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
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
38964ecfc0
Fix bedtools intersect module
2021-02-07 21:32:01 +00:00
sruthipsuresh
957983bd99
Fixed and tested 4 modules, keeping with fastp module syntax
2021-01-29 23:17:44 -06:00
sruthipsuresh
295fff35ec
Corrected containers and tested
2021-01-29 23:17:44 -06:00
sruthipsuresh
19b55fc67c
Fixed intersect, complement indentation issues
2021-01-29 23:17:44 -06:00
sruthipsuresh
fc8cdde2b4
Apply suggestions from code review
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Add all initial suggestions from review (syntax issues)
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-01-29 23:17:44 -06:00
sruthipsuresh
70de0331a5
Corrected pytest and config
2021-01-29 23:17:44 -06:00
sruthipsuresh
672f94f2af
rebased and updated all bedtools testing and modules
2021-01-29 23:17:44 -06:00
sruthipsuresh
78473edb72
Removed large testing files, will convert to updated testing
2021-01-29 23:17:44 -06:00
Sruthi Suresh
4fca435120
Fixed naming issues and links in meta.yml
2021-01-29 23:17:44 -06:00
Sruthi Suresh
a984c1be7c
Added all modules with basic functionality and updated meta.yml files.
2021-01-29 23:17:44 -06:00
drpatelh
c08e6959a5
Reorganise everything
2020-08-05 16:09:25 +01:00
JoseEspinosa
a09e3a633d
I forgot to uncomment output
2020-07-16 16:38:37 +02:00
JoseEspinosa
d30089f12d
Very preliminary implementation of passing optional params to bedtools/intersect modules
2020-07-16 16:37:33 +02:00
JoseEspinosa
759dd85c92
Removing biocontainer in favor of nf-core container
2020-07-16 10:22:09 +02:00
JoseEspinosa
98c8f44130
Bedtools intersect adapted to the current module standard
2020-07-15 18:15:49 +02:00
JoseEspinosa
b38135ff6b
Moving bedtools/intersectbed to bedtools/intersect
2020-07-14 17:40:17 +02:00
