Johnathan D
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a21cc95c69
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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>
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2021-07-26 19:07:29 +01:00 |
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