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Create subworkflow to filter reads from blacklisted regions #17

Merged
merged 45 commits into from
Oct 23, 2023
Merged

Create subworkflow to filter reads from blacklisted regions #17

merged 45 commits into from
Oct 23, 2023

Commits on Oct 19, 2023

  1. chore: Merge branch 'filter-aligned' into filter-blacklist-subwf

    @kelly-sovacool
    kelly-sovacool committed Oct 19, 2023
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  2. chore: create test datasets

    @kelly-sovacool
    kelly-sovacool committed Oct 19, 2023
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  3. test: gzip test data files

    @kelly-sovacool
    kelly-sovacool committed Oct 19, 2023
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  4. feat: create subworkflow to filter blacklist

    @kelly-sovacool
    kelly-sovacool committed Oct 19, 2023
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  5. fix: subwf path

    @kelly-sovacool
    kelly-sovacool committed Oct 19, 2023
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  6. fix: module paths

    @kelly-sovacool
    kelly-sovacool committed Oct 19, 2023
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Commits on Oct 20, 2023

  1. test: use custom test data locally 

    because the github repo is internal right now, so can't access URLs
    @kelly-sovacool
    kelly-sovacool committed Oct 20, 2023
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  2. fix: use bwa index for next step

    @kelly-sovacool
    kelly-sovacool committed Oct 20, 2023
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  3. test: create test yml file 

    had to do it manually due to nf-core tools not supporing local custom
module repos yet for subworkflows.
    @kelly-sovacool
    kelly-sovacool committed Oct 20, 2023
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  4. test: fix typos

    @kelly-sovacool
    kelly-sovacool committed Oct 20, 2023
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  5. test: fix tuple construction

    @kelly-sovacool
    kelly-sovacool committed Oct 20, 2023
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  6. test: expected 2 fasta file for paired

    @kelly-sovacool
    kelly-sovacool committed Oct 20, 2023
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  7. test: unpaired output is empty after filtering 

    towards CCBR/CHAMPAGNE#117
    @kelly-sovacool
    kelly-sovacool committed Oct 20, 2023
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  8. test: add filter_blacklist subworkflow to pytest list

    @kelly-sovacool
    kelly-sovacool committed Oct 20, 2023
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  9. chore: Merge branch 'filter-aligned' into filter-blacklist-subwf

    @kelly-sovacool
    kelly-sovacool committed Oct 20, 2023
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  10. docs: add new subwf to changelog

    @kelly-sovacool
    kelly-sovacool committed Oct 20, 2023
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  11. test: make sure custom test filenames are unique

    @kelly-sovacool
    kelly-sovacool committed Oct 20, 2023
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  12. test: tag needs to start with subworkflows

    @kelly-sovacool
    kelly-sovacool committed Oct 20, 2023
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  13. chore: Merge branch 'filter-aligned' into filter-blacklist-subwf

    @kelly-sovacool
    kelly-sovacool committed Oct 20, 2023
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  14. fix: tags -> keywords

    @kelly-sovacool
    kelly-sovacool committed Oct 20, 2023
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  15. refactor: rename bam_to_fastq to bam2fastq

    @kelly-sovacool
    kelly-sovacool committed Oct 20, 2023
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  16. refactor: move samtools/filter_aligned to samtools/filteraligned

    @kelly-sovacool
    kelly-sovacool committed Oct 20, 2023
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  17. fix: path name

    @kelly-sovacool
    kelly-sovacool committed Oct 20, 2023
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  18. refactor: move subworkflows

    @kelly-sovacool
    kelly-sovacool committed Oct 20, 2023
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  19. test: fix subworkflow subdir structure

    @kelly-sovacool
    kelly-sovacool committed Oct 20, 2023
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  20. fix: move subwf

    @kelly-sovacool
    kelly-sovacool committed Oct 20, 2023
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  21. test: fix tags

    @kelly-sovacool
    kelly-sovacool committed Oct 20, 2023
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  22. test: fix bam2fastq path

    @kelly-sovacool
    kelly-sovacool committed Oct 20, 2023
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  23. fix: paths

    @kelly-sovacool
    kelly-sovacool committed Oct 20, 2023
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  24. fix: paths

    @kelly-sovacool
    kelly-sovacool committed Oct 20, 2023
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Commits on Oct 23, 2023

  1. test: use url for custom test data

    @kelly-sovacool
    kelly-sovacool committed Oct 23, 2023
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  2. test: fix expected output

    @kelly-sovacool
    kelly-sovacool committed Oct 23, 2023
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  3. test: empty gzip file has zero lines

    @kelly-sovacool
    kelly-sovacool committed Oct 23, 2023
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  4. test: fix filter output dir

    @kelly-sovacool
    kelly-sovacool committed Oct 23, 2023
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  5. fix: samtools/filteraligned component name

    @kelly-sovacool
    kelly-sovacool committed Oct 23, 2023
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  6. chore: Merge branch 'main' into filter-blacklist-subwf

    @kelly-sovacool
    kelly-sovacool committed Oct 23, 2023
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  7. chore: Merge branch 'main' into filter-blacklist-subwf

    @kelly-sovacool
    kelly-sovacool committed Oct 23, 2023
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  8. refactor: update usage of samtools filter aligned

    @kelly-sovacool
    kelly-sovacool committed Oct 23, 2023
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  9. fix: case-sensitive include paths

    @kelly-sovacool
    kelly-sovacool committed Oct 23, 2023
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  10. test: update tags

    @kelly-sovacool
    kelly-sovacool committed Oct 23, 2023
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  11. chore: Merge branch 'main' into filter-blacklist-subwf

    @kelly-sovacool
    kelly-sovacool committed Oct 23, 2023
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  12. refactor: use picard/samtofastq in filter_blacklist 

    custom/bam2fastq probably fails due to naming scheme not matching nf-core
    @kelly-sovacool
    kelly-sovacool committed Oct 23, 2023
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  13. refactor: samtools_filter_aligned -> samtools_filteraligned 

    process names can only have 1 underscore
otherwise linting fails in subworkflows that use them
    @kelly-sovacool
    kelly-sovacool committed Oct 23, 2023
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  14. fix: typo in samtools_filteraligned

    @kelly-sovacool
    kelly-sovacool committed Oct 23, 2023
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  15. docs: show subworkflows command

    @kelly-sovacool
    kelly-sovacool committed Oct 23, 2023
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