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
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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