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
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
Florian Wuennemann
592002aa23
add picard_collectwgsmetrics ( #304 )
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* Added new module picard/collectwgsmetrics.
* Removed unused outputs from meta.yml
* Added version.txt file back to meta.yml
* Updated test.yml
* Removed md5sum from test.yaml and added contain tests.
* Update functions.nf
Fixed missing newline formatting.
* Update main.nf
Fixed missing newline formatting.
* style(picard): Remove trailing whitespace
Co-authored-by: Kevin Menden <kevin.menden@t-online.de>
Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com>
2021-03-22 17:05:59 +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
daab19a849
picard - add build to conda definition
2021-02-03 09:18:37 +00:00
Edmund Miller
d76638d6f8
style( #77 ): Fix editorconfig errors
2020-12-17 17:50:24 -06:00
drpatelh
200c946693
Add --singularity_pull_docker_container to module yml
2020-12-14 00:34:24 +00:00
drpatelh
99a2364a26
Update all other modules
2020-12-14 00:05:48 +00:00
drpatelh
047dbde0af
Add singularity containers for rnaseq pipeline modules
2020-12-13 23:41:53 +00:00
Edmund Miller
7848019cdb
test(picard): Refactor markduplicates to use pytest-workflow
2020-11-24 21:08:33 -06:00
Edmund Miller
939f5ca744
test(picard): Refactor collectmultiplemetrics to use pytest-workflow
2020-11-24 21:03:40 -06:00
Edmund Miller
234e85bdce
test(picard): Refactor mergesamfiles to use pytest-workflow
2020-11-24 19:01:12 -06:00
drpatelh
a3f46865ff
Remove Singularity image path
2020-11-12 14:55:16 +00:00
drpatelh
47d390772c
Update picard version command and default container
2020-10-19 15:17:19 +01:00
drpatelh
29f9b05433
Update docs
2020-10-15 11:13:54 +01:00
drpatelh
530789ba85
Get tests passing
2020-10-15 10:47:15 +01:00
drpatelh
1d30e2c21a
Update tools not in rnaseq pipeline too
2020-10-14 18:59:25 +01:00
drpatelh
d19a8c702d
Update picard version
2020-10-12 15:58:09 +01:00
drpatelh
e438d026bd
Unify syntax
2020-09-10 16:45:11 +01:00
drpatelh
473f1b192f
Update functions script
2020-09-10 15:59:26 +01:00
Jeremy1805
789dc4f09a
Changed options.publish_files definition in functions.nf/initOptions
2020-08-20 11:57:10 +01:00
drpatelh
08723c9d61
Add tests for mergesamfiles
2020-08-07 16:39:16 +01:00
drpatelh
3547b64eab
Add docs and tests for markduplicates
2020-08-07 16:30:28 +01:00
drpatelh
cb85acddf0
Add docs and tests for collectmultiplemetrics
2020-08-07 16:29:37 +01:00
drpatelh
f315a7b3c4
Hard copy files
2020-08-05 18:38:27 +01:00
drpatelh
993d0d5743
Add picard
2020-08-05 17:17:41 +01:00
