millironx/nf-core_modules
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14 commits

Author SHA1 Message Date
Harshil Patel
e937c7950a
Rename software/ directory to modules/ to re-organise module structure (#567) 
* Update README

* Rename pytest_software.yml to pytest_modules.yml

* Rename main software directory to modules

* Remove deprecated modules

* Rename tests software to modules

* Replace paths for tests in pytest_modules.yml

* Replace software with modules in Github Actions

* Replace software with modules in main.nf tests

* Rename software to modules in test.yml
 2021-07-07 10:10:18 +01:00
Harshil Patel
dce27b8102
Update functions.nf to be more flexible for publishing by meta keys (#423) 
* Update functions.nf

* Replace saveAs line in module main script

* Add spacing for ECLint
 2021-04-09 17:23:56 +01:00
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
dcc580e4fb Remove Conda build ids for all modules 2021-02-16 23:58:23 +00:00
drpatelh
f3b5af4ed5 Fix bedtools slip module 2021-02-07 21:32:20 +00:00
sruthipsuresh
e360617ac6 Fixed images, genomecov 2021-01-29 23:17:44 -06:00
sruthipsuresh
e3bbbb48fc Fixed slop file 2021-01-29 23:17:44 -06:00
sruthipsuresh
fc8cdde2b4 Apply suggestions from code review 
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
Sruthi Suresh
89e5473b44 Updated modules with the changed container format 2021-01-29 23:17:44 -06:00
Sruthi Suresh
6677c98b11 Updated complement and completed slop module with all parameters available. 2021-01-29 23:17:44 -06:00
Sruthi Suresh
709970e9af Completed slop module for modules with test directory and updated meta.yml file 2021-01-29 23:17:44 -06:00
Sruthi Suresh
1426d89440 Completed sloprefseq and removegenes modules (main.nf, meta.yml and functiosn.nf file). Also added the test directory with input/output/main.nf files. 2021-01-29 23:17:44 -06:00