millironx/nf-core_modules
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20 commits

Author SHA1 Message Date
Jose Espinosa-Carrasco
e621f78757
Update salmon/quant to provide '--libType A' option (#536) 
* Update salmon/quant to provide '--libType A' option

* Modify lib_type description to  be a string

* Update tests

* lyb_type can be explicitly overwrite

* Update main.nf

* Update main.nf

* Update main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-06-17 15:13:47 +02:00
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
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) 
* 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
ee90e7af77
Add default output dir for modules that create indices, updated (#336) 
* 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
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) 
* 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
3ae4c51f42 various - add build to conda definition 2021-02-03 09:20:34 +00:00
Kevin Menden
afaef3c30d
Apply suggestions from code review 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-01-29 12:40:15 +01:00
kevinmenden
3750bea2dd fixed typo 2021-01-26 16:18:46 +01:00
kevinmenden
a3185732ff added meta.yml files 2021-01-26 16:12:41 +01:00
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
115efec15c Update Salmon quant to use BAM input 2020-12-09 21:20:52 +00:00
drpatelh
42f318fe75 Update Salmon modules 2020-12-09 21:20:11 +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
e438d026bd Unify syntax 2020-09-10 16:45:11 +01:00
drpatelh
cbf8329ffd Add new modules 2020-09-10 16:09:54 +01:00