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Differential splicing analysis. #23

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merged 57 commits into from
Oct 5, 2021
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940be52
Differential splicing analysis.
johanneskoester Apr 9, 2020
e4c9f38
add new sources
johanneskoester Apr 9, 2020
054f6ad
add rules for obtaining reference data.
johanneskoester Apr 9, 2020
6935a18
cache reference data rules
johanneskoester Apr 9, 2020
76e8723
move reference data into resources directory
johanneskoester Apr 9, 2020
c5868c9
refactoring
johanneskoester Apr 9, 2020
da9589e
update reference config
johanneskoester Apr 9, 2020
31e386d
update config schema
johanneskoester Apr 9, 2020
bfcabfd
include refs.smk
johanneskoester Apr 9, 2020
714c59b
add missing env files
johanneskoester Apr 9, 2020
b1a0952
add report captions
johanneskoester Apr 9, 2020
8411fd1
Cleanup pkgs.
johanneskoester Apr 10, 2020
f1966b4
Merge branch 'master' into diffsplice
johanneskoester Apr 24, 2020
0509c11
patch docker daemon data root
johanneskoester Apr 28, 2020
24a31bb
dbg
johanneskoester Apr 28, 2020
a34d2f7
try cleaning up cache
johanneskoester Apr 28, 2020
37ddec6
use latest action with hopefully fixed space issues
johanneskoester Apr 28, 2020
4bb9ade
polish
johanneskoester Apr 28, 2020
d5c26e9
Merge branch 'main' into diffsplice
johanneskoester Sep 20, 2021
1122aff
add missing module
johanneskoester Sep 20, 2021
20ddd76
fixes
johanneskoester Sep 20, 2021
29258a9
fixes
johanneskoester Sep 20, 2021
3f1e379
add missing log files
johanneskoester Sep 20, 2021
c885c94
fmt
johanneskoester Sep 20, 2021
59afbd7
add missing log
johanneskoester Sep 20, 2021
a36cbd5
logs
johanneskoester Sep 20, 2021
1d5783e
add missing output file
johanneskoester Sep 20, 2021
cbd5f9d
fix model usage in init script
johanneskoester Sep 20, 2021
b1275b5
configure base_level
johanneskoester Sep 20, 2021
9619b79
make cutoffs configurable
johanneskoester Sep 21, 2021
9f427ef
schema
johanneskoester Sep 21, 2021
5143e1f
even less stringent thresholds
johanneskoester Sep 21, 2021
dca9c68
manual filtering
johanneskoester Sep 21, 2021
187608d
docs
johanneskoester Sep 21, 2021
7c386d6
add missing input file
johanneskoester Sep 21, 2021
3235b03
dbg
johanneskoester Sep 21, 2021
6adbcbb
adjust filtering
johanneskoester Sep 21, 2021
732cf55
dbg
johanneskoester Sep 21, 2021
2d0bc2b
dbg
johanneskoester Sep 21, 2021
1cc77bb
dbg
johanneskoester Sep 22, 2021
697fa62
dbg
johanneskoester Sep 22, 2021
2e84656
dbg
johanneskoester Sep 22, 2021
7caae45
dbg
johanneskoester Sep 22, 2021
1cc5fd2
dbg
johanneskoester Sep 22, 2021
0dbeec4
update package versions
johanneskoester Sep 22, 2021
fe56e49
fix versions
johanneskoester Sep 24, 2021
996f577
fix versions
johanneskoester Sep 24, 2021
f7663c9
fix
johanneskoester Sep 24, 2021
7471615
add alpha and cutoff
johanneskoester Sep 24, 2021
44255bf
chore: temporarily disable report testing
johanneskoester Sep 28, 2021
74e8dcb
fmt
johanneskoester Sep 29, 2021
fd8d594
convert path to str
johanneskoester Sep 29, 2021
d5cd669
perf: obtain transcript info in a separate rule
johanneskoester Oct 5, 2021
65a75e8
set ensembl release version for transcript info
johanneskoester Oct 5, 2021
9f592f3
chore: import missing files
johanneskoester Oct 5, 2021
80acd3c
refactor: addressed @dlaehnemann's comments
johanneskoester Oct 5, 2021
d59093a
fix deps
johanneskoester Oct 5, 2021
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chore: temporarily disable report testing
  • Loading branch information
johanneskoester committed Sep 28, 2021
commit 44255bf531d7b1f8fd1739c8914b12bcf3296ed5
15 changes: 9 additions & 6 deletions .github/workflows/main.yml
Original file line number Diff line number Diff line change
Expand Up @@ -52,9 +52,12 @@ jobs:
snakefile: workflow/Snakefile
args: "--use-conda --show-failed-logs --cores 2 --conda-cleanup-pkgs cache --all-temp"

- name: Test report
uses: snakemake/snakemake-github-action@v1.22.0
with:
directory: .test
snakefile: workflow/Snakefile
args: "--report report.zip"
# Disable report testing for now since we mark all output files as temporary above.
# TODO: add some kind of test mode to report generation which does not really try to include
# results.
# - name: Test report
# uses: snakemake/snakemake-github-action@v1.22.0
# with:
# directory: .test
# snakefile: workflow/Snakefile
# args: "--report report.zip"