nf-core_modules/tests/modules/variantbam/test.yml at 4866421777747fc43fb7746993465938666426d6 - millironx/nf-core_modules - Milliron X Code: Code hosting for cattle or technology, but especially anything to do with both of them

millironx/nf-core_modules

mirror of https://github.com/MillironX/nf-core_modules.git synced 2024-11-14 13:43:09 +00:00

Johnathan D a21cc95c69

Add variantbam (#618 )

* template created for variantbam (#616)

* Add bcftools reheader (#585) (#608)

* local tests and linting passing (#585)

* fix: picard filtersamreads input (#610)

* Move readlist into same input channel as bam

* Update test reflecting input restructuring

* Update tests/modules/picard/filtersamreads/main.nf

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

* fix test

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

* Added module arriba (#611)

* Updated the version of STAR in align and genomegenerate modules

* Changes in test.yml

* Changes in test.yml

* Added module arriba

* Changes in test configs

* Added module Arriba for fusion detection

* Fixed review comments

* Added an output option for discarded fusions

* Resolved some conflits

* conflicts

* Apply suggestions from code review

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

* added test for new header

* enhance module fastp: add `save_merged` (#598) (#614)

* enhance module fastp: add `save_merged` (#598)

* removed md5sum checks from log and json

* Apply suggestions from code review

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: praveenraj2018 <43108054+praveenraj2018@users.noreply.github.com>

* fixed autogenerated biocontainter links

* variantbam module passing all tests/lints (#616)

* Added an optional output junction channel in STAR (#621)

* Added an optional output channel for chimeric junctions

* Fix in test.yml

* Apply suggestions from code review

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

* removed qcreport output

fixes #616

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: praveenraj2018 <43108054+praveenraj2018@users.noreply.github.com>

2021-07-26 19:07:29 +01:00

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 - name: variantbam test_variantbam
   command: nextflow run tests/modules/variantbam -entry test_variantbam -c tests/config/nextflow.config
   tags:
     - variantbam
   files:
     - path: output/variantbam/test.bam
       md5sum: fc08f065475d60b3b06ee32920564d4b