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

Merged

MatthiasZepper merged 21 commits intonf-core:devfrom MatthiasZepper:MultiQC_FastQC_bug

Jul 12, 2024

+467-504

Commits on Jul 4, 2024

Modify FastQC output publishing to comply with the paths in MultiQC config.
MatthiasZepper
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MultiQC config updates.
MatthiasZepper
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Linting.
MatthiasZepper
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Use the correct module names to supress the Percent Duplicate column in the General Stats table of MultiQC.
MatthiasZepper
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Publish logfiles from umi-tools dedup steps.
MatthiasZepper
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Modify subworkflow bam_dedup_stats_samtools_umitools to publish dedup logs.
MatthiasZepper
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Update bam_dedup_stats_samtools_umitools subworkflow and MultiQC module.
MatthiasZepper
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Add UMI information for Watchmaker mRNA Library Prep Kit.
MatthiasZepper
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Publish the UMI-tools extract logs for MultiQC.
MatthiasZepper
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The output channel of fastq_fastqc_umitools_trimgalore/fastp is called 'umi_log' and not 'log'. The meta.yml is wrong.
MatthiasZepper
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Mark FASTQC outputs with suffixes

pinin4fjords
authored and
MatthiasZepper
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@aanil (Anandashankar Anil) correctly pointed out that some MultiQC configuration parameters used in the config were deprecated.
MatthiasZepper
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Linting
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Changelog
MatthiasZepper
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Commits on Jul 9, 2024

Undo changes to modules/nf-core/dupradar/templates/dupradar.r from Harshil Patel and me, since they should be fixed upstream in the modules directory. Reset state of file to cc1bf2c.
MatthiasZepper
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Commits on Jul 10, 2024

Commits on Jul 11, 2024