millironx/nf-core_modules
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3158 commits 30 branches 0 tags 142 MiB
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26 commits

Author SHA1 Message Date
Jasmin F
85b3c2bcf2
Apply suggestions from code review 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-05-12 15:28:19 +02:00
jasmezz
d2ef476321 Fix Prettier linting error 2022-05-12 12:19:50 +02:00
jasmezz
37cc6f250b Fixed test.yml 2022-05-12 12:14:19 +02:00
jasmezz
bd4b70439b Streamlined some output channels, formatted tests main.nf 2022-05-12 10:56:48 +02:00
Jasmin F
853e3ec087
Remove commented code 
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
 2022-05-11 15:56:10 +02:00
jasmezz
2b746abfbe Fix Prettier linting issue 2022-05-11 12:09:52 +02:00
jasmezz
5d76f1c7ff Add fasta/gff input option 2022-05-11 12:06:02 +02:00
jasmezz
24b9c397dd Apply suggestions from code review + add support for GFF annotations 2022-05-05 13:14:39 +02:00
jasmezz
6a7aec8b41 Remove prokka test workflow 2022-05-05 10:22:02 +02:00
jasmezz
fa9f0753de Apply review suggestions + add stub for prokka test workflow 2022-05-03 17:30:16 +02:00
jasmezz
a992a0207e Merge branch 'antismashlite' of github.com:jasmezz/modules into antismashlite 2022-05-02 17:58:52 +02:00
Jasmin F
b8386c42a7
Merge branch 'nf-core:master' into antismashlite 2022-05-02 17:58:19 +02:00
jasmezz
d19e65d2a2 Merge branch 'antismashlite' of github.com:jasmezz/modules into antismashlite 2022-05-02 17:56:23 +02:00
jasmezz
35cc8152b8 Fix missing test input 2022-05-02 17:55:39 +02:00
Jasmin F
883b95bed6
Merge branch 'nf-core:master' into antismashlite 2022-05-02 17:31:43 +02:00
jasmezz
4a4de550b8 Simplify/reduce container mount volumes 2022-05-02 17:30:46 +02:00
Jasmin F
39258e53d7
Update checksum in test.yml 2022-04-28 17:09:40 +02:00
Jasmin F
c740853874
Antismash db output patch 1 (#3) 
* Update main.nf

* Update meta.yml

* Update test.yml
 2022-04-28 16:42:44 +02:00
Jasmin F
61e740f79c
Add antismash download DB: missing container folders as output channels (#1567) 
* Add missing container folders as output channels

* Apply suggestions from code review

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update tool name

* Update test output checksum

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-04-27 12:40:04 +02:00
Jasmin F
9108e2e2ec
Update test output checksum 2022-04-27 12:22:05 +02:00
Jasmin F
d79433dcac
Apply suggestions from code review 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-04-27 10:08:07 +02:00
jasmezz
cc05006dbb Update antismashlite module main.nf 2022-04-26 17:15:41 +02:00
jasmezz
134272c7ee Add missing container folders as output channels 2022-04-26 17:04:57 +02:00
jasmezz
1acde9a7a1 Fix container volume mounts 2022-04-26 16:28:39 +02:00
jasmezz
1c1e813c67 Initial module creation 2022-04-22 16:47:48 +02:00
Jasmin F
d07d270743
Antismashlite download databases (#1426) 
* Create module antismashlitedownloaddatabases

* Corrected user-specification of database directory

* Updated test.yml

* Apply suggestions from code review

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Fix typo in test.yml

* Feed database files via docker/singularity mount)

* Add external db file mounts to the containers

* Fixed docker command in main.nf

* Apply prettier

* Apply prettier and add PWD

* Add more output to test.yml

* Add more output paths to test.yml

* Fixed test.yml

* Apply suggestions from code review

Add documentation of why we need to mount files to the containers.

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Fix code linting errors (remove trailing whitespaces)

* Fix code linting error (remove trailing whitespace)

* Fix errors from Prettier linting

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-04-21 10:38:17 +02:00