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Author SHA1 Message Date
Harshil Patel
d6d34a4b5b
Merge pull request #177 from MaxUlysse/master_gatk_createsequencedictionary 
Add gatk/createsequencedictionary
 2021-02-16 22:21:38 +00:00
Harshil Patel
a6d6c0b973
Update software/gatk/createsequencedictionary/main.nf 2021-02-16 22:08:11 +00:00
Harshil Patel
7c64e70c9e
Update software/gatk/createsequencedictionary/meta.yml 2021-02-16 22:07:51 +00:00
Harshil Patel
e558d5fb57
Merge pull request #174 from andersgs/ivar_consensus_fix 
ivar consensus: Add save mpileup as optional in output directive
 2021-02-16 22:04:38 +00:00
Harshil Patel
d30baa9e54
Merge pull request #178 from MaxUlysse/master_resource_requirements 
Add cpus, memory and time requirements to limit resource consumption
 2021-02-16 22:03:39 +00:00
MaxUlysse
4968458b6c chores: add cpus, memory and time requirements to limit resource consumption 2021-02-16 14:18:29 +01:00
MaxUlysse
763800a0e2 fix: correct md5sum 2021-02-16 13:54:54 +01:00
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
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
Anders Goncalves da Silva
fd854c333e
Add save mpileup as optional in output directive 2021-02-15 21:07:31 -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
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
Harshil Patel
b74ba0af1e
Merge pull request #162 from andersgs/ivar-consensus 
Add ivar consensus module
 2021-02-12 23:18:57 +00:00
Harshil Patel
c0d128fd39
Update software/bcftools/merge/main.nf 2021-02-12 23:16:52 +00:00
Anders Goncalves da Silva
9268851cde
Remove samtools option 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-02-12 15:09:50 -08:00
Anders Goncalves da Silva
1f66954180
Relabel input parameter 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-02-12 15:09:35 -08:00
JoseEspinosa
5313698705 Add bcftools merge module 2021-02-13 00:08:57 +01:00
Harshil Patel
96d3b0a18b
Update tests/software/ivar/consensus/main.nf 2021-02-12 23:02:25 +00:00
Harshil Patel
f8916060f8
Update tests/software/ivar/consensus/main.nf 2021-02-12 23:02:19 +00:00
Harshil Patel
0580fd8ded
Update software/ivar/consensus/main.nf 2021-02-12 23:02:04 +00:00
Harshil Patel
9e4539473e
Update software/ivar/consensus/main.nf 2021-02-12 23:01:53 +00:00
Harshil Patel
bc5e073cdb
Update software/ivar/consensus/main.nf 2021-02-12 22:57:06 +00:00
Anders Goncalves da Silva
cb19c7b056
Fix trailing whitespace 2021-02-12 14:46:13 -08:00
Anders Goncalves da Silva
b08bf1ea5c
Remove ref to conda build and additional params 2021-02-12 14:43:50 -08:00
Anders Goncalves da Silva
ffc849761d
Edit test to output mpileup and passing args to samtools 2021-02-12 14:43:19 -08:00
Anders Goncalves da Silva
487ec7b793
Fix test.yml 2021-02-12 14:42:42 -08:00
Anders Goncalves da Silva
24b212318b Merge branch 'master' into ivar-consensus 2021-02-12 11:51:24 -08:00
Anders Goncalves da Silva
bfc13d3379
Add options to make samtools more flexible 2021-02-12 11:50:33 -08:00