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Prepare release v0.2.0 #112

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merged 76 commits into from
Oct 27, 2023
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bc618b9
refactor: fully separate run & init (copy config) commands
kelly-sovacool Oct 11, 2023
184a577
fix: copy assets on init
kelly-sovacool Oct 11, 2023
deacddb
refactor: run tests from tests/ dir
kelly-sovacool Oct 11, 2023
3c02261
docs: document init command
kelly-sovacool Oct 11, 2023
1d2bb82
feat: support local or slurm execution
kelly-sovacool Oct 11, 2023
0ebdad3
refactor!: require python 3.10 for itertools.pairwise()
kelly-sovacool Oct 11, 2023
b985c0c
feat!: modify -profile depending on hpc if run mode is slurm
kelly-sovacool Oct 11, 2023
6682a81
chore: remove nextflow dep
kelly-sovacool Oct 11, 2023
d7079fc
docs: create release guide
kelly-sovacool Oct 11, 2023
61966ae
fix: make sure profile gets set when mode=slurm
kelly-sovacool Oct 12, 2023
9aa5772
docs: delete placeholders & start fresh
kelly-sovacool Oct 12, 2023
c5f6be8
style: sort imports alphabetically
kelly-sovacool Oct 12, 2023
be7358e
feat: run local version or from github
kelly-sovacool Oct 12, 2023
1def175
chore: document CLI updates
kelly-sovacool Oct 12, 2023
49703c9
docs: overhaul readme for biowulf
kelly-sovacool Oct 12, 2023
8b949d1
fix(cli): main.nf path must be a flag, not positional
kelly-sovacool Oct 12, 2023
4bd9c27
fix(cli): correctly pair up nextflow args
kelly-sovacool Oct 12, 2023
8155aa6
docs: describe custom genome usage
kelly-sovacool Oct 12, 2023
0134e17
docs: minor tweaks
kelly-sovacool Oct 12, 2023
540734d
fix: remove baseDir from conf
kelly-sovacool Oct 12, 2023
0c93f75
chore: assets don't need to be executable
kelly-sovacool Oct 12, 2023
d84bb71
ci: test gha pip paths
kelly-sovacool Oct 12, 2023
b0a0569
chore: update version for release candidate
kelly-sovacool Oct 12, 2023
474ede0
docs: need conda py3.11 to install successfully
kelly-sovacool Oct 12, 2023
cde5c94
fix: typo in config filename
kelly-sovacool Oct 12, 2023
95e9a0b
feat: create install script for ccbrpipeliner module
kelly-sovacool Oct 12, 2023
2228d54
chore: Merge branch 'release-v0.2.0' of https://github.com/CCBR/CHAMP…
kelly-sovacool Oct 12, 2023
6958b4f
docs: need to export path & pythonpath after installing
kelly-sovacool Oct 12, 2023
ed6cb1f
chore: Merge branch 'release-v0.2.0' of https://github.com/CCBR/CHAMP…
kelly-sovacool Oct 12, 2023
94bc9e2
docs: use py311 conda env during installation
kelly-sovacool Oct 12, 2023
a4d9ba0
fix: include assets & alphabetize
kelly-sovacool Oct 12, 2023
29b2abd
fix: need wildcard to add subdirs to package data
kelly-sovacool Oct 13, 2023
0a2c417
fix: biowulf requires min memory
kelly-sovacool Oct 13, 2023
0ea9c81
fix: correct nextflow arg parsing and allow biowulf/frce config with …
kelly-sovacool Oct 13, 2023
a336154
fix: typo
kelly-sovacool Oct 13, 2023
ed243e5
ci: don't use pip -t
kelly-sovacool Oct 13, 2023
e99f71b
chore: bump version to 0.2.0
kelly-sovacool Oct 13, 2023
a76ea34
fix: out of memory for samtools sort
kelly-sovacool Oct 13, 2023
c07dd3c
test: switch mem back to 72 GB
kelly-sovacool Oct 13, 2023
f6da4a0
fix: increase picard markdup resources
kelly-sovacool Oct 14, 2023
c3f4855
fix: make sure scripts are executable for nextflow
kelly-sovacool Oct 16, 2023
21db7cf
refactor: rename install script -- it's biowulf-specific
kelly-sovacool Oct 16, 2023
633180a
fix: don't hide errors
kelly-sovacool Oct 16, 2023
09a08b9
fix: download gem read dists file
kelly-sovacool Oct 17, 2023
f60cd43
fix: nf comment
kelly-sovacool Oct 17, 2023
98085ca
fix: assign process labels for peak callers
kelly-sovacool Oct 18, 2023
5f11030
chore: Merge branch 'release-v0.2.0' of https://github.com/CCBR/CHAMP…
kelly-sovacool Oct 18, 2023
7935fa2
fix: bump maxRetries to 2
kelly-sovacool Oct 19, 2023
e54c49c
fix: increase resources for ppqt
kelly-sovacool Oct 19, 2023
cf8b075
chore: remove nf-core/khmers
kelly-sovacool Oct 19, 2023
8e654b0
fix: update cutadapt module w/ corrected PE behavior
kelly-sovacool Oct 19, 2023
bf561fa
fix: include assets subdirs
kelly-sovacool Oct 19, 2023
446f4ef
fix(cli): recursively include data subdirs
kelly-sovacool Oct 19, 2023
867307f
fix: increase memory for process_higher label
kelly-sovacool Oct 19, 2023
d9dea8a
chore: slurm node doesn't have to be interactive
kelly-sovacool Oct 19, 2023
2b95c0e
fix: effective gsize calculation
kelly-sovacool Oct 19, 2023
e35c0b6
chore: Merge branch 'release-v0.2.0' of https://github.com/CCBR/CHAMP…
kelly-sovacool Oct 19, 2023
5109519
refactor: use filter_blacklist subworkflow from CCBR/nf-modules
kelly-sovacool Oct 23, 2023
e1a3652
chore: Merge branch 'release-v0.2.0' of https://github.com/CCBR/CHAMP…
kelly-sovacool Oct 23, 2023
b973dba
chore: update modules
kelly-sovacool Oct 23, 2023
d49f3ef
chore: don't write test dag to assets anymore
kelly-sovacool Oct 23, 2023
1165fc7
feat: install samtools/flagstat module
kelly-sovacool Oct 24, 2023
f74e1dd
feat: update CCBR nf-modules
kelly-sovacool Oct 24, 2023
891f150
fix: udpate filter_blacklist w/ bugfix
kelly-sovacool Oct 24, 2023
9460580
fix: update samtools/sort to output bai files
kelly-sovacool Oct 24, 2023
46ed621
chore: don't use process.scratch for interactive profile
kelly-sovacool Oct 24, 2023
1e34c72
feat: process to filter by alignment quality
kelly-sovacool Oct 24, 2023
0f10d23
refactor: use align_genome submodule instead of process
kelly-sovacool Oct 24, 2023
dad66d4
fix: flagstat now outputs metadata too
kelly-sovacool Oct 24, 2023
7299db6
fix: biowulf repo path
kelly-sovacool Oct 24, 2023
2bfef25
test: run QC & input normalization steps
kelly-sovacool Oct 24, 2023
655d711
chore: Merge branch 'release-v0.2.0' of https://github.com/CCBR/CHAMP…
kelly-sovacool Oct 24, 2023
861c233
style: tweak plot dimensions
kelly-sovacool Oct 25, 2023
dd5d12b
style: plot broad & narrow peaks separately
kelly-sovacool Oct 25, 2023
ee6049d
fix: don't log-scale the peak width plot axes
kelly-sovacool Oct 26, 2023
b5f0214
style: widen peak width plots
kelly-sovacool Oct 26, 2023
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fix: copy assets on init
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kelly-sovacool committed Oct 11, 2023

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commit 184a5770d88d0ecd38eb1f7889e228195bf53286
2 changes: 1 addition & 1 deletion src/__main__.py
Original file line number Diff line number Diff line change
@@ -71,7 +71,7 @@ def run(**kwargs):
@click.command()
def init(**kwargs):
"""Initialize the working directory by copying the system default config files"""
paths = ("nextflow.config", "conf/")
paths = ("nextflow.config", "conf/", "assets/")
copy_config(paths)