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New flow elprep #212

Merged
merged 26 commits into from
Nov 12, 2024
Merged

New flow elprep #212

merged 26 commits into from
Nov 12, 2024

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nvnieuwk
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@nvnieuwk nvnieuwk commented Nov 4, 2024 •
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This PR contains a new caller elprep/filter and some refactoring to make it easier to test and expand the pipeline in the future

nf-test now also uses the new sharding system and --changed-since HEAD^ to only run tests for changed files

@nvnieuwk
move bam conversion to cram_prepare_samtools_bedtools
99cbaae
@nvnieuwk
separate dbnsp annotation from vardictjava subwf
ebb3630
@nvnieuwk
move filtering to the main wf
6a35da1
@nvnieuwk
move genotyping out of the gatk4 subwf
9350160
@nvnieuwk
add elprep
10fa33c
@nvnieuwk
fix typo
4e970d5
@nvnieuwk
fix some small issues
59623f1
@nvnieuwk
correct channels
fc26fe4
@nvnieuwk
fix dbsnp subwf
660a809
@nvnieuwk
fix dbsnp flow issue
db31f34
@nvnieuwk
fix wrong map + resources
8b72777
@nvnieuwk
update vardict flow
de1f449
@nvnieuwk
small memory fix
3ae299d
@nvnieuwk
update nf-test ci command
23729f7
@nvnieuwk
nf-test ci updates
ef5a811
@nvnieuwk
use sharding and filters on nf-test
5afc3f3
@nvnieuwk
update test name
7d28f4d
@nvnieuwk
fix env issue in ci
9e736b0
@nvnieuwk
fix env issue in ci
2fd1b38
@nvnieuwk
module -> process in ci
f4654f0
@nvnieuwk
update fetch depth in ci
aa015fc
@nvnieuwk
add test for bam_call_elprep
c444fa5
@nvnieuwk
fix some more tests
acf18e8
@nvnieuwk
more test fixes
3faa540
@nvnieuwk
fix elprep/filter test
76a86a2
@nvnieuwk
fix linting + reimplement only_call and only_merge
6eaf981
@nvnieuwk nvnieuwk marked this pull request as ready for review November 5, 2024 14:42
@nvnieuwk nvnieuwk mentioned this pull request Nov 6, 2024
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ToonRosseel
ToonRosseel approved these changes Nov 8, 2024
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LGTM

@nvnieuwk nvnieuwk merged commit 0e7514e into dev Nov 12, 2024
32 checks passed
@nvnieuwk nvnieuwk deleted the new-flow-elprep branch November 12, 2024 08:37
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@ToonRosseel ToonRosseel ToonRosseel approved these changes

@matthdsm matthdsm Awaiting requested review from matthdsm

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@nvnieuwk @ToonRosseel