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1234 commits

Author SHA1 Message Date
Lauri Mesilaakso
6367c6a1ad
Merge branch 'master' into add_compression_to_bam2fq 2022-05-03 11:41:25 +03:00
nvnieuwk
f85787b19e
Merge branch 'master' into vardict-java 2022-05-03 10:17:04 +02:00
Lauri Mesilaakso
773e6f8e93
Merge branch 'master' into add_compression_to_bam2fq 2022-05-03 11:13:55 +03:00
ljmesi
59d6e6e1dd Add updated md5sums 2022-05-03 09:56:50 +02:00
Ramprasad Neethiraj
6f787aea71
Merge branch 'master' into adding_stub_to_modules 2022-05-03 09:43:16 +02:00
Nicolas Vannieuwkerke
9127f92ddd Merge branch 'vardict-java' of github.com:nvnieuwk/modules into vardict-java 2022-05-03 08:29:50 +02:00
Nicolas Vannieuwkerke
9a10e5beb5 Added the missing inputs in meta.yml + correct notation 2022-05-03 08:29:46 +02:00
Matthias De Smet
1687bfcb85
Merge branch 'master' into add-slimfastq 2022-05-03 08:22:49 +02:00
Matthias De Smet
a67c06af81
Merge branch 'master' into vardict-java 2022-05-03 08:22:19 +02:00
Jill V. Hagey, PhD
23cfb5dd42
Update test.yml 2022-05-02 18:38:48 -04:00
Jill V. Hagey, PhD
db9681029c
Update test.yml 2022-05-02 18:27:01 -04:00
Jill V. Hagey, PhD
7b0d6f96fd
Update test.yml 2022-05-02 18:20:54 -04:00
Jill V. Hagey, PhD
e5d7c80bb5
Update test.yml 2022-05-02 18:13:14 -04:00
Moritz E. Beber
16aa3915e3 feat: add module for slimfastq 2022-05-02 23:16:59 +02:00
Carpanzano
d2e1408b0f updated content for html file in test yml 2022-05-02 18:44:05 +02:00
carpanz
e8b2445878 updated file location in test yml 2022-05-02 18:43:20 +02:00
Carpanzano
1deb789502 synced withName ext.args with process name 2022-05-02 18:39:45 +02:00
Carpanzano
5136ed29c4 removed include and changed process name due to expected folder name before tokenize 2022-05-02 18:38:59 +02:00
Ramprasad Neethiraj
3194729f82
Merge branch 'master' into adding_stub_to_modules 2022-05-02 18:31:55 +02:00
Jill V. Hagey, PhD
99a8711997
Update tests/modules/srst2/srst2/test.yml 
Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com>
 2022-05-02 12:26:56 -04:00
Carpanzano
32b8f3f612 adding contain for html output in test yml 2022-05-02 18:21:26 +02:00
carpanz
6e83196634 updating test yml after removing kronadb from test 2022-05-02 18:20:36 +02:00
Carpanzano
b0a2d36ec1 removing kronadb module from testing ktimporttaxonomy test - NB: temporarily using test db while testdb is added to test-datasets 2022-05-02 18:16:08 +02:00
Sateesh Peri
c56b371713
Merge branch 'master' into srst2/srst2 2022-05-02 12:13:11 -04:00
Simone Carpanzano
3d9c8a6bb1
Merge branch 'master' into firstbranch 2022-05-02 17:43:33 +02:00
Carpanzano
c9ab26ba8e synced name of report as in test config 2022-05-02 17:41:55 +02:00
Carpanzano
76a0e3ef04 updated config kraken report name 2022-05-02 17:40:50 +02:00
jvhagey
cd45dc1550 linting test.yml 2022-05-02 11:38:39 -04:00
jvhagey
24dc2d2113 added tests 2022-05-02 11:30:19 -04:00
Carpanzano
1188264fa2 finished test yml file 2022-05-02 17:25:58 +02:00
carpanz
028dc3cb87 updated test yml file 2022-05-02 17:24:55 +02:00
Carpanzano
3cebcbfc0a remove taxonomy not used in place of db 2022-05-02 17:13:58 +02:00
Carpanzano
2e4c200a26 remove new line between includes 2022-05-02 17:13:20 +02:00
Jasmin F
235944f797
Merge branch 'master' into antismash_db_output 2022-05-02 17:11:51 +02:00
Carpanzano
700d6ab3f1 errore TDOWNLOAD 2022-05-02 16:55:18 +02:00
Carpanzano
80f107515e update nextflow.config withName 2022-05-02 16:22:22 +02:00
Carpanzano
42310cbce2 updated config to reflect names in test workflow 2022-05-02 16:14:38 +02:00
Carpanzano
38d9d81aaf update code 2022-05-02 16:10:57 +02:00
Lucpen
50cc136a78
Update tests/modules/gatk4/mutect2/main.nf 
fix spelling mistake

Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
 2022-05-02 15:14:05 +02:00
JIANHONG OU
b14f30936e
Merge branch 'nf-core:master' into motus_downloaddb 2022-05-02 08:42:09 -04:00
Lucpen
dfabf960dc
Merge branch 'master' into adding_stub_to_modules 2022-05-02 14:20:03 +02:00
JIANHONG OU
3f07761da5 remove the output check for the versions.yml. 2022-05-02 08:19:13 -04:00
Lucpen
da82e06354 fix gatk4_mutect2 test 2022-05-02 14:16:07 +02:00
Lucpen
3a4e415fe2 chores adding dummy files for stubs 2022-05-02 13:30:18 +02:00
James A. Fellows Yates
f1c2f624eb
Update tests/modules/diamond/blastx/main.nf 
Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
 2022-05-02 13:17:22 +02:00
Lucpen
de40c1bf54 chore removing file from test 2022-05-02 13:15:01 +02:00
James Fellows Yates
bd3bfe0817 Add warn of default being used 2022-05-02 12:41:24 +02:00
James Fellows Yates
67b074382e Fix tests 2022-05-02 12:29:00 +02:00
Lucpen
08d5acbeb6 feat added tests for stubs 2022-05-02 11:59:08 +02:00
James Fellows Yates
58e5c6aece Make variables consistent 2022-05-02 11:55:43 +02:00
James Fellows Yates
6986975bc0 Fix output channels allow BLAST table customisation 2022-05-02 11:39:07 +02:00
Matthias De Smet
bf416f2307
Merge branch 'master' into vardict-java 2022-05-02 10:43:47 +02:00
James Fellows Yates
996385fb0f Remove MD5sumfor DIAMOND DAA file due to occasioanlly variability 2022-05-02 09:36:34 +02:00
Ramprasad Neethiraj
9a9f3e97de fix md5sums 2022-05-01 21:51:40 +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
Carpanzano
41fd2d1557 modifiche 2022-04-29 17:52:12 +02:00
Harshil Patel
4df985a065
Merge branch 'master' into tool/bamtools-split 2022-04-29 16:38:59 +01:00
Carpanzano
6bf0a407f6 modifiche nextflow.config 2022-04-29 15:51:27 +02:00
Simone Carpanzano
d9d0eb393b
Update nextflow.config 2022-04-29 15:39:50 +02:00
Carpanzano
20787514d9 modifiche per il test 2022-04-29 15:11:21 +02:00
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
Simone Carpanzano
05e283405c
Update test_data.config 2022-04-29 00:13:01 +02:00
Simone Carpanzano
a6026e6d30
Update test_data.config 2022-04-29 00:08:27 +02:00
Simone Carpanzano
a76be27d9f
Update test_data.config 2022-04-29 00:06:55 +02:00
Simone Carpanzano
f13a0070d0
Update test_data.config 2022-04-29 00:04:49 +02:00
Simone Carpanzano
10a3718ad6
Update test_data.config 
add 'metagenome' in sarscov2
 2022-04-29 00:03:54 +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
Sateesh Peri
f5c4aecde5
Merge branch 'master' into srst2/srst2 2022-04-28 13:49:51 -04:00
Robert A. Petit III
4b6ee6fc14
Merge branch 'master' into rp3-add-shigatyper 2022-04-28 09:51:36 -06:00
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
Nicolas Vannieuwkerke
4b04ca22dd Variable name change for var2vcf conversion arguments 2022-04-28 16:38:49 +02:00
nvnieuwk
a6397fac8f
Merge branch 'master' into vardict-java 2022-04-28 15:34:46 +02:00
Nicolas Vannieuwkerke
bdff37c3d7 Added the statistical tests and conversion to vcf 2022-04-28 15:33:27 +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
nvnieuwk
c9404ed266
Merge branch 'master' into vardict-java 2022-04-28 14:30:19 +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
Matthias De Smet
c7806e7bef
Merge branch 'master' into vardict-java 2022-04-28 14:12:07 +02:00
Nicolas Vannieuwkerke
8c98a78d2a Fixed the issue with the BED file 2022-04-28 14:07:55 +02:00
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
Nicolas Vannieuwkerke
45b4a61a15 Some small updates 2022-04-28 13:31:37 +02:00
Nicolas Vannieuwkerke
9df830f79d Added the .bai and .fai files 2022-04-28 10:23:07 +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
Nicolas Vannieuwkerke
db43095b1a Split the bed file into a seperate input 2022-04-28 09:18:15 +02:00
nvnieuwk
1fd4719e9d
Merge branch 'master' into vardict-java 2022-04-28 09:09:07 +02:00
Matthias De Smet
8303c509fe
Merge branch 'master' into subwf/bam_qc 2022-04-28 08:57:24 +02:00
Jill V. Hagey, PhD
b0c5f9422b
tmp/ to changed to output/ 2022-04-27 20:21:41 -04:00
Jill V. Hagey, PhD
a575b91254
Update test.yml 2022-04-27 19:54:33 -04:00
Jill V. Hagey, PhD
5b6d4fdace
Merge branch 'nf-core:master' into srst2/srst2 2022-04-27 18:19:18 -04:00
jvhagey
839ee59ca1 adding srst2 module 2022-04-27 18:01:28 -04:00
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
Robert A. Petit III
30bd93602f
Merge branch 'master' into rp3-add-shigatyper 2022-04-27 11:37:13 -06:00
Maxime U. Garcia
10ca39a86f
add intervals possibilities to splitncigarreads (#1571) 2022-04-27 16:03:44 +02:00
Matthias De Smet
d9b2c6af1a
Merge branch 'master' into vardict-java 2022-04-27 14:04:05 +02:00
Nicolas Vannieuwkerke
7956d38e61 Fixed the test on nextflow level 2022-04-27 13:18:46 +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
nvnieuwk
dc62de1a78
Merge branch 'master' into vardict-java 2022-04-27 11:17:33 +02:00
Nicolas Vannieuwkerke
024c992ca7 created the module 2022-04-27 11:12:58 +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
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) 
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
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
Sateesh Peri
8f2561c07f
Merge branch 'master' into rp3-add-shigatyper 2022-04-22 09:01:36 -04:00
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
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
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
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) 
* 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