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6 commits

Author SHA1 Message Date
Felipe Marques de Almeida
e1a3ae6bf5
make module output meta map (#1803) 2022-06-23 12:43:06 +02:00
Alexander Peltzer
8032833e6e
Update main.nf 2022-06-10 10:53:09 +02:00
Matthias Hörtenhuber
e745e167c1
Fix formatting in yaml files, add yamllint config (#1279) 
* fix yml formatting

* allow fastq.gz and fq.gz as file input, add meta.yml and test

* fix yaml files

* Revert "allow fastq.gz and fq.gz as file input, add meta.yml and test"

This reverts commit 34002d7a7a8c7f7bb4600c3377f35c87849f71a4.

* prettier magic!

* fix comments for yamllint

* remove node version number

* fix linting errors

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2022-02-15 11:15:27 +00:00
Mahesh Binzer-Panchal
e20e57f90b
Add when: block (#1261) 2022-02-04 09:53:32 +01:00
Regina Hertfelder Reynolds
1b24005f07
Add bcl2fastq2 to cellranger dockerfile (#1115) 
* refactor: add bcl2fastq to cellranger dockerfile

bcl2fastq required for the cellranger mkfastq module and was therefore
added to the cellranger dockerfile. Further, cellranger was updated to
the latest version, 6.1.2., with naming and containers across
cellranger modules updated accordingly.

* chore: add bcl2fastq zip to .gitignore

* style: fix code linting error

* test(cellranger): Add tiles to mkfastq

* additional dockerfile for mkfastq

* update readme and dockerfiles

* update readme

* fix: update container for mkfastq

* docs: correct typos in readme

* test: update md5sum following cellranger update

* test: update md5sum following cellranger update

* fix: new line for external args in mkfastq

* test: update mkfastq tiles argument

* test: comment out mkfastq tests until smaller test data found

* test: stub-run mkfastq test until smaller test data found

* test: fix incorrect file path for mkfastq

Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com>
Co-authored-by: ggabernet <gisela.gabernet@qbic.uni-tuebingen.de>
Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>
 2022-01-25 19:58:22 +01:00
Edmund Miller
e2ba70ed9a
Add Cell Ranger mkfastq, mkgtf, and count (#979) 
* feat(cellranger): Add initial count module

Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>

* feat(cellranger): Add mkgtf module

* test(cellranger): Fix count test with mkgtf

* fix(cellranger): Generalize gtf attribute filters

* chore: Add .gitignore for cellranger tar

* build(cellranger): Update dockerfile

https://joshtronic.com/2021/09/12/fixed-repository-debian-security-buster-updates-changed-suite-from-stable-to-oldstable/

* Apply suggestions from code review

Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update modules/cellranger/mkgtf/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* style: Capitalize README

* test(cellranger): Update pytest_modules

* feat(cellranger): Add initial mkfastq module

* ci: Update pytest modules

* refactor(cellranger): Update modules to new syntax

* docs(cellranger): Update meta files

There is some terrible copy-pasting going on.

* fix(cellranger): Add args

Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-12-02 14:27:20 +00:00