millironx/nf-core_modules
1
0
Fork 0
mirror of https://github.com/MillironX/nf-core_modules.git synced 2024-11-14 05:43:08 +00:00
Code Issues Releases Packages Activity
2103 commits 30 branches 0 tags 142 MiB
Commit graph

2103 commits

This branch
This branch
All branches
Author SHA1 Message Date
Harshil Patel
2134031879
Bump SAMtools version for custom/getchromsizes (#1572) 2022-04-27 19:15:11 +02:00
Maxime U. Garcia
10ca39a86f
add intervals possibilities to splitncigarreads (#1571) 2022-04-27 16:03:44 +02:00
Jasmin F
61e740f79c
Add antismash download DB: missing container folders as output channels (#1567) 
* Add missing container folders as output channels

* Apply suggestions from code review

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update tool name

* Update test output checksum

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-04-27 12:40:04 +02:00
Jasmin F
9108e2e2ec
Update test output checksum 2022-04-27 12:22:05 +02:00
Jasmin F
31547edc1e
Update tool name 2022-04-27 10:14:14 +02:00
Jasmin F
d79433dcac
Apply suggestions from code review 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-04-27 10:08:07 +02:00
James A. Fellows Yates
f03afbd337
Merge branch 'master' into antismash_db_output 2022-04-27 08:30:50 +02:00
Harshil Patel
85ec13ff1f
Add Trimgalore output for unpaired reads (#1568) 
* 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) 
* 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) 
* 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) 
* 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 
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 
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 
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 
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 
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 
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 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2022-04-22 19:34:00 +02:00
Jasmin F
9957689568
Add missing bacteroides_fragilis genome.gbff.gz (#1558) 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-04-22 17:51:18 +02:00
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) 
* 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
Matthias De Smet
7e883da904 Revert "make use of dependent on input array size" 
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) 
* 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) 
* 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