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 )
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* 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
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Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-02-12 15:09:50 -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
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
e9aa037e7b
Add function to enable output of mpileup
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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
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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
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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
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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
