Mahesh Binzer-Panchal
83a266ea70
Merge branch 'master' into meryl_unionsum
2022-05-09 16:16:08 +02:00
FriederikeHanssen
adc4ff868c
Merge branch 'master' into samtools_convert
2022-05-09 16:15:24 +02:00
nvnieuwk
4b8bd9ebf9
Merge branch 'master' into new-module-rtg/vcfeval
2022-05-09 15:51:31 +02:00
Mahesh Binzer-Panchal
da93beaf60
Update pytests
2022-05-09 13:50:49 +00:00
Nicolas Vannieuwkerke
f6262b4a10
fixed some issues
2022-05-09 15:47:07 +02:00
Mahesh Binzer-Panchal
8d86988632
Merge branch 'master' into meryl/histogram
2022-05-09 15:39:32 +02:00
nvnieuwk
d6dd4c2e2d
Update tests/modules/rtgtools/vcfeval/test.yml
...
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2022-05-09 15:35:16 +02:00
Rike
ef5f145342
Generalize Bam2Cram do either conversion
2022-05-09 15:22:54 +02:00
Annick Renevey
ac3034696b
update md5sum
2022-05-09 15:19:16 +02:00
Mahesh Binzer-Panchal
0c567f5474
Merge branch 'master' into meryl_unionsum
2022-05-09 15:03:27 +02:00
Mahesh Binzer-Panchal
f0f414d519
Update pytests
2022-05-09 13:00:10 +00:00
Annick Renevey
eed874ace7
update arriba tests
2022-05-09 14:55:59 +02:00
Mahesh Binzer-Panchal
6621768550
Update pytest outputs
2022-05-09 12:54:31 +00:00
Jasmin F
453d5b66a4
Add Bacteroides fragilis GFF file
2022-05-09 14:46:18 +02:00
Mahesh Binzer-Panchal
ce97c87b5d
Merge branch 'master' into meryl_unionsum
2022-05-09 13:51:55 +02:00
Mahesh Binzer-Panchal
7a5d5f5766
Merge branch 'master' into kat_hist
2022-05-09 13:18:18 +02:00
Mahesh Binzer-Panchal
a43bc940d6
Add suggestions from code review
2022-05-09 11:15:14 +00:00
Mahesh Binzer-Panchal
129f57ccd9
Add meryl histogram
2022-05-09 08:50:28 +00:00
Mahesh Binzer-Panchal
ad4f8389cb
Add meryl unionsum
2022-05-09 08:33:21 +00:00
Mahesh Binzer-Panchal
32b0fdc9d9
Merge branch 'master' into meryl_count
2022-05-09 10:05:28 +02:00
Mahesh Binzer-Panchal
9ebeb6a702
Update test
2022-05-09 08:05:07 +00:00
Matthias De Smet
3dc18365f6
Merge branch 'master' into new-module-rtg/vcfeval
2022-05-09 10:04:29 +02:00
Mahesh Binzer-Panchal
4591ea2205
atomize
2022-05-09 07:58:58 +00:00
Matthias De Smet
2b91985aa0
Merge branch 'master' into new-module-rtg/vcfeval
2022-05-09 09:43:48 +02:00
Nicolas Vannieuwkerke
d18af7358a
Moved untarring the genome sdf folder to the test itself
2022-05-09 09:20:42 +02:00
Lucpen
bdaed264a7
Merge branch 'master' into correcting_stubs
2022-05-09 08:54:22 +02:00
James A. Fellows Yates
8a83ad0518
Merge branch 'master' into motus_profile
2022-05-09 08:16:16 +02:00
MaxUlysse
3d428e2933
fix spacing
2022-05-07 15:28:40 +02:00
MaxUlysse
1013be2623
fix path to script
2022-05-07 15:22:52 +02:00
Jose Espinosa-Carrasco
e2acf28c8f
Merge branch 'master' into maxulysse-patch-1
2022-05-06 23:53:27 +02:00
Matthias De Smet
0752b82c9f
Merge branch 'master' into update/snapaligner
2022-05-06 18:57:37 +02:00
Matthias De Smet
dd458e3388
fix tags
2022-05-06 18:57:17 +02:00
Maxime U. Garcia
ac217479e9
Update tests/config/test_data.config
...
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
2022-05-06 18:18:32 +02:00
Maxime U. Garcia
ec7b460fa4
add missing file
2022-05-06 17:54:35 +02:00
Mahesh Binzer-Panchal
67481c6d54
Start Meryl count
2022-05-06 15:04:04 +00:00
Mahesh Binzer-Panchal
1e55ad987f
Merge branch 'master' into kat_hist
2022-05-06 16:35:51 +02:00
nvnieuwk
5153e10840
Merge branch 'master' into new-module-rtg/vcfeval
2022-05-06 16:19:17 +02:00
Nicolas Vannieuwkerke
8c857dee3a
Fixed the sdf folder fetching
2022-05-06 16:16:57 +02:00
Lucpen
8e5fda3b10
Merge branch 'master' into correcting_stubs
2022-05-06 15:37:08 +02:00
Lucpen
971a17a3ab
fix datatest for stubs
2022-05-06 15:34:18 +02:00
Mahesh Binzer-Panchal
7a85760d08
remove 'auto' test
2022-05-06 13:33:27 +00:00
Lucpen
0fa36e6777
fix added correct entry workflow in test.yml
2022-05-06 15:26:34 +02:00
JIANHONG OU
9b50036e9b
add test_bam and -m parameter for motus_profile
2022-05-06 08:56:42 -04:00
JIANHONG OU
c301a406dd
Merge branch 'nf-core:master' into motus_profile
2022-05-06 08:33:43 -04:00
Nicolas Vannieuwkerke
84b354ab6a
Added the rtgtools/vcfeval module
2022-05-06 14:23:40 +02:00
JIANHONG OU
26d5b4da72
Update tests/modules/motus/profile/main.nf
...
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-05-06 08:19:54 -04:00
Matthias De Smet
26d2231e85
fix linting
2022-05-06 14:16:38 +02:00
Matthias De Smet
3930ba227b
merge snapaligner modes into one
2022-05-06 14:10:44 +02:00
Mahesh Binzer-Panchal
a9f23bb477
Merge branch 'master' into busco
2022-05-06 13:49:01 +02:00
Mahesh Binzer-Panchal
35c5828f43
Add --auto-lineage option and remove single_end
...
Co-authored-by: Jill V. Hagey, PhD <jvhagey@gmail.com>
2022-05-06 11:48:21 +00:00
Jose Espinosa-Carrasco
035655e35d
Merge branch 'master' into modules/md5sum
2022-05-06 12:34:14 +02:00
Mahesh Binzer-Panchal
c19e7da59d
Apply suggestions from code review
...
Remove versions md5sum
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2022-05-06 10:55:48 +02:00
Matthias De Smet
09e729ad41
added sha256sum
2022-05-06 10:28:14 +02:00
Mahesh Binzer-Panchal
d83281eac9
Merge branch 'master' into kat_hist
2022-05-06 10:02:44 +02:00
Mahesh Binzer-Panchal
9194fb845e
Add module kat hist
2022-05-06 07:54:10 +00:00
Matthias De Smet
853b623969
new module: md5sum
2022-05-06 09:20:40 +02:00
Ramprasad Neethiraj
db56d80060
Merge branch 'master' of https://github.com/nf-core/modules into feat/update_cnvpytor
2022-05-06 00:10:28 +02:00
Ramprasad Neethiraj
e4e4f8090c
combine multiple pytor
2022-05-05 23:59:12 +02:00
JIANHONG OU
b8efa2ae7c
Merge branch 'master' into motus_profile
2022-05-05 13:41:54 -04:00
JIANHONG OU
fb5c5d310a
update motus module.
2022-05-05 13:38:46 -04:00
Sateesh Peri
faf45edc5e
Merge branch 'master' into busco
2022-05-05 12:48:39 -04:00
Ramprasad Neethiraj
db2acba71b
Merge branch 'master' into feat/update_cnvpytor
2022-05-05 17:31:10 +02:00
Sateesh Peri
3414d3aba3
Merge branch 'master' into busco
2022-05-05 10:08:55 -04:00
JIANHONG OU
c8f2c44e22
Merge remote-tracking branch 'origin' into motus_profile
2022-05-05 09:41:13 -04:00
JIANHONG OU
a8bc386ea3
Merge branch 'master' into motus_downloaddb
2022-05-05 09:36:25 -04:00
JIANHONG OU
566c11dacc
Merge branch 'master' into motus_downloaddb
2022-05-05 08:28:10 -04:00
Francesco L
97f318eea6
Merge branch 'master' into firstbranch
2022-05-05 14:25:00 +02:00
Carpanzano
a700a9c15e
Merge branch 'firstbranch' of github.com:carpanz/modules into firstbranch
2022-05-05 13:52:45 +02:00
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
jasmezz
24b9c397dd
Apply suggestions from code review + add support for GFF annotations
2022-05-05 13:14:39 +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
jasmezz
6a7aec8b41
Remove prokka test workflow
2022-05-05 10:22:02 +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
jasmezz
fa9f0753de
Apply review suggestions + add stub for prokka test workflow
2022-05-03 17:30:16 +02:00
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
jasmezz
a992a0207e
Merge branch 'antismashlite' of github.com:jasmezz/modules into antismashlite
2022-05-02 17:58:52 +02:00
Jasmin F
b8386c42a7
Merge branch 'nf-core:master' into antismashlite
2022-05-02 17:58:19 +02:00
jasmezz
d19e65d2a2
Merge branch 'antismashlite' of github.com:jasmezz/modules into antismashlite
2022-05-02 17:56:23 +02:00
jasmezz
35cc8152b8
Fix missing test input
2022-05-02 17:55:39 +02:00
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
Jasmin F
883b95bed6
Merge branch 'nf-core:master' into antismashlite
2022-05-02 17:31:43 +02:00
jasmezz
4a4de550b8
Simplify/reduce container mount volumes
2022-05-02 17:30:46 +02:00
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
JIANHONG OU
0f24e4dcff
add input database and intermediate bam file.
2022-05-02 08:37:12 -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 )
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* 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
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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 )
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* 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 )
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* 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 )
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* 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
JIANHONG OU
61799e80ab
Merge branch 'nf-core:master' into motus_profile
2022-04-28 08:09:47 -04:00
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 )
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* 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 )
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* 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
jasmezz
cc05006dbb
Update antismashlite module main.nf
2022-04-26 17:15:41 +02:00
Sofia Stamouli
1f77bc130b
Update minimap2/align module ( #1537 )
2022-04-26 16:32:20 +02:00
jasmezz
1acde9a7a1
Fix container volume mounts
2022-04-26 16:28:39 +02:00
Maxime U. Garcia
569e07f0af
add samtools/bamtocram modules ( #1561 )
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* 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
Jasmin F
6467e23809
Merge branch 'nf-core:master' into antismashlite
2022-04-25 14:21:54 +02:00
JIANHONG OU
98d318c0e0
init
2022-04-24 07:55:17 -04:00
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 )
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* 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
jasmezz
1c1e813c67
Initial module creation
2022-04-22 16:47:48 +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
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
Matthias De Smet
35231d3949
update picard/collecthsmetrics ( #1542 )
...
* update picard/collecthsmetrics
* syntax fixes, bugfixes
* add tests
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
2022-04-22 10:13:57 +02:00
Ramprasad Neethiraj
c7329a3a57
add stubs for stranger ( #1543 )
2022-04-22 10:10:43 +02:00
Lucpen
12afb6b0fa
Update samtools view to add input path(index) ( #1539 )
...
* feat added index as input, to allow module to be used for subsampling
* fix test
* feat added index to meta.yml
* Update modules/samtools/view/meta.yml
feat corrected description of idea pattern file in meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-04-22 10:01:47 +02:00
Robert A. Petit III
47d8d476b8
make prettier
2022-04-21 12:55:56 -06:00
Robert A. Petit III
0095bc91f7
add module for shigatyper
2022-04-21 18:49:42 +00:00
Matthias De Smet
f4c69bc427
Module/bclconvert ( #1485 )
...
* bclconvert: initial commit
* add most of tool
* attempt at adding testing stub
* add dockerfile + instructions
* add container to module
* update readme
* more attempts at making stubs work
* finish stub run
* fix ci issues
* more fixes to stub
* add read version check to stub
* fix some tests
* update readme
* fix version number
* syntax fix
* revert edit to output directory
* Update modules/bclconvert/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/bclconvert/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* update meta.yaml
* update thread usage
* Update modules/bclconvert/main.nf
Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com>
* Escape env variable
* Update modules/bclconvert/Dockerfile
Co-authored-by: Mark Whelan <7407040+MrMarkW@users.noreply.github.com>
* fix comments by @Emiller88
* fix task.cpus
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com>
Co-authored-by: Mark Whelan <7407040+MrMarkW@users.noreply.github.com>
2022-04-21 15:39:22 +02:00
Francesco L
abe025677c
update to kraken2: breaking change - output channels renamed ( #1525 )
...
* updated kraken2 module to include optional classification of each input reads, and make fastq outputs optional
NB: this is a breaking change, because the output channels have been renamed as a consequence of changes
* updated yml
* pigz command made optional, in order to be executed only if fastq of classified/unclassified reads are saved
* updated test yaml file for kraken2
* fixed TODOs and renamed variables and outputs
* untar in conda cannot keep same md5sum of version, and therefore md5sum check removed
* improved description of the options
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-04-21 14:33:59 +02:00
Matthias De Smet
d85f9c7011
add subworkflow bam_qc_picard
2022-04-21 13:16:23 +02:00
Jasmin F
d07d270743
Antismashlite download databases ( #1426 )
...
* Create module antismashlitedownloaddatabases
* Corrected user-specification of database directory
* Updated test.yml
* Apply suggestions from code review
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Fix typo in test.yml
* Feed database files via docker/singularity mount)
* Add external db file mounts to the containers
* Fixed docker command in main.nf
* Apply prettier
* Apply prettier and add PWD
* Add more output to test.yml
* Add more output paths to test.yml
* Fixed test.yml
* Apply suggestions from code review
Add documentation of why we need to mount files to the containers.
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Fix code linting errors (remove trailing whitespaces)
* Fix code linting error (remove trailing whitespace)
* Fix errors from Prettier linting
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-04-21 10:38:17 +02:00
Maxime U. Garcia
37bf3936f3
add decompress possibilities to bgzip ( #1540 )
...
* add decompress possibilities to bgzip
* spacing
2022-04-20 16:26:56 +02:00
louperelo
6c45773c0b
add module AMPlify ( #1498 )
...
* add module AMPlify
* Apply suggestions from code review
Thanks for the review!
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
* removed trailing whitespaces
* Apply suggestions from code review
Thanks again!
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
* Apply suggestions from code review
Thank you for the suggestions!
Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Apply suggestions from code review
Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
* including review suggestions
* fix versions.yml
* add model_dir input
* add model_dir to meta.yml
* complete faa pattern in meta.yml
* add fa.gz to pattern
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-04-20 11:53:26 +02:00
Maxime U. Garcia
705f8c9ac4
Add samtools/collatefastq module ( #1536 )
...
* add samtools/collatefastq module
* update yml file
* improve output
2022-04-20 10:05:17 +02:00
Maxime U. Garcia
7630e278f3
update gatk4 yml for spark ( #1538 )
2022-04-19 16:51:59 +02:00
Matthias De Smet
bddb88dfaf
Merge branch 'master' into tool/bamtools-split
2022-04-19 15:33:49 +02:00
Matthias De Smet
07982d6cb1
fix command line, fix meta.yml
2022-04-19 15:31:39 +02:00
Matthias De Smet
b35264e919
bugfixes
2022-04-19 15:11:37 +02:00
Matthias De Smet
553c1bcf9d
Merge branch 'master' into tool/elprep-merge
2022-04-19 11:28:04 +02:00
Matthias De Smet
ccef7f8579
alignment
2022-04-19 11:26:01 +02:00
Anders Jemt
a6cb75174b
Add variant catalog ch to stranger ( #1508 )
...
* Add optional variant catalog input
* fix for no variant catalog test
Co-authored-by: ljmesi <37740329+ljmesi@users.noreply.github.com>
Co-authored-by: Lauri Mesilaakso <john.mesilaakso@gmail.com>
2022-04-19 10:53:39 +02:00
JIANHONG OU
ee04fc2737
add module motus_downloaddb
2022-04-14 12:56:42 -04:00
Sofia Stamouli
be4ae28c3c
Add centrifuge_kreport module ( #1514 )
2022-04-13 15:33:51 +02:00
Sofia Stamouli
8856f127c5
Update input in kaiju_kaiju module ( #1522 )
2022-04-13 14:53:08 +02:00
Sofia Stamouli
39b4b45ba0
Update test_data.config to include kaiju.tar.gz ( #1520 )
2022-04-13 13:31:32 +02:00
Matthias De Smet
0f7c046477
first commit
2022-04-13 12:51:17 +02:00
Maxime U. Garcia
409af2f27c
Improve syntax/logic coherence in all gatk4 plugins ( #1459 )
...
* feat: code polishing
* Apply suggestions from code review
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
* code polishing
* more code polishing
* code polishing
* tests for applybqsrspark
* fix typo
* no need to check md5sum for versions.yml
* fix: use correct syntax
* code polishing again
* add tests for markduplicatesspark
* simplify mergevcfs tests
* add tests for baserecalibratorspark
* fix: path to entry
* code polishing
* fix linting
* simplify module
* update meta.yml
* fix pair mode
* fix: MITO mode
* more tests
* fix command
* bad copy paste
* fix typos
* fix tests
* fix test
* update meta.yml
* correct versions.yml in all test.yml
* code polishing
* code polishing
* more code polishing
* fix args
* add tmpdir for all
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2022-04-12 17:15:39 +02:00
Matthias De Smet
b59713e623
Tool/snap aligner single ( #1510 )
...
* first commit
* add tool
* fix tests
* fix indents
* Update modules/snapaligner/single/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* fix comments
* fix versions
* prettier
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-04-12 11:20:35 +02:00
Matthias De Smet
09125979cc
Tool/snap aligner paired ( #1509 )
...
* first commit
* edit main.nf
* edit tests
* run prettier
* fix test
* indent script
* Update modules/snapaligner/paired/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/snapaligner/paired/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* fix version nr
* update meta
* fix versions
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-04-12 11:02:10 +02:00
FriederikeHanssen
ffedf09b6e
Revert manta changes ( #1518 )
...
* Fix typo
* Revert to have target bed matched with sample info
* Add comment on design decision
2022-04-12 10:40:06 +02:00
James A. Fellows Yates
2d38566eca
Add MEGAN/RMA2INFO ( #1513 )
...
* fix: remove left-over unnecessary code
* Add megan/rma2info
* Attempt at fixing test
* Right yml formatting
* Get the versios reporting correct
2022-04-12 08:35:36 +02:00
FriederikeHanssen
897c33d5da
Samtools version update ( #1507 )
...
* Fix typo
* update version to 1.15.1
* Fix md5sums
* update mulled containers
* update md5sums
* update md5sums
2022-04-11 14:26:28 +02:00
Matthias De Smet
d4160c669b
Tool/crosscheckfingerprints ( #1505 )
...
* first commit
* first commit
* update test.yml
* update test.yml
* Update modules/picard/crosscheckfingerprints/main.nf
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
* Update modules/picard/crosscheckfingerprints/main.nf
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
* add support for vcf haplotype maps
* update test
* update test data config, use test data
* fix exit code
* Update modules/picard/crosscheckfingerprints/main.nf
Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
* Update modules/picard/crosscheckfingerprints/main.nf
Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
* remove unused stub
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
2022-04-08 10:02:10 -04:00
Matthias De Smet
e19a9a2474
new tool: staden_io_lib ( #1499 )
...
* new tool: staden_io_lib
* update docker containers
* add test.yml
* add fai index input
* typo
* fix version.yml
* update md5sum
* omit md5sum for cram
* move scramble to submodule
* add missing in/output
* remove some comments
Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
2022-04-08 09:54:15 -04:00
Matthias De Smet
f57f085912
new tool snap-aligner/index ( #1506 )
...
* add snapaligner/index
* output fixes
* fix outputs
* fix tests
* update inputs
* fix more bugs
* fix linting
* Update modules/snapaligner/index/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/snapaligner/index/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* fix comments
* fix indents
* fix escaping
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-04-08 14:41:08 +02:00
FriederikeHanssen
9ae34a01d1
Fix Controlfreec: Add stub runs to test single sample input & make conda work with R scripts ( #1504 )
...
* Fix typo
* Add stub runs for testing input without matched normals
* Add missing -stub-run
* remove empty file checksum tests and change workflow names
* test controlfreec naming
* fix output file names
* fix output file names
* fix output file names
* fix conda and container path difference for R scripts
* update tar version to work with conda
* fix version number in docker
* try to fix path to script, pretty sure it won't work
* try new ways to set path with wildcard
* try which
* add which but with escape
* remove comment
2022-04-08 11:43:40 +02:00
Lucpen
f079367416
Picard liftover vcf ( #1431 )
...
* Building Picard liftovervcf module
* Building Picard liftovervcf module_test
* Building Picard liftovervcf pytest
* Module for picard liftover vcf created
* Fixed files after linting test
* Fixed trailing whitespace
* Checked files with prettier
* further formatting with prettier
* Fixed test.yml
* Fixed input variable names
* Changed contain test.liftef.vcf
* Changed contain in test.yml test.liftef.vcf
* Run prittier
* Going back to previous version of test.yml
* downgrading picard to 2.26.10 from 2.26.11
* Update modules/picard/liftovervcf/main.nf
Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
* Update modules/picard/liftovervcf/main.nf
Print available memory
Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
* Output from .vcf to .vcf.gz
* Added spaces to align emit
* Update modules/picard/liftovervcf/meta.yml
Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
* Update modules/picard/liftovervcf/meta.yml
Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
* Update modules/picard/liftovervcf/meta.yml
Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
* Removing md5sum test
Co-authored-by: jemten <jemten@users.noreply.github.com>
Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
2022-04-07 07:50:58 -04:00
Sofia Stamouli
d2726fcf75
Update centrifuge/centrifuge ( #1495 )
2022-04-07 11:46:34 +02:00
Matthias De Smet
dc95e67e15
New tool: biobambam/bamsormadup ( #1478 )
...
* add bamsormadup
* fix yaml
* add test.yml
* Update tests/modules/biobambam/bamsormadup/test.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* test meta.yaml: remove md5sums
* Tool bamsormadup:
- add (optional) reference input
- add bam index ouput
- add cram output option
- make metrics output: more general
* fix input and output formats
* update input file description
* drop sam output, goes against nf-core regs; add input check for cram files
* fix typo
* Update modules/biobambam/bamsormadup/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* improve ref fasta name
* fix if else shorthand
* fix syntax error
* kind of fix tests
* set fixed suffix for metrics file to keep it in line with picard and bammarkduplicates2
* fix command line
* update test.yml
* add support for multiple input bams
* Update modules/biobambam/bamsormadup/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/biobambam/bamsormadup/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update tests/modules/biobambam/bamsormadup/test.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-04-06 08:18:23 +02:00
Matthias De Smet
797ce3254e
Update: biobambam/bammarkduplicates2 to v2.0.183 ( #1493 )
...
* bump version, remove md5sums from test
* re-add md5sums
2022-04-05 11:06:46 +02:00
Moritz E. Beber
879d42c5e2
Refactor adapterremoval ( #1491 )
...
* refactor: insert .fastq file extensions
* style: insert whitespace
* refactor: create paired output
* refactor: rename settings from log
Requested by @jfy133
* tests: correct expected output
* fix: remove settings option due to default
* chore: rename output patterns
* refactor: omit paired files in single-end
* refactor: rename output to settings
2022-04-04 21:40:35 +02:00
Edmund Miller
13cc32399c
feat(homer): Add groseq subworkflow ( #1492 )
...
* feat(homer): Add groseq subworkflow
* fix(homer): Update groseq paths
* test(homer): Update groseq bam md5sums
* test(homer): Update bed process args wildcard
* test(homer): Update groseq bed md5s
* style: Run prettier
* style(homer): Align comments
Co-authored-by: Friederike Hanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
* docs(homer): Add groseq meta.yml
Co-authored-by: Friederike Hanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2022-04-04 18:21:37 +00:00
Sofia Stamouli
6a11c5a222
Fix untar for centrifuge ( #1472 )
2022-04-04 10:18:11 +02:00
James A. Fellows Yates
f1c5384c31
Add PRINSEQPLUSPLUS ( #1481 )
...
* fix: remove left-over unnecessary code
* Add prinseq++
* Remove last todo
* Fix tests due to variability of output FASTQs (reads can be ordered differently between runs)
* Apply suggestions from code review
2022-04-03 16:06:22 +02:00
Ramprasad Neethiraj
67c1bc9568
Add stubs to cnvpytor module ( #1473 )
...
* callcnvs stub and tests
* partition stub and test
* histogram stub and test
* importreaddepth stub and tests
* update module scripts
Co-authored-by: Sima Rahimi <sima.rahimi@gu.se>
2022-04-01 17:35:15 +02:00
James A. Fellows Yates
8ce6810787
Update DASTool to 1.1.4 ( #1471 )
...
* fix: remove left-over unnecessary code
* Update DASTool
* Fix tests
* Fix test.ymls
* Fix container build version
* Make tests less strict to account for variability
* Apply suggestions from code review
Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
* Add missing description
Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
2022-04-01 11:33:07 +02:00
Jose Espinosa-Carrasco
5e7daa7b96
Add task.ext.args to phantompeakqualtools and finish the module ( #1474 )
...
* Add --max--ppsize option
* Add args to phantompeakqualtools and all the missing files (test, yml, ...)
* Fix tests
* Add the nextflow.config
* Fix tests
2022-03-31 22:59:21 +01:00
Sébastien Guizard
794f84534b
New Module: gstama/polyacleanup ( #1468 )
...
* 📦 NEW: Add gstama/polyacleanup
polyacleanup script remove remaining polyA tails from FLNC reads (Pacbio isoseq3)
* 🐛 FIX: Prettier: replace simple quote by double quote
* 🐛 FIX: Update TEMPLATE to nf-core 2.4
* 👌 IMPROVE: Compress outputs
Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
2022-03-31 09:11:51 -04:00
Ramprasad Neethiraj
eeda4136c0
Update cat module ( #1469 )
...
* fix cat stub
* add test
* commit suggestions
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
2022-03-31 13:42:44 +02:00
Moritz E. Beber
0de6406217
feat: add module for seqkit stats ( #1466 )
2022-03-30 23:01:17 +02:00
Ramprasad Neethiraj
fd5f6f5f4f
Revert recent changes made to some of the modules ( #1463 )
...
* revert changes to modules
* fix tests
* fix kraken2
* fix untar
* fix cat
* add blank lines
* fix typo
2022-03-30 20:21:06 +02:00
Jose Espinosa-Carrasco
dbb46c9b63
Bump chromap version 0.2.1 ( #1462 )
2022-03-29 16:44:19 +02:00
Ramprasad Neethiraj
49b18b1639
add stub to modules used in raredisease pipeline ( #1206 )
...
* add stub section
* add stub for bcftools norm
* add stub to more modules
* fix expansionhunter tests
* revert changes -picard
* Update stub to write version no.s to a file
* add picard
* revert picard again
* add stubs to more modules
* fix bwamem2
* add bcftools view
* add stubs
* fix svdb query
* review suggestions
2022-03-28 17:48:39 +02:00
James A. Fellows Yates
240ee4328c
Dastool update to allow non-gzipped inputs ( #1458 )
...
* fix: remove left-over unnecessary code
* Make gzipping optional for DAS_Tool scaffolds2bin
* Add optional unzipping
* Make gunzip optional for DAS_Tool scaffolds2bin
* Apply suggestions from code review
Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
* Update modules/dastool/scaffolds2bin/meta.yml
Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
2022-03-28 16:29:46 +02:00
Tanja Normark
1f483d9203
Add kaiju_kaiju module ( #1448 )
...
* Added kaiju_kaiju module
* Update modules/kaiju/kaiju/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/kaiju/kaiju/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/kaiju/kaiju/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update keywords
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update output file naming
* Update output file naming
* update spacing for lint
* Update input file patterns
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-03-28 14:28:50 +02:00
Edmund Miller
5832fbc225
Fix homer/maketagdirectory output collision ( #1456 )
...
* fix(homer): Update tagdir to have a prefix
Otherwise they have a naming collision
* test(homer): Update paths
* style(homer): Align ,'s
* chore(homer): Update md5sums
2022-03-27 03:17:42 +00:00
FriederikeHanssen
5acf301ddd
add freec2circos script ( #1454 )
...
* add freec2circos script
* remove todo statements
2022-03-26 21:25:29 +01:00
FriederikeHanssen
28e5211b35
add makegraph script ( #1452 )
...
* add makegraph script
* allow renaming of output files
* allow renaming of output files
2022-03-25 20:49:08 +01:00
FriederikeHanssen
8a64e73af2
add freec2bed script ( #1453 )
2022-03-25 20:31:52 +01:00
FriederikeHanssen
4efa8da5c5
controlfreec significance ( #1451 )
...
* controlfreec significance
* move freec files to own subfolder
* Fix meta.yml naming
* Fix meta.yml naming
* Fix linting
* Forgot to refactor
* forgot more refactoring
* Too much refactoring on output paths
* Too little refactoring here
* update checksum
2022-03-25 18:22:17 +01:00
Edmund Miller
27936729f2
Add samtools to homer/maketagdirectory to use bam files ( #1437 )
...
* fix(homer): Update dependancies for maketagdirectory
Closes #1363
* test(homer): Add tests for bam usage
* style(homer): Rename meta test
* fix(homer): Update args order and add missing \\
* docs(homer): Add DESeq2 and edgeR
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
* test(homer): Update md5sum
* test(homer): bam => sam
* fix(homer): Use nextflow conda recipe instead of biocontainers with commas
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2022-03-25 17:13:30 +00:00
Edmund Miller
7111e571cc
Split preseq lcextrap and ccurve ( #1440 )
...
* fix(preseq): Update lcextrap file name
* chore(preseq): Bump lcextrap image
* feat: Initialize preseq c_curve
* docs(preseq): Update documentation
2022-03-25 17:11:40 +00:00
Simon Pearce
a066456735
Add tests for umitools extract and dedup ( #1429 )
...
* NGSCheckMate v1
* Add some tests for UMItools
* Added tests for dedup
* Include pytest
* Delete main.nf
* Delete meta.yml
* Delete main.nf
* Delete nextflow.config
* Delete test.yml
* add prettier
* Add direct test on bam
* Update tests/modules/umitools/dedup/main.nf
Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com>
* Update tests/modules/umitools/dedup/main.nf
Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com>
* Update tests/config/pytest_modules.yml
Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com>
* Not ignore-umi
Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk>
Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com>
2022-03-25 14:25:07 +00:00
Edmund Miller
1fb1801dcb
refactor(homer): Update output path for bedGraph ( #1438 )
...
This allow for caching because otherwise it modifies the tag directory input
2022-03-25 13:54:09 +00:00
