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Add UMI reads processing capability #145

Merged
merged 26 commits into from
Jul 22, 2020
Merged

Add UMI reads processing capability #145

merged 26 commits into from
Jul 22, 2020

Commits on Mar 4, 2020

  1. added software to environment file

    Francesco committed Mar 4, 2020
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  2. added UMI options to param help

    Francesco committed Mar 4, 2020
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  3. split inputreads into an additional channel for UMI processing

    Francesco committed Mar 4, 2020
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  4. added UMI code block

    Francesco committed Mar 4, 2020
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  5. connected UMI output to mapping process

    Francesco committed Mar 4, 2020
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  6. corrected missing tuple

    Francesco committed Mar 4, 2020
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  7. fixed reference in umi file mapping

    Francesco committed Mar 4, 2020
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  8. fixing channel used twice for fasta by sentieon

    Francesco committed Mar 4, 2020
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  9. wrongly duplicated channel with typo

    Francesco committed Mar 4, 2020
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Commits on Mar 5, 2020

  1. using ch_fasta as in mapping for umi mapping

    Francesco committed Mar 5, 2020
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  2. reduced test config for laptop run

    Francesco committed Mar 5, 2020
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  3. added documentation for UMI input options

    Francesco committed Mar 5, 2020
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  4. improved helper 

    Co-Authored-By: Maxime Garcia <maxime.garcia@scilifelab.se>
    @lescai @maxulysse
    lescai and maxulysse committed Mar 5, 2020
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  5. Update docs/usage.md 

    Co-Authored-By: Maxime Garcia <maxime.garcia@scilifelab.se>
    @lescai @maxulysse
    lescai and maxulysse committed Mar 5, 2020
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  6. Apply suggestions from code review 

    Co-Authored-By: Maxime Garcia <maxime.garcia@scilifelab.se>
    @lescai @maxulysse
    lescai and maxulysse committed Mar 5, 2020
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  7. Update main.nf

    @lescai
    lescai committed Mar 5, 2020
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  8. Update docs/usage.md

    @lescai
    lescai committed Mar 5, 2020
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  9. Update main.nf

    @lescai
    lescai committed Mar 5, 2020
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  10. Update docs/usage.md

    @lescai
    lescai committed Mar 5, 2020
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Commits on Mar 6, 2020

  1. updated changelog

    Francesco committed Mar 6, 2020
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  2. Merge branch 'umi' of github.com:nibscles/sarek into umi

    Francesco committed Mar 6, 2020
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  3. Merge branch 'dev' into umi

    @maxulysse
    maxulysse committed Mar 6, 2020
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  4. Merge branch 'dev' into umi

    @maxulysse
    maxulysse committed Mar 6, 2020
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Commits on Jul 20, 2020

  1. Merge branch 'dev' into umi

    @maxulysse
    maxulysse committed Jul 20, 2020
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  2. Apply suggestions from code review

    @maxulysse
    maxulysse committed Jul 20, 2020
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Commits on Jul 22, 2020

  1. Apply suggestions from code review

    @maxulysse
    maxulysse committed Jul 22, 2020
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