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8 commits

Author SHA1 Message Date
James A. Fellows Yates
daab0a77dd
Add HAMRONIZATION/FARGENE and updates all HARMONIZATION tools to 1.1.1 (#2107) 
* Update main.nf

* Update meta.yml

* Re-add logos as not staged in a way that works with MultiQC config files

* Update main.nf

* Remove now unnecessary input channel

* Remove unused channel from tests

* Update hAMRonization to 1.1.1 and add hAMRonization farGene

* Fix hamronizatio ntests

* Prettier

* Fix fargene linting

* Correct file

* Fix fargene output

* Apply suggestions from code review

Co-authored-by: Jasmin F <73216762+jasmezz@users.noreply.github.com>

* Fix summarise tests

* Prettier

Co-authored-by: Jasmin F <73216762+jasmezz@users.noreply.github.com>
 2022-09-27 15:32:18 +02:00
James A. Fellows Yates
90aef30f43
Set process label to process_single for modules with no task.cpus usage (#2076) 
* Set process label to `process_single` for modules with no `task.cpus` usage

* Fix tests of 'borked' modules

* prettier

* More modules are single-threaded and can use process_single

* Adding process_single to hmmer/esl* modules

* Fix failing tests

* Prettier

Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk>
Co-authored-by: Daniel Lundin <erik.rikard.daniel@gmail.com>
 2022-09-19 11:54:47 +02:00
Jasmin F
7f7f6bc913
Add module hamronization/abricate (#1925) 
* Add hamronization/abricate

* Update input pattern in meta.yml

* Update location of hamronization test data

* Apply suggestions from code review
 2022-07-26 12:55:53 +02:00
louperelo
1368164eb5
add module hamronization/amrfinderplus (#1888) 
* add module hamronization/amrfinderplus

* deleted comments

* Apply suggestions from code review

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

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-07-15 10:54:42 +02:00
louperelo
057a889d3b
new module hamronization/rgi (#1844) 
* new module hamronization/rgi

* remove comments

* Update modules/hamronization/rgi/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-07-01 12:03:08 +02:00
Edmund Miller
f080015754
Prettier (#1405) 
* style: Add prettier config files

* build: Add prettier vscode extension

* ci: Replace markdownlint and yamllint with prettier

* style: Run prettier

* style: Use indent of 2 for markdown as well

https://github.com/nf-core/tools/pull/1470#issuecomment-1071028358

* style: Fix indent

* style: Let editorconfig take over tab widths

* style: yaml => yml

* ci: Run prettier once

Co-authored-by: Phil Ewels <phil.ewels@scilifelab.se>

Co-authored-by: Phil Ewels <phil.ewels@scilifelab.se>
 2022-03-18 14:27:50 +01:00
James A. Fellows Yates
61c88c6233
Add hamronization/summarize (#1366) 
* fix: remove left-over unnecessary code

* Add hamronizer/deeparg

* Add hamronisation/summarise

* Update test.yml

* Update modules/hamronization/summarize/meta.yml

Co-authored-by: Jasmin F <73216762+jasmezz@users.noreply.github.com>

* line up outputs

Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
Co-authored-by: Jasmin F <73216762+jasmezz@users.noreply.github.com>
 2022-03-03 08:02:04 +01:00
James A. Fellows Yates
4983f77796
Add hamronization/deeparg (#1364) 
* fix: remove left-over unnecessary code

* Add hamronizer/deeparg

* Add when condition

* Apply suggestions from code review

* Update modules/hamronization/deeparg/meta.yml
 2022-03-02 13:04:22 +01:00