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22 commits

Author SHA1 Message Date
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
James A. Fellows Yates
70f7f07a37
Apply suggestions from code review 
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
 2022-06-09 08:33:37 +02:00
James Fellows Yates
939653a47e Changes after code review 2022-06-09 08:26:04 +02:00
James Fellows Yates
4d7afa21e2 Add GATK indelrealigner tests 2022-06-08 21:14:08 +02:00
James A. Fellows Yates
1fc0d3de4b
Merge branch 'gatk3-indelrealigner' into upstream-for-indel 2022-06-08 20:30:19 +02:00
James A. Fellows Yates
0d087b4890
Update modules/gatk/realignertargetcreator/main.nf 2022-06-03 21:33:54 +02:00
James A. Fellows Yates
d292f822e4
Merge branch 'master' into gatk-realigntargetcreator 2022-06-03 21:33:22 +02:00
James A. Fellows Yates
e827a042ce
Update modules/gatk/unifiedgenotyper/main.nf 
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
 2022-06-03 21:24:03 +02:00
James Fellows Yates
a565d9072a Add GATK UnifiedGenotyper 2022-06-02 21:39:39 +02:00
James Fellows Yates
a14855dbe8 Start meta 2022-06-02 21:22:21 +02:00
James Fellows Yates
544b62df45 Star work on GATK UG 2022-06-02 21:11:17 +02:00
James Fellows Yates
de88adc926 Standardise parameters (no tests yet until realigntarget creator ready) 2022-06-02 20:35:34 +02:00
James Fellows Yates
9a4f22e8d1 Merge branch 'gatk-realigntargetcreator' of github.com:jfy133/nf-core-modules into gatk-realigntargetcreator 2022-06-02 20:32:03 +02:00
James Fellows Yates
c469a2b35e Fux tests 2022-06-02 20:32:00 +02:00
James Fellows Yates
599b264280 Standaridse parameters 2022-06-02 20:27:16 +02:00
James A. Fellows Yates
b1edcc6e94
Update modules/gatk/realignertargetcreator/main.nf 2022-06-02 20:26:09 +02:00
James A. Fellows Yates
43ef3841d1
remove duplciate path 2022-06-02 20:25:12 +02:00
James Fellows Yates
14c63f9ccc Changes after review 2022-06-02 20:24:14 +02:00
James Fellows Yates
7633d7816b Add GATK(3)/realignertargetcreator 2022-05-31 20:35:54 +02:00
James Fellows Yates
d39ba08e02 Prepare main module code 2022-05-31 20:19:49 +02:00
James Fellows Yates
c1ac3fbb59 Skeleton 2022-05-31 20:13:48 +02:00
James Fellows Yates
7ffe98ac8b Add gatk/indelrealigner 2022-05-30 21:12:21 +02:00