Commit graph

1036 commits

Author SHA1 Message Date
James Fellows Yates
6986975bc0 Fix output channels allow BLAST table customisation 2022-05-02 11:39:07 +02:00
James Fellows Yates
996385fb0f Remove MD5sumfor DIAMOND DAA file due to occasioanlly variability 2022-05-02 09:36:34 +02:00
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
Harshil Patel
4df985a065
Merge branch 'master' into tool/bamtools-split 2022-04-29 16:38:59 +01:00
James A. Fellows Yates
23c42e9b76
Merge branch 'master' into tool/elprep-merge 2022-04-29 15:11:09 +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
3997d28a77
Merge branch 'master' into subwf/bam_qc 2022-04-29 11:39:18 +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
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
Matthias De Smet
b72ec05d69 drop md5sum from versions.yml 2022-04-29 08:19:42 +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)
* 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
8ad861a645 add fasta index 2022-04-28 13:52:03 +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
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
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
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
Sofia Stamouli
1f77bc130b
Update minimap2/align module (#1537) 2022-04-26 16:32:20 +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
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
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
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
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
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
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