Harshil Patel
85ec13ff1f
Add Trimgalore output for unpaired reads ( #1568 )
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* Add Trimgalore output for unpaired reads
* Use glob instead of outprefix
2022-04-26 19:15:24 +01:00
James A. Fellows Yates
5bf24cdad7
Merge branch 'master' into antismash_db_output
2022-04-26 17:16:28 +02:00
jasmezz
134272c7ee
Add missing container folders as output channels
2022-04-26 17:04:57 +02:00
Sofia Stamouli
1f77bc130b
Update minimap2/align module ( #1537 )
2022-04-26 16:32:20 +02:00
Jose Espinosa-Carrasco
6a46e7cf11
Allow to pass arguments to the phantompeakqualtools script itself ( #1562 )
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* Allow to pass arguments to the script itself
* Place args2 correctly
* Define args2 aaaaarrrrgggg
* Testing locally before commiting is a good practice
* Update modules/phantompeakqualtools/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-04-25 19:07:43 +02:00
Maxime U. Garcia
569e07f0af
add samtools/bamtocram modules ( #1561 )
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* add new samtools/bamtocram module
* fix md5sum
* remove md5sum
* Update modules/samtools/bamtocram/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-04-25 14:32:49 +02:00
Matthias De Smet
978f665c0a
Merge branch 'master' into tool/elprep-merge
2022-04-24 10:08:29 +02:00
Sateesh Peri
378fa5fbb4
new module: GAMMA ( #1532 )
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* initial version of gamma module
* remove trailing whitespace
* prettier fix
* hardcode version number
* Update modules/gamma/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/gamma/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/gamma/meta.yml
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
* update meta and prettier
* add whitespaces
* add fasta output and tests
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-04-23 10:12:06 -04:00
Matthias De Smet
c3f13fdaf6
Merge branch 'master' into tool/bamtools-split
2022-04-22 19:36:18 +02:00
Matthias De Smet
da56a2d509
Update modules/bamtools/split/main.nf
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Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-04-22 19:36:08 +02:00
Matthias De Smet
2d32267fcd
Update modules/bamtools/split/main.nf
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Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-04-22 19:36:01 +02:00
Matthias De Smet
e9c44f3d85
Update tests/modules/bamtools/split/test.yml
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Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-04-22 19:35:34 +02:00
Matthias De Smet
6efb022f69
Update tests/modules/bamtools/split/test.yml
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Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-04-22 19:34:44 +02:00
Matthias De Smet
b73662c8d9
Update tests/modules/bamtools/split/main.nf
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Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-04-22 19:34:32 +02:00
Matthias De Smet
7bcede7474
Update modules/bamtools/split/meta.yml
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Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-04-22 19:34:14 +02:00
Matthias De Smet
2a2ac290c3
Update modules/bamtools/split/meta.yml
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Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-04-22 19:34:00 +02:00
Robert A. Petit III
4e21cb95ca
Merge branch 'master' into rp3-add-shigatyper
2022-04-22 10:26:29 -06:00
Jasmin F
9957689568
Add missing bacteroides_fragilis genome.gbff.gz ( #1558 )
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Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-04-22 17:51:18 +02:00
Robert A. Petit III
a83202e710
Merge branch 'master' into rp3-add-shigatyper
2022-04-22 08:49:50 -06:00
Robert A. Petit III
c2d2399107
Update modules/shigatyper/main.nf
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Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
2022-04-22 08:49:44 -06:00
Jose Espinosa-Carrasco
b3e56c83c6
Remove task.cpus from the command ( #1559 )
2022-04-22 15:29:49 +01:00
Harshil Patel
6d88f2da8c
Rename process from STRINGTIE to STRINGTIE_STRINGTIE ( #1546 )
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* Rename process from STRINGTIE to STRINGTIE_STRINGTIE
* Bump Stringtie version to 2.2.1 and remove empty files in tests
* Fix tests for stringtie/merge
Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>
2022-04-22 15:13:06 +01:00
Harshil Patel
9aadd9a6d3
Replace vanilla Linux Biocontainer with Ubuntu ( #1557 )
2022-04-22 14:50:07 +01:00
CMGG ICT Team
3bcae8e71e
fix testing errors
2022-04-22 15:19:52 +02:00
CMGG ICT Team
b4af3f1475
test fixes
2022-04-22 15:02:41 +02:00
Sateesh Peri
8f2561c07f
Merge branch 'master' into rp3-add-shigatyper
2022-04-22 09:01:36 -04:00
Matthias De Smet
7e883da904
Revert "make use of dependent on input array size"
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This reverts commit 413980e93a
2022-04-22 14:50:50 +02:00
Matthias De Smet
d293cffc6a
update tests
2022-04-22 14:42:43 +02:00
Matthias De Smet
d617a50371
add extra test
2022-04-22 14:39:25 +02:00
Matthias De Smet
413980e93a
make use of dependent on input array size
2022-04-22 14:33:16 +02:00
James A. Fellows Yates
8874f2de4f
Merge branch 'nf-core:master' into master
2022-04-22 14:09:22 +02:00
Matthias De Smet
e37b982bd7
Merge branch 'master' into subwf/bam_qc
2022-04-22 13:38:23 +02:00
CMGG ICT Team
9a2dad935c
update config
2022-04-22 13:13:39 +02:00
Matthias De Smet
a6e7ecb3a3
Merge branch 'master' into tool/bamtools-split
2022-04-22 13:07:16 +02:00
Matthias De Smet
d57024ddc0
Merge branch 'master' into tool/elprep-merge
2022-04-22 13:05:30 +02:00
Matthias De Smet
c17d1a7a7b
fix output glob ( #1552 )
2022-04-22 13:04:41 +02:00
Matthias De Smet
d9348f3714
Merge branch 'master' into tool/bamtools-split
2022-04-22 13:04:16 +02:00
Matthias De Smet
b1749445d7
fix output glob ( #1551 )
2022-04-22 12:50:17 +02:00
Matthias De Smet
fefffb9bb0
fix output glob
2022-04-22 12:36:32 +02:00
Matthias De Smet
20728acde6
Merge branch 'master' into tool/bamtools-split
2022-04-22 11:57:22 +02:00
Matthias De Smet
2f6382168c
update meta.yml
2022-04-22 11:51:54 +02:00
Matthias De Smet
c4072f274c
fix formatting, fix code style
2022-04-22 11:39:22 +02:00
Matthias De Smet
b4d2e374a0
Merge branch 'master' into tool/elprep-merge
2022-04-22 11:35:48 +02:00
CMGG ICT Team
8dad38afc7
fix test.yml
2022-04-22 11:35:14 +02:00
Sofia Stamouli
538dbac98b
Kaiju2table module ( #1545 )
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* Add kaiju2table module
2022-04-22 11:26:30 +02:00
Matthias De Smet
4af5be8de3
Merge branch 'master' into tool/elprep-merge
2022-04-22 11:10:23 +02:00
Matthias De Smet
9e3daae8ef
New module: elprep filter ( #1524 )
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* first commit
* syntax fix
* fix input
* output sam during test for md5sum
* replace md5sum with contains
* add new test data, add extra in/outputs
* cli fixes
* fix outputs
* Update modules/elprep/filter/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/elprep/filter/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/elprep/filter/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* fix suggestions by @jfy133
* Bit more verbose explanation for bool vals
* define variables
* fix prettier
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-04-22 11:08:03 +02:00
Matthias De Smet
a1757897cb
Merge branch 'master' into tool/elprep-merge
2022-04-22 10:20:59 +02:00
Matthias De Smet
90b203d3e9
Tool/elprep split ( #1533 )
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* tool: elprep split
* fixes for testing
* fix tests
* fix test outputs
* create test-yaml
* fix suggestions by @jfy133
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-04-22 10:20:05 +02:00
Matthias De Smet
35231d3949
update picard/collecthsmetrics ( #1542 )
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* update picard/collecthsmetrics
* syntax fixes, bugfixes
* add tests
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
2022-04-22 10:13:57 +02:00
