Kevin Menden
b59e8054e4
fix rseqc/junctionsaturation ( #553 )
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* bump bcftools filter
* junctionsaturation meta.yml and test
* pytest config entry
* bump bcftools version down again
* fix test
* fix bcftools
2021-07-02 13:31:09 +02:00
Harshil Patel
b5f6a1da79
Fix linting failures ( #552 )
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* Modules TLC
* Fix all the tests
* Fix linting failures
* Soft-link build files to bypass lint error
* Update software/rseqc/junctionannotation/main.nf
2021-07-01 19:50:14 +01:00
Jose Espinosa-Carrasco
95e02f913f
Update comments with new style ( #497 )
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* Update comment style on functions.nf files
* Update test main.nf comments
* Add meta for ggread
2021-05-12 14:56:46 +01:00
Kevin Menden
1d874bb0d0
Finish rseqc modules ( #439 )
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* initial 'modules create' of minia
* fixed tests
* finished meta.yml
* fixed filters.yml
* resolved issues in pytest_software.yml
* add newline
* Update software/minia/main.nf
* fixing a bunch of module tests
* remove vscode
* fixed minia
* added rseqc/bamstat tests
* added tests/meta.yml for rseqc/inferexperiment
* added test/meta.yml for rseqc/inner_distances
* added meta.yml and tests/main.nf for junctionannotation (test not running)
* added test/meta.yml for rseqc/readdistribution
* finished test/meta.yml for rseqc/readduplication
* added entries to pytest_software.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-13 08:49:32 +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
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
773d4d89f2
rseqc - add build to conda definition
2021-02-03 09:18:20 +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
e9e81e8691
Revert RSeQC version
2020-10-12 17:47:13 +01:00
drpatelh
a1b705d412
Update RSeQC version
2020-10-12 16:04:04 +01:00
drpatelh
cbf8329ffd
Add new modules
2020-09-10 16:09:54 +01:00
