Commit graph

2028 commits

Author SHA1 Message Date
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
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
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
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
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
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
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
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
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
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
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
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)
* 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
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
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