millironx/nf-core_modules
1
0
Fork 0
mirror of https://github.com/MillironX/nf-core_modules.git synced 2024-11-11 04:33:10 +00:00
Code Issues Releases Packages Activity
2088 commits 30 branches 0 tags 142 MiB
Commit graph

2088 commits

This branch
This branch
All branches
Author SHA1 Message Date
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) 
* 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
Jasmin F
39258e53d7
Update checksum in test.yml 2022-04-28 17:09:40 +02:00
Jasmin F
c740853874
Antismash db output patch 1 (#3) 
* Update main.nf

* Update meta.yml

* Update test.yml
 2022-04-28 16:42:44 +02:00
Jasmin F
f6526ced41
Merge branch 'nf-core:master' into antismash_db_output 2022-04-28 16:30:30 +02:00
Praveen Raj S
b3e9b88e80
csi output in TABIX (#1579) 
* 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) 
* 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) 
* 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
Matthias De Smet
fdaef46c90
Merge branch 'master' into subwf/bam_qc 2022-04-28 14:00:30 +02:00
Matthias De Smet
4618c542e9 fix metrics output 2022-04-28 13:59:46 +02:00
Matthias De Smet
2fc857955f fix index omission 2022-04-28 13:53:48 +02:00
Matthias De Smet
8ad861a645 add fasta index 2022-04-28 13:52:03 +02:00
Matthias De Smet
55dfe1d8ab fix hsmetrics input 2022-04-28 13:43:59 +02:00
Matthias De Smet
e0a8af8693 fix outputs 2022-04-28 13:42:24 +02:00
Praveen Raj S
68f1c27169
Changed tbi as optional output in GATK4 HaplotypeCaller (#1576) 
* Changed tbi as optional output. HC cannot index a VCF from large chromosomes.

* Apply suggestions from code review

* Update modules/gatk4/haplotypecaller/main.nf

Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
 2022-04-28 13:41:20 +02:00
Matthias De Smet
dee8ec9e91 fix typos 2022-04-28 12:53:17 +02:00
Matthias De Smet
b92efb7abf add nextflow.config 2022-04-28 10:21:47 +02:00
Matthias De Smet
881e9db4bf update tests 2022-04-28 10:19:30 +02:00
Matthias De Smet
3cbf5c63e5
Update subworkflows/nf-core/bam_qc_picard/main.nf 
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
 2022-04-28 10:09:25 +02:00
Matthias De Smet
433aaece46
Update tests/subworkflows/nf-core/bam_qc_picard/main.nf 
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
 2022-04-28 10:05:31 +02:00
Matthias De Smet
8fb8199f31 fix copilot suggestion 2022-04-28 10:05:07 +02:00
Matthias De Smet
2b29ff5883 drop params.options 2022-04-28 10:03:02 +02:00
Matthias De Smet
8303c509fe
Merge branch 'master' into subwf/bam_qc 2022-04-28 08:57:24 +02:00
Harshil Patel
1b5d3f5ac2
Bump STAR version to 2.7.10a for RSEM modules (#1573) 
* Bump STAR version to 2.7.10a for RSEM modules

* Fix tests
 2022-04-27 19:21:26 +01:00
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