millironx/nf-core_modules
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17 commits

Author SHA1 Message Date
Kevin Menden
043a7d1e3c
remove deprecated test tags (#440) 
* remove deprecated test tags

* fix bowtie, gatk4/applybsqr

* fix gatk4 baserecalibrator

* fixed shovill

* fixed yara/mapper

* fixed kallistobustools/ref paths
 2021-04-13 18:03:09 +01:00
Edmund Miller
a3684d9594
Lint modules ci (#389) 
* ci: Add modules lint step

Moved it ahead of the nextflow install so ideally it'll fail before we
bother doing any more setup

* ci: _ => /

* Update tests/config/pytest_software.yml

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-04-08 09:10:52 +01:00
FriederikeHanssen
86df111707
Seqkit/split2 test path update (#372) 
* Update test path

* Fix bracket

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-03-24 17:05:43 +01:00
Harshil Patel
acb1a12a56
Re-organise all test data (#354) 
* Re-organise all test data

* Fix ECLint

* Fix ECLint agaaainn

* Now is not the time EClint
 2021-03-24 09:53:41 +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
FriederikeHanssen
7627e656ee Add all tests back in 2021-02-24 09:57:23 +01:00
FriederikeHanssen
8a7333c13b lower case path 2021-02-24 09:53:11 +01:00
FriederikeHanssen
7f6e5d9ab5 try to make a single test pass on GHA, passes locally 2021-02-24 09:48:55 +01:00
FriederikeHanssen
e67515809a try to only make paired-end test work, pass locally with conda & docker 2021-02-23 15:47:16 +01:00
FriederikeHanssen
13733b2581 Add beautiful md5sums 2021-02-23 14:57:07 +01:00
FriederikeHanssen
5e365d5eff Make all these tests pass 2021-02-23 14:09:46 +01:00
FriederikeHanssen
25a2a16f2d Try to make a single test pass 2021-02-23 13:34:50 +01:00
FriederikeHanssen
312bf85f70 use reasonable option params 2021-02-23 11:26:54 +01:00
FriederikeHanssen
9c51e05125 remove wrong md5 sums 2021-02-23 11:25:45 +01:00
FriederikeHanssen
c7d2bc8d43 Add tests for different options 2021-02-23 11:14:51 +01:00
FriederikeHanssen
ec63f335d5 Add split2 options 2021-02-22 22:43:32 +01:00
FriederikeHanssen
5f9aa7264e Add tests 2021-02-17 17:25:41 +01:00