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fastp: number of reads before/after filtering #1811

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dwishsan opened this issue Dec 7, 2022 · 1 comment
Open

fastp: number of reads before/after filtering #1811

dwishsan opened this issue Dec 7, 2022 · 1 comment

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@dwishsan
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dwishsan commented Dec 7, 2022

Description of feature

Hello!

Thank you for the awesome tool that is MultiQC :)

I think that it would be nice to print the number of reads before and after filtering with the fastp module.
I used this code will do the job within the fastp_general_stats_table:

        headers["before_filtering_total_reads"] = {
            "title": "{} Reads Before Filtering".format(config.read_count_prefix),
            "description": "Total reads before filtering ({})".format(config.read_count_desc),
            "min": 0,
            "scale": "Blues",
            "modify": lambda x: x * config.read_count_multiplier,
            "shared_key": "read_count",
        }
        headers["after_filtering_total_reads"] = {
            "title": "{} Reads After Filtering".format(config.read_count_prefix),
            "description": "Total reads after filtering ({})".format(config.read_count_desc),
            "min": 0,
            "scale": "Blues",
            "modify": lambda x: x * config.read_count_multiplier,
            "shared_key": "read_count",
        }

This print before and after-trimming total reads next to each other in the General Stats table.
Maybe there will be some conflict related to #1744

@ewels
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ewels commented Dec 15, 2022

Thanks for this! It would be great if you could submit this as a pull request 🙏🏻 Then it's easier for me to review and merge, plus we'll see right away if there's a conflict 😊

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