Commit graph

19 commits

Author SHA1 Message Date
Harshil Patel
d9396adbdf
Update software version command (#269) 2021-03-15 12:21:21 +00:00
Jose Espinosa-Carrasco
572abb00b3
Remove def from module options definition in main (#270)
* Remove def from module options definition in main

* Fix bismark_deduplicate tests

* Fix bwameth_align tests

* Fixing gatk4 conda tests ("=" instead of ':' in build id)

* Same as previous commit (Fix gatk4 test)

* Fix qualimap bamqc test (no md5 check for pngs)

* Fix seqkit split2 tests. Changed to new test data

* Fix samtools tests. Some were missing initOptions include

* Removing TOOL SUBTOOL template module since now it is included on tools repo
2021-03-15 12:16:43 +00:00
drpatelh
9098ba41c8 Update ivar consensus 2021-02-23 20:36:03 +00:00
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
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
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
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
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
Anders Goncalves da Silva
8f546a1f95 Add ivar consensus 2021-02-09 10:26:35 -08:00