millironx/nf-core_modules
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Author SHA1 Message Date
SusiJo
810564deca
Merge branch 'master' into gatk_spark 2022-05-31 15:24:58 +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
94dd8f63df
Merge pull request #1710 from jfy133/fix-filtlong 
Fix filtlong - makes running without shortreads work correctly, and also ensures all tests produce …
 2022-05-31 14:54:54 +02:00
SusiJo
9ef09e6add adjusted newlines 2022-05-31 14:54:39 +02:00
SusiJo
205576279f ran prettier again 2022-05-31 14:50:55 +02:00
James A. Fellows Yates
0b895871d7
Merge branch 'master' into fix-filtlong 2022-05-31 14:49:44 +02:00
James Fellows Yates
430def06fa Switch from md5sum to string due to conda flakiness 2022-05-31 14:45:41 +02:00
SusiJo
d484aa1906 adjusted tabs 2022-05-31 14:45:23 +02:00
SusiJo
e083bfafa0 ran prettier 2022-05-31 14:38:45 +02:00
SusiJo
1e396d767f Merge remote-tracking branch 'upstream/master' into gatk_spark 2022-05-31 14:36:14 +02:00
SusiJo
ea526051a4 new test.yml 2022-05-31 14:35:42 +02:00
SusiJo
3117b2973c added test for metrics 2022-05-31 14:35:29 +02:00
SusiJo
e0e8273f74 adjusted input to use queryname sorted bams 2022-05-31 14:35:18 +02:00
SusiJo
39e34418c9 added metrics as optional output 2022-05-31 14:34:50 +02:00
James A. Fellows Yates
667a0bc24c
Merge pull request #1708 from sguizard/bamtools/convert/remove_TODO 
👌 IMPROVE: Remove last TODO
 2022-05-31 13:41:41 +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
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