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[WIP] Timstof support #41

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[WIP] Timstof support #41

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Commits on Jun 26, 2023

  1. initial commit on the branch

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    jspaezp committed Jun 26, 2023
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Commits on Jun 27, 2023

  1. added params to the encyclopedia run

    @jspaezp
    jspaezp committed Jun 27, 2023
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Commits on Jul 21, 2023

  1. (wip) addition of skyline

    @jspaezp
    jspaezp committed Jul 21, 2023
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  2. added branching to the skyline quant step

    @jspaezp
    jspaezp committed Jul 21, 2023
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  3. (wip) improvement on skyline job passing

    @jspaezp
    jspaezp committed Jul 21, 2023
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Commits on Jul 24, 2023

  1. made blib conversion 2 step

    @jspaezp
    jspaezp committed Jul 24, 2023
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  2. Update test.yml

    @jspaezp
    jspaezp committed Jul 24, 2023
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  3. minor addition to tests cicd

    @jspaezp
    jspaezp committed Jul 24, 2023
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  4. updated docker image

    @jspaezp
    jspaezp committed Jul 24, 2023
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  5. moved skyline logic out of agg

    @jspaezp
    jspaezp committed Jul 24, 2023
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  6. added skyline template asset

    @jspaezp
    jspaezp committed Jul 24, 2023
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  7. handled no-merge use case

    @jspaezp
    jspaezp committed Jul 24, 2023
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  8. added asset

    @jspaezp
    jspaezp committed Jul 24, 2023
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Commits on Jul 25, 2023

  1. Update test.yml

    @jspaezp
    jspaezp committed Jul 25, 2023
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  2. bumped ims conversion version

    @jspaezp
    jspaezp committed Jul 25, 2023
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  3. Merge branch 'feature/timstof_data' of github.com:TalusBio/nf-encyclo… 

    …pedia into feature/timstof_data
    @jspaezp
    jspaezp committed Jul 25, 2023
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  4. updated msstats tests for resolutoin

    @jspaezp
    jspaezp committed Jul 25, 2023
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  5. fixed input piping to ims

    @jspaezp
    jspaezp committed Jul 25, 2023
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  6. changed log handling in skyline steps

    @jspaezp
    jspaezp committed Jul 25, 2023
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  7. changed log handling in skylines first step

    @jspaezp
    jspaezp committed Jul 25, 2023
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  8. updated position in skyline adds

    @jspaezp
    jspaezp committed Jul 25, 2023
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  9. handled decompression

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    jspaezp committed Jul 25, 2023
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  10. handled decompression on grouping stage

    @jspaezp
    jspaezp committed Jul 25, 2023
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  11. escaped bash variables

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    jspaezp committed Jul 25, 2023
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  12. bugfix minor typo on file type

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    jspaezp committed Jul 25, 2023
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  13. bugfix minor typo on file type

    @jspaezp
    jspaezp committed Jul 25, 2023
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Commits on Jul 26, 2023

  1. changed way to list files in bash

    @jspaezp
    jspaezp committed Jul 26, 2023
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  2. fixed yet another bug in the bash side of the workflow

    @jspaezp
    jspaezp committed Jul 26, 2023
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  3. changed val to path in skyline step

    @jspaezp
    jspaezp committed Jul 26, 2023
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  4. added debugging prints

    @jspaezp
    jspaezp committed Jul 26, 2023
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  5. yet another fix

    @jspaezp
    jspaezp committed Jul 26, 2023
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  6. added more debugging info and added handling of raw files

    @jspaezp
    jspaezp committed Jul 26, 2023
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  7. handled empty else clause

    @jspaezp
    jspaezp committed Jul 26, 2023
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  8. added a lot of extra params

    @jspaezp
    jspaezp committed Jul 26, 2023
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  9. added unused parameter

    @jspaezp
    jspaezp committed Jul 26, 2023
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  10. fixed name in a parameter

    @jspaezp
    jspaezp committed Jul 26, 2023
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  11. fixed name in a parameter

    @jspaezp
    jspaezp committed Jul 26, 2023
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  12. fixed name in a parameter

    @jspaezp
    jspaezp committed Jul 26, 2023
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  13. moved parameters from termplate to import

    @jspaezp
    jspaezp committed Jul 26, 2023
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  14. added rt filter

    @jspaezp
    jspaezp committed Jul 26, 2023
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Commits on Jul 28, 2023

  1. moved ims params to sky template creation

    @jspaezp
    jspaezp committed Jul 28, 2023
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  2. added mem logging and decoys

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    jspaezp committed Jul 28, 2023
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