Jose Espinosa-Carrasco
95e02f913f
Update comments with new style ( #497 )
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* Update comment style on functions.nf files
* Update test main.nf comments
* Add meta for ggread
2021-05-12 14:56:46 +01:00
Harshil Patel
65a3422686
Add default publish_dir for index processes ( #428 )
2021-04-10 20:49:09 +01:00
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
Harshil Patel
242fdb2f73
Version bumps and minor module updates ( #406 )
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* Version bumps and minor module updates
* Fix Pangolin tests
* Fix SPAdes tests
* stageAs @phue
2021-04-06 13:38:41 +01:00
Jose Espinosa-Carrasco
ee90e7af77
Add default output dir for modules that create indices, updated ( #336 )
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* Add default output dir for modules that create indices
* Change path for index module test output
* Fix bowtie2/align tests
* Fixing bowtie/align tests
* Fix genomegenerate test
* Fixing README linting
2021-03-23 17:55:01 +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
dcc580e4fb
Remove Conda build ids for all modules
2021-02-16 23:58:23 +00:00
drpatelh
34e451dd2e
rsem - add build info for mulled container
2021-02-03 11:04:59 +00:00
drpatelh
26e04dd298
rsem - add build info for mulled container
2021-02-03 11:04:51 +00:00
Edmund Miller
d76638d6f8
style( #77 ): Fix editorconfig errors
2020-12-17 17:50:24 -06:00
Harshil Patel
b236d0c834
Update main.nf
2020-12-17 10:24:01 +00:00
drpatelh
047dbde0af
Add singularity containers for rnaseq pipeline modules
2020-12-13 23:41:53 +00:00
drpatelh
e5c7ecc89c
Use STAR to build initial index for RSEM
2020-11-30 11:29:24 +00:00
drpatelh
a3f46865ff
Remove Singularity image path
2020-11-12 14:55:16 +00:00
drpatelh
14525ed50d
Remove functions file
2020-10-14 18:29:50 +01:00
drpatelh
6bb3d5caea
Update container
2020-10-12 16:20:35 +01:00
drpatelh
64377d4035
Bug fixes
2020-10-12 16:20:22 +01:00
Harshil Patel
fb44f36f66
Update main.nf
2020-09-16 19:08:24 +01:00
drpatelh
cbf8329ffd
Add new modules
2020-09-10 16:09:54 +01:00
