Harshil Patel
dce27b8102
Update functions.nf to be more flexible for publishing by meta keys ( #423 )
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* Update functions.nf
* Replace saveAs line in module main script
* Add spacing for ECLint
2021-04-09 17:23:56 +01:00
Patrick Hüther
8a44258548
remove params section from meta.yml ( #282 )
2021-03-19 13:16:50 +01:00
Harshil Patel
9b99b33401
Rename .github/filters.yml -> tests/config/pytest_software.yml ( #271 )
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* Rename pytest filters.yml
* Change filters.yml name
* Update resoures for ivar trim
2021-03-15 12:51:30 +00:00
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
1094af2206
Add missing docs
2021-02-24 12:54:45 +00:00
drpatelh
89cd71309c
Output log file for MultiQC
2021-02-23 20:36:23 +00:00
drpatelh
9098ba41c8
Update ivar consensus
2021-02-23 20:36:03 +00:00
Harshil Patel
a282ecd8c7
Merge pull request #172 from andersgs/ivar-variant
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Add ivar variants
2021-02-16 23:20:30 +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
7cae9b1842
Add gff to meta yaml
2021-02-15 20:49:37 -08:00
Anders Goncalves da Silva
26189f4132
Change ternary expressions back to traditional format
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Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-02-15 19:56:22 -08:00
Anders Goncalves da Silva
4f8ab8bd69
Rename gff to features
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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
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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
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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
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Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-02-15 19:51:45 -08:00
Anders Goncalves da Silva
f841483a70
Fix URL for containers
2021-02-15 13:23:35 -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
9e3c4e598c
Add meta to ivar variants
2021-02-15 09:29:10 -08:00
Anders Goncalves da Silva
2fe3210f88
Add ivar variants
2021-02-15 09:27:59 -08:00
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
25f3d46f68
Update software/ivar/trim/meta.yml
2021-02-13 08:17:03 +00:00
Anders Goncalves da Silva
bbdca4fa76
Fix output files
2021-02-12 16:14:46 -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
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
Anders Goncalves da Silva
1f66954180
Relabel input parameter
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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
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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
