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a21cc95c69
* 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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