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Fixing contamination_filter and mirdeep2 #294

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wants to merge 25 commits into from
Closed

Fixing contamination_filter and mirdeep2 #294

wants to merge 25 commits into from

Commits on Oct 12, 2023

  1. Re-organized code mirna_quant to make it simpler to read

    @sguizard
    sguizard committed Oct 12, 2023
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  2. Switched to HTML less hairpin.fa and mature.fa

    @sguizard
    sguizard committed Oct 12, 2023
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Commits on Oct 16, 2023

  1. detect bowtie2 idx instead of bowtie1 idx

    @sguizard
    sguizard committed Oct 16, 2023
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  2. print mirQuant inputs

    @sguizard
    sguizard committed Oct 16, 2023
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  3. debug mirdeeprun

    @sguizard
    sguizard committed Oct 16, 2023
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  4. remove previous debug print

    @sguizard
    sguizard committed Oct 16, 2023
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  5. add more debug messages

    @sguizard
    sguizard committed Oct 16, 2023
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  6. remove prints

    @sguizard
    sguizard committed Oct 16, 2023
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  7. remove metq from mature and hairpin

    @sguizard
    sguizard committed Oct 16, 2023
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  8. connect clean hairpin / mature to mirdeep2

    @sguizard
    sguizard committed Oct 16, 2023
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  9. remove meta from fasta in mirdeep2_run

    @sguizard
    sguizard committed Oct 16, 2023
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  10. Clean debug prints

    @sguizard
    sguizard committed Oct 16, 2023
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  11. Merge branch 'debug' into fix-contamination_filter

    @sguizard
    sguizard committed Oct 16, 2023
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Commits on Oct 17, 2023

  1. update bowtie map contaminant with right options

    @sguizard
    sguizard committed Oct 17, 2023
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  2. define args variable

    @sguizard
    sguizard committed Oct 17, 2023
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  3. FIx? - include fastqc trim to multiQC

    @sguizard
    sguizard committed Oct 17, 2023
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  4. Refresh pipeline summary

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    sguizard committed Oct 17, 2023
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  5. Fix version: missing quotes and misaligned END_VER

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    sguizard committed Oct 17, 2023
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  6. Update doc with HTML less fa

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    sguizard committed Oct 17, 2023
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Commits on Oct 18, 2023

  1. update mirtrace ouput directory

    @sguizard
    sguizard committed Oct 18, 2023
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  2. update fastqc config

    @sguizard
    sguizard committed Oct 18, 2023
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  3. Update mirdeep2 publish_dir path

    @sguizard
    sguizard committed Oct 18, 2023
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Commits on Oct 27, 2023

  1. Merge branch 'fix-mirdeep2_and_contamination_filter' into dev

    @sguizard
    sguizard committed Oct 27, 2023
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  2. Prettier readme

    @sguizard
    sguizard committed Oct 27, 2023
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Commits on Jan 12, 2024

  1. Merge branch 'umi-handling' into dev

    @apeltzer
    apeltzer committed Jan 12, 2024
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