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Author SHA1 Message Date
MaxUlysse
28dc9227d7 fix: remove memory requirements and simplify URI 2021-02-16 13:54:40 +01:00
MaxUlysse
30e3f2c5f5 fix: ECLint check: trailing whitespace 2021-02-16 13:42:34 +01:00
MaxUlysse
053dd6ee1b add minimal cpu,memory and time requirements 2021-02-16 13:40:22 +01:00
MaxUlysse
7f35a1742d chores: add gatk/createsequencedictionary module 2021-02-16 13:40:06 +01:00
Harshil Patel
7d5ac60aa1
Merge pull request #176 from nf-core/MaxUlysse-patch-1 
Update meta.yml
 2021-02-16 10:43:18 +00:00
Maxime Garcia
303687d42a
Update .github/PULL_REQUEST_TEMPLATE.md 2021-02-16 11:30:29 +01:00
MaxUlysse
8c4d201dd5 chores: remove deprecated bwamem2/index modules cf #166 2021-02-16 11:27:25 +01:00
Maxime Garcia
d8706c12b3
Update meta.yml 
typo
 2021-02-16 11:22:15 +01:00
MaxUlysse
9472f2fa2d chores: Remove deprecated version of the module 2021-02-16 11:11:27 +01:00
MaxUlysse
a285bfe8a6 fix: add guidelines to PRs and issues 2021-02-16 11:07:43 +01:00
Anders Goncalves da Silva
fd854c333e
Add save mpileup as optional in output directive 2021-02-15 21:07:31 -08:00
Anders Goncalves da Silva
eeedb959c9
Clean out comments 2021-02-15 21:04:17 -08:00
Anders Goncalves da Silva
b99972f3a0
Move params to nextflow invocation 2021-02-15 20:59:45 -08:00
Anders Goncalves da Silva
89f65e0875 Merge branch 'master' into ivar-variant 2021-02-15 20:50:35 -08:00
Anders Goncalves da Silva
7cae9b1842
Add gff to meta yaml 2021-02-15 20:49:37 -08:00
Anders Goncalves da Silva
c12a558f15
Add tests without mpileup 2021-02-15 20:49:27 -08:00
Anders Goncalves da Silva
26189f4132
Change ternary expressions back to traditional format 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-02-15 19:56:22 -08:00
Anders Goncalves da Silva
3188b8e30e
Add explicit gff is false param 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-02-15 19:55:34 -08:00
Anders Goncalves da Silva
ee4c2828a0
Update gff assignment to string 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-02-15 19:55:12 -08:00
Anders Goncalves da Silva
39401ccd07
Add gff as input 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-02-15 19:54:36 -08:00
Anders Goncalves da Silva
8b6989f2d7
Add gff as input 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-02-15 19:54:19 -08:00
Anders Goncalves da Silva
4f8ab8bd69
Rename gff to features 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-02-15 19:53:30 -08:00
Anders Goncalves da Silva
8c483d4c6a
Add gff as input for proper staging 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-02-15 19:53:13 -08:00
Anders Goncalves da Silva
6259b72081
Fix output format 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-02-15 19:52:30 -08:00
Anders Goncalves da Silva
ef1e1b2539
Fix indentation 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-02-15 19:51:45 -08:00
Harshil Patel
8eb3acc43f
Merge pull request #171 from JoseEspinosa/mosdepth 
Add mosdepth module
 2021-02-15 23:13:01 +00:00
Harshil Patel
f97c78b3fb
Update software/mosdepth/main.nf 2021-02-15 22:49:53 +00:00
Anders Goncalves da Silva
f841483a70
Fix URL for containers 2021-02-15 13:23:35 -08:00
Anders Goncalves da Silva
9a5aa0f145
Fix tests to work with gff param 2021-02-15 11:51:04 -08:00
Anders Goncalves da Silva
e8d1171b5d
Make gff a param and not an optional input 2021-02-15 11:50:52 -08:00
Anders Goncalves da Silva
4af7414419
Add tests for ivar variants 2021-02-15 09:29:40 -08:00
Anders Goncalves da Silva
9e3c4e598c
Add meta to ivar variants 2021-02-15 09:29:10 -08:00
Anders Goncalves da Silva
4ab3ccc905
Add ivar variants 2021-02-15 09:28:10 -08:00
Anders Goncalves da Silva
2fe3210f88
Add ivar variants 2021-02-15 09:27:59 -08:00
Maxime Garcia
b28604efca
Merge pull request #166 from MaxUlysse/master_bwa-mem2 
chores: add bwa-mem2 index + mem
 2021-02-15 18:14:50 +01:00
JoseEspinosa
6e92a6a080 Adding mosdepth module 2021-02-15 14:33:44 +01:00
Maxime Garcia
ec0bf0145e
Merge branch 'master' into master_bwa-mem2 2021-02-15 13:08:52 +01:00
Harshil Patel
3d53917b47
Merge pull request #170 from andersgs/ivar_trim 
Add ivar trim
 2021-02-13 08:24:12 +00:00
Harshil Patel
4af9417b6d
Update software/ivar/trim/main.nf 2021-02-13 08:20:06 +00:00
Harshil Patel
a5686ed14e
Update software/ivar/trim/main.nf 2021-02-13 08:19:55 +00:00
Harshil Patel
f51f8c6400
Update tests/software/ivar/trim/main.nf 2021-02-13 08:18:32 +00:00
Harshil Patel
9d6f29fc61
Update tests/software/ivar/trim/main.nf 2021-02-13 08:17:15 +00:00
Harshil Patel
25f3d46f68
Update software/ivar/trim/meta.yml 2021-02-13 08:17:03 +00:00
Harshil Patel
cdd9be0a2d
Update tests/software/ivar/trim/main.nf 2021-02-13 08:16:44 +00:00
Anders Goncalves da Silva
bbdca4fa76
Fix output files 2021-02-12 16:14:46 -08:00
Anders Goncalves da Silva
47670a12ad
Fix ivar trim test.yml 2021-02-12 16:03:18 -08:00
Anders Goncalves da Silva
ed74d366bf
Clean up ivar trim main.nf 2021-02-12 16:03:07 -08:00
Anders Goncalves da Silva
7c9766962d
Add ivar trim meta.yml 2021-02-12 16:02:48 -08:00
Anders Goncalves da Silva
6dca7799e6
Add ivar trim 2021-02-12 16:02:10 -08:00
Harshil Patel
63a20e7b5c
Merge pull request #168 from JoseEspinosa/bcftools_merge 
Add bcftools merge module
 2021-02-12 23:20:30 +00:00