Commit graph

14 commits

Author SHA1 Message Date
Harshil Patel
b3278a1e63
Modules TLC (#551)
* Modules TLC

* Fix all the tests
2021-07-01 16:13:01 +01:00
Jose Espinosa-Carrasco
95e02f913f
Update comments with new style (#497)
* Update comment style on functions.nf files

* Update test main.nf comments

* Add meta for ggread
2021-05-12 14:56:46 +01:00
Yuk Kei Wan
6ad50f8ec4
Add stringtie merge module (from nanoseq modules) (#475)
* add stringtie merge module

* add md5sum and path for stringtie.merged.gtf

* fix errors

* try fixing stringtie check error

* add tag

* remove unreproducible md5sum

* address PR suggestions

* hopefully fix linting error
2021-05-03 07:18:51 +02:00
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
2b9129b3f9 Change txt channel output 2021-02-09 23:09:22 +00:00
drpatelh
3ae4c51f42 various - add build to conda definition 2021-02-03 09:20:34 +00:00
Edmund Miller
d76638d6f8
style(#77): Fix editorconfig errors 2020-12-17 17:50:24 -06:00
drpatelh
047dbde0af Add singularity containers for rnaseq pipeline modules 2020-12-13 23:41:53 +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
74f27803b4 Update stringtie version 2020-10-12 15:55:07 +01:00
drpatelh
cbf8329ffd Add new modules 2020-09-10 16:09:54 +01:00