millironx/nf-core_modules
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16 commits

Author SHA1 Message Date
Maxime U. Garcia
25f88dee3c
Update samtools from 1.10 to 1.12 (#530) 
* feat: remove social preview image to use GitHub OpenGraph

* feat: update samtools from 1.10 to 1.12

* fix: CI tests

* fix: add meta.yml file for samtools/merge

* Update software/samtools/merge/meta.yml

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>

* Update software/samtools/merge/meta.yml

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
 2021-06-07 13:07:32 +02:00
Harshil Patel
d1c6082a66
Update modules required for rnaseq pipeline (#449) 
* Update HISAT2 build module

* Bump preseq version

* Fix tests

* Add meta.yml for preseq to fix linting

* Auto-detect --genomeSAindexNbases for smaller genomes

* Add placeholder to use human data for the tests

* Add CSI output option to samtools/index

* Fix samtools/index tests
 2021-04-16 08:56:47 +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
Harshil Patel
3df3d671f2
Fix nf-core modules lint tests (#275) 
* Fix Conda definition bug

* Add process label
 2021-03-16 17:16:47 +00:00
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
383d35bc7d samtools - add build to conda definition 2021-02-03 09:17:38 +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
e438d026bd Unify syntax 2020-09-10 16:45:11 +01:00
drpatelh
137db462a7 Add samtools 2020-08-05 17:17:47 +01:00
drpatelh
c08e6959a5 Reorganise everything 2020-08-05 16:09:25 +01:00
Paolo Di Tommaso
70daf8be30
Minor style improvents 
This commit provides a minor refactoring with som
Nextflow code style improvments:
- Replaces `.toGiga()` with `.giga`
- Replaces `tag { foo }` with `tag "$foo"`
- Move publishDir before input declarations. Directives should be
  before the first input. Tho this is not enforced, it may be in
  future versions.
- Replaces input `file` with `path`
- Remove unnecessary parentheses
 2020-07-27 12:11:42 +02:00
Phil Ewels
014fef2e92 Rename tools to software 2020-07-11 14:27:21 +02:00
Renamed from tools/samtools/index/main.nf (Browse further)