Commit graph

2899 commits

Author SHA1 Message Date
jtangrot
05e4e2cdde Add idcutoff as input 2022-05-26 20:16:45 +02:00
Harshil Patel
f89b76afa4
Merge pull request #1701 from matthdsm/update/mosdepth
Mosdepth: add all remaining outputs
2022-05-25 19:46:37 +01:00
Harshil Patel
72a31b76eb
Update main.nf 2022-05-25 19:42:15 +01:00
Harshil Patel
241a1de035
Update main.nf 2022-05-25 19:38:12 +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
038fced07e
Merge pull request #1698 from mahesh-panchal/mash_screen_patch
Patch mash screen
2022-05-25 17:00:01 +02:00
Mahesh Binzer-Panchal
3d532405a5
Merge branch 'master' into mash_screen_patch 2022-05-25 16:51:42 +02:00
Robert A. Petit III
c50e097cd1
Merge pull request #1696 from jvhagey/gamma-update
adding upzip to gamma/gamma
2022-05-25 10:06:03 -04:00
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
jvhagey
127665d27b fixed test.yml 2022-05-24 19:27:09 -04:00
jvhagey
bb999395aa fixed pytest_modules.yml 2022-05-24 19:19:38 -04:00
Mahesh Binzer-Panchal
de74c0a83b
Merge pull request #1620 from mahesh-panchal/kat_hist
Add module kat hist
2022-05-25 00:23:38 +02:00
Mahesh Binzer-Panchal
3d51956b88
Merge branch 'master' into kat_hist 2022-05-24 23:10:13 +02:00
Ramprasad Neethiraj
00db06eb9e
Merge pull request #1685 from genomic-medicine-sweden/rhocall
add bcftools/roh
2022-05-24 22:39:32 +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
60793adea2
Merge pull request #1694 from SusiJo/cnvkit/reference
Add prefix to cnvkit/reference
2022-05-24 15:11:06 +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
Harshil Patel
2c0b0df088
Merge pull request #1693 from matthdsm/update/mosdepth
mosdepth: cram compatiblility
2022-05-24 13:52:18 +01:00
Matthias De Smet
8381a5e5dd add window test 2022-05-24 14:43:40 +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
Harshil Patel
f9aa1e0bdb
Merge pull request #1692 from SusiJo/cnvkit/reference
Changed tag of module
2022-05-24 12:49:15 +01:00
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
Matthias De Smet
5bc2d419a9 fix fail test 2022-05-24 13:23:00 +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
300e607a61
Merge pull request #1689 from drpatelh/umitools
Update umitools/dedup module to make --output-stats optional
2022-05-24 09:24:03 +01:00
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
0e1bbe5b4a
Merge pull request #1690 from SusiJo/cnvkit_reference
Add cnvkit/reference module
2022-05-24 09:08:13 +02:00
SusiJo
0f0d555f96
Merge branch 'master' into cnvkit_reference 2022-05-24 08:03:44 +02:00
SusiJo
61ebf89fb8
Merge pull request #1680 from SusiJo/cnvkit_bam
Modified cnvkit/batch module: cram2bam conversion
2022-05-24 08:03:26 +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