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Various MultiQC issues: FastQC sections for raw and trimmed reads // umi-tools dedup and extraction plots, custom content styling. #1308

Merged
merged 21 commits into from
Jul 12, 2024
Merged

Various MultiQC issues: FastQC sections for raw and trimmed reads // umi-tools dedup and extraction plots, custom content styling. #1308

merged 21 commits into from
Jul 12, 2024

Commits on Jul 4, 2024

  1. Modify FastQC output publishing to comply with the paths in MultiQC c… 

    …onfig.
    @MatthiasZepper
    MatthiasZepper committed Jul 4, 2024
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  2. MultiQC config updates.

    @MatthiasZepper
    MatthiasZepper committed Jul 4, 2024
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  3. Linting.

    @MatthiasZepper
    MatthiasZepper committed Jul 4, 2024
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  4. Use the correct module names to supress the Percent Duplicate column … 

    …in the General Stats table of MultiQC.
    @MatthiasZepper
    MatthiasZepper committed Jul 4, 2024
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  5. Publish logfiles from umi-tools dedup steps.

    @MatthiasZepper
    MatthiasZepper committed Jul 4, 2024
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  6. Modify subworkflow bam_dedup_stats_samtools_umitools to publish dedup… 

    … logs.
    @MatthiasZepper
    MatthiasZepper committed Jul 4, 2024
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  7. Update bam_dedup_stats_samtools_umitools subworkflow and MultiQC module.

    @MatthiasZepper
    MatthiasZepper committed Jul 4, 2024
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  8. Add UMI information for Watchmaker mRNA Library Prep Kit.

    @MatthiasZepper
    MatthiasZepper committed Jul 4, 2024
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  9. Publish the UMI-tools extract logs for MultiQC.

    @MatthiasZepper
    MatthiasZepper committed Jul 4, 2024
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  10. The output channel of fastq_fastqc_umitools_trimgalore/fastp is calle… 

    …d 'umi_log' and not 'log'. The meta.yml is wrong.
    @MatthiasZepper
    MatthiasZepper committed Jul 4, 2024
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  11. Mark FASTQC outputs with suffixes

    @pinin4fjords @MatthiasZepper
    pinin4fjords authored and MatthiasZepper committed Jul 4, 2024
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  12. @aanil (Anandashankar Anil) correctly pointed out that some MultiQC c… 

    …onfiguration parameters used in the config were deprecated.
    @MatthiasZepper
    MatthiasZepper committed Jul 4, 2024
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  13. Linting

    @MatthiasZepper
    MatthiasZepper committed Jul 4, 2024
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  14. Changelog

    @MatthiasZepper
    MatthiasZepper committed Jul 4, 2024
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Commits on Jul 9, 2024

  1. Undo changes to modules/nf-core/dupradar/templates/dupradar.r from Ha… 

    …rshil Patel and me, since they should be fixed upstream in the modules directory. Reset state of file to cc1bf2c.
    @MatthiasZepper
    MatthiasZepper committed Jul 9, 2024
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Commits on Jul 10, 2024

  1. bump module and temporarily patch for nf-core/modules#5943

    @pinin4fjords
    pinin4fjords committed Jul 10, 2024
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  2. Correct the diff

    @pinin4fjords
    pinin4fjords committed Jul 10, 2024
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  3. Update MultiQC to v1.23

    @MatthiasZepper
    MatthiasZepper committed Jul 10, 2024
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Commits on Jul 11, 2024

  1. Update dupradar from modules repo and remove patch.

    @MatthiasZepper
    MatthiasZepper committed Jul 11, 2024
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  2. Update module for snapshot fix

    @pinin4fjords
    pinin4fjords committed Jul 11, 2024
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  3. Fix prefixes for FASTQC

    @pinin4fjords
    pinin4fjords committed Jul 11, 2024
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