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Release v2.1.1 #83

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May 6, 2024
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6ef61ef
tweak usage.md
allaway Oct 13, 2023
539f54b
Update usage.md
allaway Oct 13, 2023
dac1e31
Update usage.md
allaway Oct 13, 2023
f7be719
consistency of colnames
allaway Oct 13, 2023
9bf7b9a
[automated] Fix linting with Prettier
nf-core-bot Oct 13, 2023
b4c15ee
Merge pull request #68 from allaway/dev
FriederikeHanssen Oct 13, 2023
e5fc18d
Template update for nf-core/tools version 2.11
nf-core-bot Dec 19, 2023
c4cf474
Template update for nf-core/tools version 2.11.1
nf-core-bot Dec 20, 2023
5400508
Template update for nf-core/tools version 2.12
nf-core-bot Jan 29, 2024
09ab01e
update samtools
asp8200 Feb 13, 2024
7fd7f8d
update tests
asp8200 Feb 13, 2024
3dd5b17
Merge branch 'dev' into nf-core-template-merge-2.12
maxulysse Feb 13, 2024
4d695ce
fix nf-core lint
maxulysse Feb 13, 2024
1543f81
Merge pull request #73 from nf-core/nf-core-template-merge-2.12
maxulysse Feb 13, 2024
abf3f94
Merge branch 'nf-core:master' into update_samtools
asp8200 Feb 13, 2024
0695ecb
Adding fasta_fai input-channel in call to SAMTOOLS_STATS
asp8200 Feb 13, 2024
f102b4e
Handling input-channels of tuples including meta
asp8200 Feb 13, 2024
8d238d5
removing docker.userEmulation from nextflow.config
asp8200 Feb 13, 2024
3122b17
Merge pull request #74 from asp8200/update_samtools
maxulysse Feb 14, 2024
5492540
Template update for nf-core/tools version 2.13
nf-core-bot Feb 20, 2024
6a88686
update all modules
asp8200 Feb 20, 2024
7547723
tests and environment.yml for cat/fastq
asp8200 Feb 20, 2024
8103265
Fixing #22
asp8200 Feb 21, 2024
254d231
Merging dev-branch into template
asp8200 Feb 21, 2024
b741444
Template update for nf-core/tools version 2.13.1
nf-core-bot Feb 29, 2024
c1a9383
Merge pull request #78 from asp8200/nf-core-template-merge-2.13_resol…
maxulysse Mar 7, 2024
b559a1c
Merge branch 'dev' into nf-core-template-merge-2.13.1
maxulysse Mar 7, 2024
7915a0d
Update nextflow.config
maxulysse Mar 7, 2024
f6c5b10
Merge pull request #80 from nf-core/nf-core-template-merge-2.13.1
maxulysse Mar 7, 2024
35af2c4
Merge branch 'dev' into fix_22
asp8200 Mar 11, 2024
767a274
Update changelog
asp8200 Mar 11, 2024
0c02877
Merge pull request #77 from asp8200/fix_22
maxulysse Mar 11, 2024
61b4b66
merge dev and resolve conflicts
asp8200 Mar 11, 2024
798099c
resolve conflicts
asp8200 Mar 11, 2024
721f673
Update changelog
asp8200 Mar 11, 2024
cc7ad45
Merge pull request #76 from asp8200/updating_all_modules
maxulysse Mar 11, 2024
adaefc4
Add fct getGenomeAttribute to main.nf
asp8200 Mar 12, 2024
f742f96
Removing redundant definition of getGenomeAttribute
asp8200 Mar 12, 2024
5608a1e
Update changelog
asp8200 Mar 12, 2024
b6bcae3
Merge pull request #81 from asp8200/fix_getGenomeAttribute
maxulysse Mar 13, 2024
baebdeb
Update changelog for release v2.1.1
asp8200 Mar 13, 2024
851a626
Ran nf-core bump-version
asp8200 Mar 13, 2024
008854c
Merge pull request #82 from nf-core/update_changelog
asp8200 Mar 13, 2024
54a8e8a
Removing option stub from CI-test of download
asp8200 Mar 13, 2024
98ce868
Updating changelog
asp8200 Mar 13, 2024
795889b
update changelog
asp8200 Mar 13, 2024
e96b009
Merge pull request #84 from nf-core/fix_download_test
asp8200 Mar 13, 2024
2aef0e2
impot fasta_fai
asp8200 Mar 15, 2024
bd05f59
remove redundant definition of fasta_fai
asp8200 Mar 15, 2024
7a5ee93
Remove comment
asp8200 Mar 15, 2024
32487a8
Revert to former msg concerning tests
asp8200 Mar 15, 2024
db5efc6
Merge pull request #85 from asp8200/import_fasta_fai
asp8200 Apr 30, 2024
f071dfe
Update main.nf
maxulysse May 6, 2024
bf98197
feat(subworkflow): update utils_nfcore_pipeline
maxulysse May 6, 2024
49e9b0a
Merge pull request #88 from maxulysse/utils_nfcore_pipeline
maxulysse May 6, 2024
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update samtools
  • Loading branch information
asp8200 committed Feb 13, 2024
commit 09ab01e8fb4e969478880e77c9e1b321c2e61e49
16 changes: 8 additions & 8 deletions modules.json
Original file line number Diff line number Diff line change
Expand Up @@ -27,42 +27,42 @@
},
"samtools/collatefastq": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62",
"installed_by": ["modules"]
},
"samtools/faidx": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62",
"installed_by": ["modules"]
},
"samtools/flagstat": {
"branch": "master",
"git_sha": "570ec5bcfe19c49e16c9ca35a7a116563af6cc1c",
"git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62",
"installed_by": ["modules"]
},
"samtools/idxstats": {
"branch": "master",
"git_sha": "e662ab16e0c11f1e62983e21de9871f59371a639",
"git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62",
"installed_by": ["modules"]
},
"samtools/index": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62",
"installed_by": ["modules"]
},
"samtools/merge": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62",
"installed_by": ["modules"]
},
"samtools/stats": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62",
"installed_by": ["modules"]
},
"samtools/view": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62",
"installed_by": ["modules"]
}
}
Expand Down
6 changes: 3 additions & 3 deletions modules/nf-core/samtools/collatefastq/main.nf

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

8 changes: 4 additions & 4 deletions modules/nf-core/samtools/collatefastq/meta.yml

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

22 changes: 14 additions & 8 deletions modules/nf-core/samtools/faidx/main.nf

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

18 changes: 16 additions & 2 deletions modules/nf-core/samtools/faidx/meta.yml

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

6 changes: 3 additions & 3 deletions modules/nf-core/samtools/flagstat/main.nf

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

2 changes: 2 additions & 0 deletions modules/nf-core/samtools/flagstat/meta.yml

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

6 changes: 3 additions & 3 deletions modules/nf-core/samtools/idxstats/main.nf

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

2 changes: 2 additions & 0 deletions modules/nf-core/samtools/idxstats/meta.yml

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

6 changes: 3 additions & 3 deletions modules/nf-core/samtools/index/main.nf

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

4 changes: 4 additions & 0 deletions modules/nf-core/samtools/index/meta.yml

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

15 changes: 10 additions & 5 deletions modules/nf-core/samtools/merge/main.nf

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

29 changes: 25 additions & 4 deletions modules/nf-core/samtools/merge/meta.yml

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

8 changes: 4 additions & 4 deletions modules/nf-core/samtools/stats/main.nf

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

14 changes: 12 additions & 2 deletions modules/nf-core/samtools/stats/meta.yml

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

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