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
|
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
|
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
|
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 |
|
Anders Goncalves da Silva
|
a4bba006bd
|
Add reference fasta as input
|
2021-02-12 11:26:55 -08:00 |
|
Anders Goncalves da Silva
|
6b22bb9782
|
Add meta.yml
|
2021-02-12 11:25:40 -08:00 |
|
JoseEspinosa
|
0688230863
|
Revert since fixes to test were not working
This reverts commit d7a219e88d .
|
2021-02-12 18:02:32 +01:00 |
|
JoseEspinosa
|
8e23e1839d
|
Trying to fix tests
|
2021-02-12 17:56:51 +01:00 |
|
JoseEspinosa
|
6e8b63fc26
|
Add cat fastq module
|
2021-02-12 17:22:07 +01:00 |
|
Maxime Garcia
|
27be87ac72
|
Merge pull request #135 from drpatelh/bwa
Update indices syntax for BWA index and mem modules
|
2021-02-12 12:45:38 +01:00 |
|
Anders Goncalves da Silva
|
e9aa037e7b
|
Add function to enable output of mpileup
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
|
2021-02-10 10:02:06 -08:00 |
|
Anders Goncalves da Silva
|
06770d5f02
|
Specify the exact bioconda recipe build
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
|
2021-02-10 10:01:25 -08:00 |
|
Anders Goncalves da Silva
|
362a630f8b
|
Change suffix of mpileup ouput file
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
|
2021-02-10 10:00:54 -08:00 |
|
Anders Goncalves da Silva
|
884c4658b8
|
Make mpileup saving optional
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
|
2021-02-10 10:00:22 -08:00 |
|
Jose Espinosa-Carrasco
|
1e771ac8a0
|
Merge pull request #164 from drpatelh/fixes
Add missing build ids and rename *.txt channels
|
2021-02-10 14:19:00 +01:00 |
|
drpatelh
|
b9afca2b05
|
Underscore not .
|
2021-02-10 12:53:17 +00:00 |
|
drpatelh
|
d2508e3c03
|
Amend prefix for bcftools stats
|
2021-02-10 12:51:47 +00:00 |
|
drpatelh
|
e63279e6a2
|
Pin pangoLearn version
|
2021-02-10 10:28:27 +00:00 |
|
drpatelh
|
b03846600d
|
Tidy up
|
2021-02-09 23:26:45 +00:00 |
|
drpatelh
|
6795fe04b8
|
Rename output channel
|
2021-02-09 23:26:18 +00:00 |
|
drpatelh
|
2b9129b3f9
|
Change txt channel output
|
2021-02-09 23:09:22 +00:00 |
|
drpatelh
|
d50d070c06
|
Change txt channel output
|
2021-02-09 23:09:18 +00:00 |
|
drpatelh
|
0b33b6d081
|
Add missing build ids
|
2021-02-09 23:03:13 +00:00 |
|
JoseEspinosa
|
e8dc199dc8
|
Adding conda build to blast modules
|
2021-02-09 23:04:12 +01:00 |
|
JoseEspinosa
|
2fa14f2ec8
|
Adding conda build to bcftools modules
|
2021-02-09 23:00:19 +01:00 |
|
Harshil Patel
|
3f431014a4
|
Update software/bedtools/getfasta/main.nf
|
2021-02-09 21:34:40 +00:00 |
|
Anders Goncalves da Silva
|
8f546a1f95
|
Add ivar consensus
|
2021-02-09 10:26:35 -08:00 |
|
JoseEspinosa
|
68b85d9191
|
Merge remote-tracking branch 'upstream/master' into bedtools_getfasta
|
2021-02-09 18:23:24 +01:00 |
|
JoseEspinosa
|
e118bc049a
|
Add bedtools getfasta module
|
2021-02-09 17:56:51 +01:00 |
|
JoseEspinosa
|
12ae7b0bff
|
Adding blast blastn module
|
2021-02-09 16:58:36 +01:00 |
|
JoseEspinosa
|
c23b355b35
|
Add blast makeblastdb module
|
2021-02-09 15:44:34 +01:00 |
|
JoseEspinosa
|
c93e96101a
|
Add untar module
|
2021-02-09 11:50:32 +01:00 |
|
JoseEspinosa
|
20771ae1bc
|
Remove meta from input/output meta.yml
|
2021-02-09 11:02:31 +01:00 |
|
JoseEspinosa
|
b09416a0d0
|
Correcting meta.yml
|
2021-02-09 10:51:57 +01:00 |
|
JoseEspinosa
|
f7f06dd6e8
|
Add gunzip module
|
2021-02-09 10:05:55 +01:00 |
|
Harshil Patel
|
46e5df2cf7
|
Merge pull request #151 from drpatelh/bedtools
Follow up fixes for bedtools modules added in #79
|
2021-02-09 01:54:31 +00:00 |
|
Harshil Patel
|
84cf5ea2ef
|
Merge pull request #153 from JoseEspinosa/bedtools_maskfasta
Add bedtools maskfasta module
|
2021-02-08 23:11:00 +00:00 |
|
JoseEspinosa
|
02d10c25a3
|
Add bedtools maskfasta module
|
2021-02-08 23:41:10 +01:00 |
|
JoseEspinosa
|
f4e322f88d
|
Merging upstream changes
# Conflicts:
# .github/filters.yml
|
2021-02-08 18:09:41 +01:00 |
|
JoseEspinosa
|
fe412797dd
|
Adressing general comments on PR #134
|
2021-02-08 15:11:36 +01:00 |
|