Lucpen
6b64f9cb6c
feat added stub to modules
2022-05-02 10:34:14 +02:00
Harshil Patel
76ac37c529
Merge pull request #1592 from jfy133/diamond-update
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Bump DIAMOND modules to 2.0.15
2022-04-29 20:11:26 +01:00
James Fellows Yates
44ed38beb8
Merge branch 'diamond-update' of github.com:jfy133/nf-core-modules into diamond-update
2022-04-29 21:06:09 +02:00
James Fellows Yates
39530b5ca7
Bump DIAMOND version to 2.0.15
2022-04-29 21:05:12 +02:00
Matthias De Smet
a9e8dbbdec
Merge pull request #1535 from matthdsm/tool/bamtools-split
2022-04-29 18:43:44 +02:00
Harshil Patel
4df985a065
Merge branch 'master' into tool/bamtools-split
2022-04-29 16:38:59 +01:00
Edmund Miller
0d8acda00c
Use issue forms
2022-04-29 14:35:29 +00:00
Edmund Miller
a8a4d76a65
chore: Add container version
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Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2022-04-29 14:34:20 +00:00
Edmund Miller
fb02d6e85f
chore: add OS version to bug report
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Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2022-04-29 14:34:20 +00:00
Edmund Miller
8bee7d4748
chore: Add image tag to bug report
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Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2022-04-29 14:34:20 +00:00
Edmund Miller
ef0483586a
chore: Use forms for feature request
2022-04-29 14:34:20 +00:00
Edmund Miller
816803dbe9
chore: Add checkboxes for bug report
2022-04-29 14:34:20 +00:00
Edmund Miller
2da712f6f3
chore: Use forms for new modules
2022-04-29 14:34:20 +00:00
Edmund Miller
cb29ae2187
chore: Use forms for bug report
2022-04-29 14:34:20 +00:00
Matthias De Smet
86484f3361
Merge pull request #1534 from matthdsm/tool/elprep-merge
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Tool/elprep merge
2022-04-29 15:18:45 +02:00
James A. Fellows Yates
23c42e9b76
Merge branch 'master' into tool/elprep-merge
2022-04-29 15:11:09 +02:00
James A. Fellows Yates
fa8edd917f
Merge pull request #1587 from jfy133/diamond-update
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Update DIAMOND/blast* to support all output formats
2022-04-29 15:08:18 +02:00
Matthias De Smet
9d0f03d96a
Update modules/elprep/merge/main.nf
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Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-04-29 15:07:09 +02:00
Matthias De Smet
7de207f93f
Merge branch 'master' into diamond-update
2022-04-29 15:02:54 +02:00
Matthias De Smet
bdbf629d93
Merge branch 'master' into tool/bamtools-split
2022-04-29 14:33:28 +02:00
Matthias De Smet
edadc9d216
Merge branch 'master' into tool/elprep-merge
2022-04-29 14:32:12 +02:00
Matthias De Smet
0ec3dea37f
Merge pull request #1541 from matthdsm/subwf/bam_qc
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New subworkflow: bam_qc_picard
2022-04-29 14:31:38 +02:00
Matthias De Smet
7e391c3a3b
Update subworkflows/nf-core/bam_qc_picard/main.nf
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Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2022-04-29 14:26:06 +02:00
Matthias De Smet
343c0ebe20
Update subworkflows/nf-core/bam_qc_picard/main.nf
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Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2022-04-29 14:26:00 +02:00
Matthias De Smet
20e3767657
Update subworkflows/nf-core/bam_qc_picard/main.nf
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Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2022-04-29 14:24:25 +02:00
Matthias De Smet
71ccf0e207
Update subworkflows/nf-core/bam_qc_picard/main.nf
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Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2022-04-29 14:24:19 +02:00
Matthias De Smet
73600b0339
Update subworkflows/nf-core/bam_qc_picard/main.nf
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Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2022-04-29 14:20:15 +02:00
Matthias De Smet
3997d28a77
Merge branch 'master' into subwf/bam_qc
2022-04-29 11:39:18 +02:00
Matthias De Smet
c55032d10e
Merge pull request #1584 from matthdsm/bump/picard
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bump picard version across the board
2022-04-29 11:38:21 +02:00
Matthias De Smet
771d5a19f1
fix reference arg
2022-04-29 11:12:24 +02:00
Matthias De Smet
20ebb89ff9
update to long args
2022-04-29 10:52:40 +02:00
James A. Fellows Yates
983d61763d
Merge branch 'master' into diamond-update
2022-04-29 10:28:38 +02:00
James Fellows Yates
7df2fae746
Clean up test data
2022-04-29 10:26:38 +02:00
James Fellows Yates
42564565b9
Update diamond/blastx diamond/blastp to support all possible output formats
2022-04-29 10:26:17 +02:00
Matthias De Smet
b2e4342105
fix args in nextflow.config
2022-04-29 10:21:22 +02:00
Matthias De Smet
bda132191d
fix args in nextflow.config
2022-04-29 10:13:39 +02:00
CMGG ICT Team
0e01d703ea
remove version md5sum from fixmateinformation
2022-04-29 10:12:52 +02:00
Matthias De Smet
e263f267a7
Merge branch 'master' into bump/picard
2022-04-29 09:48:15 +02:00
Lauri Mesilaakso
1a5a9e7b40
Fix typo ( #1586 )
2022-04-29 09:37:23 +02:00
Matthias De Smet
ec10f98d55
picard CollectWgsMetrics: update to new cli args ( #1578 )
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* update to new cli args
* remove bam index from tuple, not needed by program
* bump picard version
Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
2022-04-29 09:32:32 +02:00
James A. Fellows Yates
4e73a9e9c5
Merge branch 'nf-core:master' into master
2022-04-29 09:10:07 +02:00
Matthias De Smet
b72ec05d69
drop md5sum from versions.yml
2022-04-29 08:19:42 +02:00
Matthias De Smet
00467ac64a
update command line syntax for all tools
2022-04-29 07:57:11 +02:00
Matthias De Smet
6ca6de91f8
bump picard version across the board
2022-04-29 07:47:24 +02:00
Matthias De Smet
da94b776ef
Merge branch 'master' into subwf/bam_qc
2022-04-28 22:12:48 +02:00
Matthias De Smet
4d913d337d
Merge branch 'master' into tool/bamtools-split
2022-04-28 21:17:46 +02:00
Matthias De Smet
a7ed1477ee
Merge branch 'master' into tool/elprep-merge
2022-04-28 21:14:30 +02:00
Praveen Raj S
b3e9b88e80
csi output in TABIX ( #1579 )
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* Added: csi output to TABIX
* Added: tests for csi
* Fix tiddit/sv (#1580 )
* Fix fasta ref option for TIDDIT_SV
* Add md5sum's to tiddit/sv tests
Co-authored-by: Daniel Cooke <dcooke@well.ox.ac.uk>
* Fix: prettier issues
Co-authored-by: Daniel Cooke <daniel.cooke@invitae.com>
Co-authored-by: Daniel Cooke <dcooke@well.ox.ac.uk>
2022-04-28 14:41:01 +02:00
JIANHONG OU
cdefbec669
add kimporttext module ( #1560 )
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* add kimporttext module
* fix the Prettier error.
* fix the Prettier error.
* fix the test.yml
* fix the test.yml
* Update modules/krona/ktimporttext/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/krona/ktimporttext/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/krona/ktimporttext/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/krona/ktimporttext/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/krona/ktimporttext/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* update the test files;
simplify the main script of krona/ktimporttext.
* update the test file url for krona ktimporttext
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-04-28 08:16:26 -04:00
Daniel Cooke
57cb730e78
Fix tiddit/sv ( #1580 )
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* Fix fasta ref option for TIDDIT_SV
* Add md5sum's to tiddit/sv tests
Co-authored-by: Daniel Cooke <dcooke@well.ox.ac.uk>
2022-04-28 14:06:38 +02:00
