Workflow Steps and Code Snippets

721 tagged steps and code snippets that match keyword MultiQC

Snakemake workflow: dna-seq-gatk-variant-calling (v2.1.1)

wrapper:
    "0.59.2/bio/multiqc"

SnakeMake MultiQC From line 42 of rules/qc.smk

Snakemake workflow: dna-seq-gatk-variant-calling (v2.1.1)

wrapper:
    "0.59.2/bio/multiqc"

SnakeMake MultiQC From line 42 of rules/qc.smk

Snakemake workflow: dna-seq-gatk-variant-calling (v2.1.1)

wrapper:
    "0.59.2/bio/multiqc"

SnakeMake MultiQC From line 42 of rules/qc.smk

Snakemake workflow: dna-seq-gatk-variant-calling (v2.1.1)

wrapper:
    "0.59.2/bio/multiqc"

SnakeMake MultiQC From line 42 of rules/qc.smk

WES analysis pipeline

wrapper:
    "0.50.4/bio/multiqc"

SnakeMake MultiQC From line 198 of rules/preprocessing.smk

Snakemake pipeline for detection limit test from laser-microdissected samples

shell:
    """
    multiqc \
        --title {params.library} \
        --force \
        --filename {params.library} \
        --outdir {params.out_dir} \
        --dirs \
        --dirs-depth 1 \
        {input} \
    2> {log} 1>&2
    """

SnakeMake MultiQC From line 18 of rules/report_library.smk

shell:
    """
    multiqc \
        --filename reads \
        --title reads \
        --force \
        --outdir {params.dir} \
        {input} \
    2> {log} 1>&2
    """

SnakeMake MultiQC From line 13 of rules/report_step.smk

shell:
    """
    multiqc \
        --title fastp \
        --force \
        --filename fastp \
        --outdir {params.dir} \
        {input} \
    2> {log} 1>&2
    """

SnakeMake MultiQC fastp From line 37 of rules/report_step.smk

shell:
    """
    multiqc \
        --title {params.title} \
        --force \
        --filename {params.title} \
        --outdir {params.dir} \
        --module kraken \
        {input} \
    2> {log} 1>&2
    """

SnakeMake MultiQC Kraken From line 61 of rules/report_step.smk

shell:
    """
    multiqc \
        --title {params.title} \
        --force \
        --filename {params.title} \
        --outdir {params.dir} \
        --dirs \
        --dirs-depth 1 \
        {input.reports} \
    2> {log} 1>&2
    """

SnakeMake MultiQC From line 97 of rules/report_step.smk

tool / biotools

MultiQC

multiqc

MultiQC aggregates results from multiple bioinformatics analyses across many samples into a single report. It searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.

References: