this Oct 23, 2023
@kelly-sovacool
refactor: use filter_blacklist subworkflow from CCBR/nf-modules
5109519
@kelly-sovacool
chore: Merge branch 'release-v0.2.0' of https://github.com/CCBR/CHAMP…
e1a3652 
…AGNE into release-v0.2.0
@kelly-sovacool
chore: update modules
b973dba
@kelly-sovacool
chore: don't write test dag to assets anymore
d49f3ef
@kelly-sovacool
feat: install samtools/flagstat module
1165fc7
@kelly-sovacool
feat: update CCBR nf-modules
f74e1dd
@kelly-sovacool
fix: udpate filter_blacklist w/ bugfix
891f150
@kelly-sovacool
fix: update samtools/sort to output bai files
9460580
@kelly-sovacool
chore: don't use process.scratch for interactive profile
46ed621
@kelly-sovacool
feat: process to filter by alignment quality
1e34c72
@kelly-sovacool
refactor: use align_genome submodule instead of process
0f10d23
@kelly-sovacool
fix: flagstat now outputs metadata too
dad66d4
@kelly-sovacool
fix: biowulf repo path
7299db6
@kelly-sovacool
test: run QC & input normalization steps
2bfef25
@kelly-sovacool
chore: Merge branch 'release-v0.2.0' of https://github.com/CCBR/CHAMP…
655d711 
…AGNE into release-v0.2.0
@kelly-sovacool
style: tweak plot dimensions
861c233
@kelly-sovacool
style: plot broad & narrow peaks separately
dd5d12b
@kelly-sovacool
fix: don't log-scale the peak width plot axes
ee6049d
@kelly-sovacool
style: widen peak width plots
b5f0214
@kelly-sovacool kelly-sovacool marked this pull request as ready for review October 27, 2023 13:54
@kelly-sovacool kelly-sovacool merged commit a84255f into main Oct 27, 2023
2 checks passed
@kelly-sovacool kelly-sovacool deleted the release-v0.2.0 branch October 27, 2023 13:54
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