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chore: develop to master #387

Merged
merged 55 commits into from
Jan 26, 2024
Merged

chore: develop to master #387

merged 55 commits into from
Jan 26, 2024

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jonca79
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@jonca79 jonca79 commented Jan 19, 2024

This PR:

(If this is a release PR, no need to add following. Leave this part empty)
(Use the following lines to create a PR text body. Make sure to remove all non-relevant one after you're done)
(Repeat each field as many times as necessary)

Added: for new features.
Changed: for changes in existing functionality.
Deprecated: for soon-to-be removed features.
Removed: for now removed features.
Fixed: for any bug fixes.
Security: in case of vulnerabilities.

Review and tests:

  • Tests pass
  • If you've fixed a bug or added code that should be tested, add tests!
  • Code review
  • CHANGELOG.md is updated
  • New code is executed and covered by tests, and test approve

jonca79 and others added 30 commits November 29, 2023 11:20
@jonca79
feat: new outputfile structure based on sample
c08bb4a
@jonca79
feat: add amino acid change to coverage_and_mutations
a66f501
@jonca79
fix: bugfix
2dbc810
@jonca79
feat: updated hydra-genetics version
b7eadaa
@jonca79
fix: corrected input variables for hotspot_report.smk
6758fa4
@jonca79
fix: corrected input variables for hotspot_report.py
076f5fd
@jonca79
fix: corrected input file for hotspot_report.smk
8ce6512
@jonca79
feat: update to latest common container
eef00aa
@jonca79
fix: remove unused time consuming step in fusioncatcher
635a40b
@jonca79
fix: remove newline after purity in cnvkit_call command
b820ab5
@jonca79
fix: update hydra-genetics to v1.10.1
be2682d
@jonca79
fix: input file bugfix
bfa94a6
@jonca79
fix: updated to bugfixed common container
1449abd
@jonca79
feat: decrease germline support needed to improve cnv visualization o…
c6cd922 
…f deletions
@jonca79
feat: decrease support needed for germline SNVs
efb2827
@jonca79
feat: restructured rna fusion report for improved interpretation
373021c
@jonca79
fix: bugfixes
7fcd240
@jonca79
fix: bugfix
e9f2511
@jonca79
fix: reverse sorting and add chr to fusioncatcher
794f8f7
@jonca79
fix: remove extra header columns
6bb5d42
@jonca79
fix: housekeeping dict
7105a88
@jonca79
feat: added dedup coverage
01046e6
@jonca79
test: pycodestyle
0a4e6b5
@jonca79
test: fix breaking pulp version
969f6d7
@jonca79
test: Update requirements.txt
4634f47
@jonca79
fix: changed sorting and bugfixes
355d99e
@jonca79
feat: added umi vcf filters
dd1cbe2
@jonca79
fix: pulp version
f37c08a
@jonca79
Merge pull request #382 from genomic-medicine-sweden/speed_up_fusionc…
e5a5a66 
…atcher

fix: remove unused time consuming step in fusioncatcher
@jonca79
Merge pull request #383 from genomic-medicine-sweden/rm_purity_newline
2b8b156 
fix: remove newline after purity in cnvkit_call command
@jonca79 jonca79 requested a review from Smeds as a code owner January 19, 2024 09:02
jonca79 and others added 17 commits January 19, 2024 10:09
@jonca79
fix: corrected results path for soft-filtered umi vcf
a8ed44c
@jonca79
Merge pull request #381 from genomic-medicine-sweden/fix_coverage_and…
2acb887 
…_mutations

feat: add amino acid change to coverage_and_mutations
@jonca79
Merge pull request #388 from genomic-medicine-sweden/fix_umi_output
30a6901 
fix: corrected results path for soft-filtered umi vcf
@jonca79
fix: remove extra sample folder in output
39fefd8
@jonca79
Merge pull request #390 from genomic-medicine-sweden/output_folder
dec6f17 
fix: remove extra sample folder in output
@maehler
feat: update reports module to 0.3.1 (#389)
9346b03
@jonca79
fix: added missing double mutations to report
ed1a526
@jonca79
Merge pull request #392 from genomic-medicine-sweden/missing_double_m…
d282c9f 
…utations

fix: added missing double mutations to report
@jonca79
feat: update Jenkins main test
5b30a35
@jonca79
fix: update jenkins start scripts
8cdaf1f
@jonca79
fix: update profile with mounted home
b3d56e2
@jonca79
fix: update profile with mounted home
1947e3a
@jonca79
fix: update profile with mounted home
0b1be40
@jonca79
fix: update profile with mounted home
7665c8b
@jonca79
fix: updated jenkins output for develop
887584b
@jonca79
fix: corrected filepath for rna in develop
85abf47
@jonca79
fix: removed spaces in jenkins test develop
05eb8ef
@jonca79 jonca79 merged commit c959b25 into master Jan 26, 2024
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3 participants
@jonca79 @Smeds @maehler