Commit graph

1117 commits

Author SHA1 Message Date
James A. Fellows Yates
615cb0722f
Merge branch 'master' into fix-filtlong 2022-05-31 20:25:16 +02:00
FriederikeHanssen
19037ed8f4
Merge branch 'master' into get_tbi_files_from_gatk4_mergevcfs 2022-05-31 17:42:27 +02:00
asp8200
4199a05aeb Removing redundant empty line 2022-05-31 15:34:34 +00:00
Nicolas Vannieuwkerke
80366924fd added gatk4/composestrtablefile 2022-05-31 16:08:13 +02:00
James Fellows Yates
089f761f0b Actually add the changes 2022-05-31 15:49:57 +02:00
Anders Sune Pedersen
5513d095f5 Adding tbi-files to the output from GATK4_MERGEVCFS. #1709 2022-05-31 15:37:26 +02:00
nvnieuwk
a6c7635b73
Merge branch 'master' into add-tbi-to-bcftools-concat 2022-05-31 15:20:03 +02:00
Nicolas Vannieuwkerke
51b0a6e4f3 Added optional input of index files to bcftools/concat 2022-05-31 15:15:58 +02:00
James A. Fellows Yates
0b895871d7
Merge branch 'master' into fix-filtlong 2022-05-31 14:49:44 +02:00
James Fellows Yates
723852bf3d Fixes running without shortreads, and also ensures all tests produce non-empty fastq.gz files 2022-05-31 13:38:18 +02:00
Sébastien Guizard
a3ae526521
Merge branch 'master' into bamtools/convert/remove_TODO 2022-05-30 17:36:36 +01:00
Sebastien Guizard
d463cd5dd6 👌 IMPROVE: Remove last TODO 2022-05-30 17:26:51 +01:00
jtangrot
5f0d75bb37 Merge branch 'vsearch_usearch_global' of https://github.com/jtangrot/nf-core_modules into vsearch_usearch_global 2022-05-30 13:05:00 +02:00
Jeanette Tångrot
69e00b55d3
Update modules/vsearch/usearchglobal/main.nf
Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
2022-05-30 13:03:45 +02:00
jtangrot
c67c15f243 Make input tuple 2022-05-30 13:01:06 +02:00
Matthias De Smet
63db63757c bump picard versions 2022-05-30 10:15:40 +02:00
jtangrot
2e16c90fce Fix whitespace 2022-05-30 09:57:05 +02:00
jtangrot
01d86439f5 Add idcutoff as input 2022-05-30 08:50:27 +02:00
jtangrot
589ce2d73a Add options for output file type 2022-05-30 08:50:27 +02:00
jtangrot
1c99ffd876 Add vserach usearch_global 2022-05-30 08:50:27 +02:00
Harshil Patel
fb6c7bca3d Bump container version for STAR to 2.7.10a 2022-05-27 11:35:04 +01:00
Sateesh Peri
ead3679829
Merge branch 'master' into rp3-add-snippy 2022-05-26 03:04:19 -04:00
Harshil Patel
72a31b76eb
Update main.nf 2022-05-25 19:42:15 +01:00
Matthias De Smet
bc7002b0c9
Merge branch 'master' into update/mosdepth 2022-05-25 19:20:45 +02:00
Matthias De Smet
72ff2732e3 add all remaining outputs to mosdepth 2022-05-25 19:19:39 +02:00
Mahesh Binzer-Panchal
3d532405a5
Merge branch 'master' into mash_screen_patch 2022-05-25 16:51:42 +02:00
Mahesh Binzer-Panchal
c452f56289 Patch mash screen 2022-05-25 12:29:14 +00:00
Jill V. Hagey, PhD
b1dd1d8a52
Merge branch 'nf-core:master' into gamma-update 2022-05-24 19:28:06 -04:00
Mahesh Binzer-Panchal
3d51956b88
Merge branch 'master' into kat_hist 2022-05-24 23:10:13 +02:00
jvhagey
b8aaea7429 updating paths in test.yml 2022-05-24 16:27:00 -04:00
jvhagey
f1fc7fc38e adding upzip 2022-05-24 15:15:07 -04:00
Ramprasad Neethiraj
fe90615f57 Merge branch 'rhocall' of github.com:genomic-medicine-sweden/modules into rhocall 2022-05-24 16:17:59 +02:00
Ramprasad Neethiraj
b0dba3ee75 update description 2022-05-24 16:17:15 +02:00
Ramprasad Neethiraj
c91947f8a1
Merge branch 'master' into rhocall 2022-05-24 16:07:55 +02:00
Mahesh Binzer-Panchal
9a5d6a815b
Merge branch 'master' into kat_hist 2022-05-24 15:46:12 +02:00
SusiJo
3077e4d34c
Merge branch 'master' into cnvkit/reference 2022-05-24 15:00:29 +02:00
SusiJo
8208140d21 missing meta.id changed 2022-05-24 14:59:52 +02:00
SusiJo
6b425735b9 Merge remote-tracking branch 'origin/master' into cnvkit/reference 2022-05-24 14:20:55 +02:00
SusiJo
749edce069 add prefix 2022-05-24 14:20:19 +02:00
Mahesh Binzer-Panchal
c8ffecfe86
Merge branch 'master' into kat_hist 2022-05-24 13:57:45 +02:00
Matthias De Smet
c51c047b2e
Merge branch 'master' into update/mosdepth 2022-05-24 13:50:22 +02:00
Matthias De Smet
a2a8e09762
Update modules/mosdepth/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-05-24 13:45:52 +02:00
Mahesh Binzer-Panchal
afb5f226e6
Merge branch 'master' into kat_hist 2022-05-24 13:06:31 +02:00
Matthias De Smet
858cbe80c6 add must fail test 2022-05-24 12:43:49 +02:00
Matthias De Smet
7e777c6626 add error is is provided twice 2022-05-24 12:25:31 +02:00
Matthias De Smet
b5850fd471 add stub 2022-05-24 12:16:03 +02:00
Harshil Patel
393f23274d
Merge branch 'master' into cnvkit/reference 2022-05-24 11:14:50 +01:00
Harshil Patel
29a4f112be
Update main.nf 2022-05-24 11:14:32 +01:00
Matthias De Smet
01fb8851c3 mosdept: cram compatiblility 2022-05-24 11:47:58 +02:00
Harshil Patel
ec141dba08
Merge branch 'master' into umitools 2022-05-24 09:23:20 +01:00
SusiJo
5db94ea0ee changed tag of module 2022-05-24 10:17:41 +02:00
Ramprasad Neethiraj
b4982ff6e3
Merge branch 'master' into rhocall 2022-05-24 09:41:30 +02:00
SusiJo
0f0d555f96
Merge branch 'master' into cnvkit_reference 2022-05-24 08:03:44 +02:00
SusiJo
0708f343de
Merge branch 'master' into cnvkit_bam 2022-05-24 07:49:51 +02:00
SusiJo
50128b0c86
Merge branch 'master' into cnvkit_reference 2022-05-24 07:49:44 +02:00
SusiJo
63c038ad68
Merge branch 'nf-core:master' into cnvkit_bam 2022-05-24 07:37:24 +02:00
SusiJo
b3e2f70651
Merge branch 'master' into cnvkit/antitarget 2022-05-24 07:36:07 +02:00
SusiJo
33a72367c6
Merge branch 'nf-core:master' into cnvkit_reference 2022-05-24 07:30:29 +02:00
Harshil Patel
84f02a08a5 Update umitools/dedup module to make --output-stats optional 2022-05-23 22:31:09 +01:00
Sateesh Peri
da0ead705e
Merge branch 'master' into update/picard 2022-05-23 13:38:18 -04:00
SusiJo
58c5ec2f4e
rm line
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2022-05-23 18:53:28 +02:00
SusiJo
86b5951c14
rm line
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2022-05-23 18:48:30 +02:00
SusiJo
24905e26e2
rm line
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2022-05-23 18:48:13 +02:00
SusiJo
ddb964a4bf
rm line
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2022-05-23 18:48:04 +02:00
SusiJo
bbee9e3c3b add new module cnvkit/reference 2022-05-23 18:35:50 +02:00
SusiJo
5d5eacee63
Merge branch 'nf-core:master' into cnvkit/antitarget 2022-05-23 16:52:33 +02:00
SusiJo
4f9d672e55 added new module cnvkit/antitarget 2022-05-23 16:52:06 +02:00
FriederikeHanssen
754afa9ff3
Merge branch 'master' into gatk_filter 2022-05-23 15:37:44 +02:00
Ramprasad Neethiraj
9fb327fec7 Merge branch 'master' of https://github.com/nf-core/modules into rhocall 2022-05-23 13:06:00 +02:00
Rike
175ea9b7f9 fix version 2022-05-23 12:15:33 +02:00
SusiJo
fd31f64266
Merge branch 'master' into cnvkit_bam 2022-05-23 11:31:56 +02:00
Mahesh Binzer-Panchal
e06fb752c3
Merge branch 'master' into kat_hist 2022-05-23 08:52:13 +02:00
Rike
5d72500d60 remove variables used for test data generation, add tbi 2022-05-22 13:34:56 +02:00
Matthias De Smet
c390385cf5 revert wgsmetrics' 2022-05-22 06:44:17 +02:00
Matthias De Smet
d6a0238cd1
Merge branch 'master' into update/picard 2022-05-21 08:34:33 +02:00
Matthias De Smet
a5a6973fcf picard: make reference sequence optional 2022-05-21 08:33:49 +02:00
Ramprasad Neethiraj
635edc0022 fix typo 2022-05-20 17:07:42 +02:00
Ramprasad Neethiraj
2542c9d176 add tests 2022-05-20 16:46:19 +02:00
Mahesh Binzer-Panchal
2926ec0abb Add mash screen 2022-05-20 13:23:11 +00:00
Ramprasad Neethiraj
c70b169f61 create modules 2022-05-20 13:34:54 +02:00
SusiJo
9096be5464 improve readability 2022-05-20 13:29:49 +02:00
SusiJo
bdf222649d remove unnecessary if statement 2022-05-20 13:25:57 +02:00
SusiJo
153c900d0e
refine comment
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2022-05-20 13:08:38 +02:00
SusiJo
2e5aa0dbb4
refine comment
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2022-05-20 13:08:26 +02:00
SusiJo
3b3921cfa3
refine comment
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2022-05-20 13:07:57 +02:00
SusiJo
f392c4bed5 removed params section & added description fasta 2022-05-20 13:05:43 +02:00
SusiJo
129270d7bc adjusted conda env & singularity container 2022-05-20 10:37:46 +02:00
SusiJo
dd2f48810a
Merge branch 'nf-core:master' into cnvkit_bam 2022-05-20 09:14:21 +02:00
SusiJo
5a1297cc7d added optional pdf/png outputs 2022-05-20 09:12:47 +02:00
SusiJo
064712c4ea added cram_bam conversion & tumor_only check 2022-05-20 09:11:45 +02:00
Rike
bb3e64647b Merge remote-tracking branch 'origin/master' into gatk_filter 2022-05-18 15:52:47 +02:00
FriederikeHanssen
44e9cf56fa
Merge branch 'master' into gatk_cnnscore 2022-05-18 15:32:36 +02:00
Rike
e8221cf98e Merge remote-tracking branch 'origin' into gatk_cnnscore 2022-05-18 14:27:25 +02:00
Rike
10840a0562 Conda not suported 2022-05-18 14:26:21 +02:00
James A. Fellows Yates
965fabdd54
Merge branch 'master' into motus_profile 2022-05-18 11:25:48 +01:00
Rike
5ae757121f Add indices and meta 2022-05-17 23:38:26 +02:00
Rike
05837a011d Add comment 2022-05-17 23:06:52 +02:00
Rike
15fba1dd7c add filter variant tranches 2022-05-17 23:01:24 +02:00
Rike
e0fcbb428d Add CNNScoreVariants 2022-05-17 19:09:46 +02:00
Jose Espinosa-Carrasco
3614c19206
Merge branch 'master' into biobambam/bammerge 2022-05-17 15:07:37 +02:00