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Author SHA1 Message Date
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
James Fellows Yates
7ffe98ac8b Add gatk/indelrealigner 2022-05-30 21:12:21 +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
Jeanette Tångrot
3bb32b2def
Merge pull request #1705 from jtangrot/vsearch_usearch_global 
Vsearch usearch global
 2022-05-30 14:28:01 +02:00
jtangrot
6ae405c5da prettier 2022-05-30 13:35:12 +02:00
jtangrot
6aac5c2c40 Update test 2022-05-30 13:30:27 +02:00
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
5132b004c7 Merge branch 'vsearch_usearch_global' of https://github.com/jtangrot/nf-core_modules into vsearch_usearch_global 2022-05-30 08:55:33 +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
b86d792055
Merge pull request #1703 from drpatelh/star 
Bump container version for STAR to 2.7.10a
 2022-05-27 12:29:59 +01:00
Harshil Patel
ad578cafcc Fix tests 2022-05-27 12:14:10 +01:00
Harshil Patel
fb6c7bca3d Bump container version for STAR to 2.7.10a 2022-05-27 11:35:04 +01:00
jtangrot
05e4e2cdde Add idcutoff as input 2022-05-26 20:16:45 +02:00
Sateesh Peri
ead3679829
Merge branch 'master' into rp3-add-snippy 2022-05-26 03:04:19 -04:00
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
SusiJo
b34e5ea6bf rm unnecessary spark_user 2022-05-25 16:38:48 +02:00
SusiJo
1400f2e683 fixed tests - mixed chr21 + chr22 2022-05-25 16:38:30 +02:00
SusiJo
dd6d838cd7 override userEmulation 2022-05-25 16:37:44 +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
jasmezz
77b5986463 Create ampir module 2022-05-25 13:27:10 +02:00
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