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1288 commits

Author SHA1 Message Date
Carpanzano
9083d3bb3d integrating suggestions from PR comments, including recovery of tests for kronadb and more detailed explanation of input database in yml file 2022-05-05 13:51:41 +02:00
MaxUlysse
40dd662fd2 update ensemblvep and snpeff modules 2022-05-05 12:57:14 +02:00
James A. Fellows Yates
e60c6f9bfd
Merge branch 'master' into firstbranch 2022-05-05 10:57:27 +02:00
Mahesh Binzer-Panchal
58ea709f7f
Merge branch 'master' into busco 2022-05-05 09:34:14 +02:00
ljmesi
888e122f05 Merge branch 'add_compression_to_bam2fq' of https://github.com/Genomic-Medicine-Linkoping/modules into add_compression_to_bam2fq 2022-05-05 08:32:48 +02:00
ljmesi
be8ce6de2a Remove variable md5sum from the tests 2022-05-05 08:32:45 +02:00
James A. Fellows Yates
35b5ba673f
Merge branch 'master' into motus_downloaddb 2022-05-04 20:58:08 +02:00
Lauri Mesilaakso
e757966566
Merge branch 'master' into add_compression_to_bam2fq 2022-05-04 18:41:36 +03:00
Carpanzano
38faf040ec missing change in ext.args config 2022-05-04 16:54:15 +02:00
Nicolas Vannieuwkerke
3c07602443 Added the version.yml 2022-05-04 16:51:09 +02:00
Carpanzano
e7b92a7616 fixing md5sum changes 2022-05-04 16:43:22 +02:00
Simone Carpanzano
162f8edf54
Merge branch 'master' into firstbranch 2022-05-04 16:35:25 +02:00
Carpanzano
6b8ca501ed fixing suggestions from PR 2022-05-04 16:34:52 +02:00
Nicolas Vannieuwkerke
42bdc5471e Changed the pytest location of happy 2022-05-04 15:40:34 +02:00
Nicolas Vannieuwkerke
f875aec46b Split the module into two parts 2022-05-04 15:29:48 +02:00
Mahesh Binzer-Panchal
5986a3efbf
Merge branch 'master' into busco 2022-05-04 15:09:54 +02:00
Nicolas Vannieuwkerke
3c66138672 Linting issue + removed the contains lines 2022-05-04 14:49:17 +02:00
Nicolas Vannieuwkerke
5889d6c923 Another possible fix for the pytest issues 2022-05-04 14:46:15 +02:00
Nicolas Vannieuwkerke
583ea13800 Another try to fix the pytest issues 2022-05-04 14:22:55 +02:00
Nicolas Vannieuwkerke
17dbd2bb82 Linting issue fixed 2022-05-04 14:18:56 +02:00
Nicolas Vannieuwkerke
c1393bf999 Possible fix for the pytest errors? 2022-05-04 14:14:01 +02:00
nvnieuwk
c9808cb97f
Merge branch 'master' into new-module-hap.py 2022-05-04 14:01:02 +02:00
Nicolas Vannieuwkerke
37338ecee3 Finished the module 2022-05-04 14:00:02 +02:00
Mahesh Binzer-Panchal
f65abe1e9a Prettier 2022-05-04 11:54:51 +00:00
Ramprasad Neethiraj
6541e151bc
Merge branch 'master' into feat/update_cnvpytor 2022-05-04 13:54:46 +02:00
Mahesh Binzer-Panchal
73a8df9522 Fix no genes found test and update test.yml 2022-05-04 11:52:42 +00:00
Nicolas Vannieuwkerke
c517ce9b4d Added the module and some simple testing 2022-05-04 13:42:12 +02:00
Mahesh Binzer-Panchal
8df20218bf Add more tests and capture summaries 
Co-authored-by: Jill V. Hagey, PhD <jvhagey@gmail.com>
 2022-05-04 09:22:43 +00:00
Mahesh Binzer-Panchal
3bb0711b06
Merge branch 'master' into busco 2022-05-04 09:15:46 +02:00
Lauri Mesilaakso
530b5ac661
Merge branch 'master' into add_compression_to_bam2fq 2022-05-04 09:53:46 +03:00
Chris Cheshire
79e64cdd1f
Merge branch 'master' into expected_error_fix 2022-05-03 22:21:28 +01:00
Lauri Mesilaakso
12f79c2101
Merge branch 'master' into add_compression_to_bam2fq 2022-05-03 17:03:02 +03:00
ljmesi
a39fa4e003 Fix checksum for one file 2022-05-03 15:47:49 +02:00
Mahesh Binzer-Panchal
636abad8f1
Merge branch 'master' into busco 2022-05-03 15:38:25 +02:00
Nicolas Vannieuwkerke
96d4a31cc1 Moved the BED file to the main tuple 2022-05-03 15:31:05 +02:00
Mahesh Binzer-Panchal
5f4781adaa
Merge branch 'master' into busco 2022-05-03 15:27:10 +02:00
Mahesh Binzer-Panchal
57db28386e Support batch fasta analysis 2022-05-03 13:26:49 +00:00
ljmesi
034352dbbf Merge branch 'add_compression_to_bam2fq' of https://github.com/Genomic-Medicine-Linkoping/modules into add_compression_to_bam2fq 2022-05-03 15:18:12 +02:00
ljmesi
5510ea39fe Test --no-name to solve inconsistent checksums 2022-05-03 15:18:09 +02:00
Ramprasad Neethiraj
26311aba2a fix minor errors 2022-05-03 15:04:37 +02:00
Ramprasad Neethiraj
be085c0173 Merge branch 'master' of https://github.com/nf-core/modules into feat/update_cnvpytor 2022-05-03 14:55:42 +02:00
Ramprasad Neethiraj
19cfb4e951 update meta files 2022-05-03 14:53:56 +02:00
Ramprasad Neethiraj
46e5752b82 update tests 2022-05-03 14:32:45 +02:00
Lauri Mesilaakso
a65e76e3dd
Merge branch 'master' into add_compression_to_bam2fq 2022-05-03 14:30:54 +03:00
Chris Cheshire
6f35537d40
Merge branch 'master' into expected_error_fix 2022-05-03 12:21:51 +01:00
Chris Cheshire
829183ee84
Merge branch 'master' into rp3-add-shigatyper 2022-05-03 12:16:54 +01:00
Chris Cheshire
6015478b72
Merge branch 'master' into add-slimfastq 2022-05-03 12:11:19 +01:00
Chris Cheshire
d7fb969a74
Merge branch 'master' into rp3-add-shigatyper 2022-05-03 12:10:23 +01:00
Chris Cheshire
40e6bd9dc1 bowtie2|fix tags error 2022-05-03 12:07:04 +01:00
Chris Cheshire
0f1ee7e50d bowtie2|test fixes 2022-05-03 12:04:51 +01:00
Chris Cheshire
61f68913fe
Merge branch 'master' into expected_error_fix 2022-05-03 11:49:35 +01:00
Chris Cheshire
768073be63 bowtie2|Added support for large indexes 2022-05-03 11:46:19 +01:00
Mahesh Binzer-Panchal
ddbe6e8f40
Merge branch 'master' into busco 2022-05-03 10:48:03 +02:00
Mahesh Binzer-Panchal
9a72548ee1 Update busco module 2022-05-03 08:42:56 +00:00
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