Workflow Steps and Code Snippets

261 tagged steps and code snippets that match keyword fastp

Snakemake pipeline for detection limit test from laser-microdissected samples 

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shell:
    """
    if [[ {params.is_paired} = True ]] ; then
        fastp \
            --in1 {input.forward_} \
            --in2 {input.reverse_} \
            --out1 >(bgzip -l 1 -@ {threads} > {output.forward_}) \
            --out2 >(bgzip -l 1 -@ {threads} > {output.reverse_}) \
            --unpaired1 >(bgzip -l 1 -@ {threads} > {output.unpaired1}) \
            --unpaired2 >(bgzip -l 1 -@ {threads} > {output.unpaired2}) \
            --html {output.html} \
            --json {output.json} \
            --compression 1 \
            --verbose \
            --adapter_sequence {params.adapter_forward} \
            --adapter_sequence_r2 {params.adapter_reverse} \
            --length_required {params.length_required} \
            --thread {threads} \
            {params.extra} \
        2> {log} 1>&2
    else
        fastp \
            --in1 {input.forward_} \
            --out1 >(bgzip -l 1 -@ {threads} > {output.forward_}) \
            --html {output.html} \
            --json {output.json} \
            --compression 1 \
            --verbose \
            --adapter_sequence {params.adapter_forward} \
            --length_required {params.length_required} \
            --thread {threads} \
            {params.extra} \
        2> {log} 1>&2
    fi
    """
SnakeMake fastp From line 26 of rules/fastp.smk 
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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

Bioinfo Macro Host Genome Short Variant Discovery Workflow 

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shell:
    """
    fastp \
        --in1 {input.forward_} \
        --in2 {input.reverse_} \
        --out1 {output.forward_} \
        --out2 {output.reverse_} \
        --unpaired1 {output.unpaired1} \
        --unpaired2 {output.unpaired2} \
        --html {output.html} \
        --json {output.json} \
        --compression 1 \
        --verbose \
        --adapter_sequence {params.adapter_forward} \
        --adapter_sequence_r2 {params.adapter_reverse} \
        --thread {threads} \
        {params.extra} \
    2> {log} 1>&2
    """
SnakeMake fastp From line 27 of rules/fastp.smk 
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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

Repository containing bioinformatic code for macro-scale host transcriptomic data processing (v0.0.1) 

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shell:
    """
    fastp \
        --in1 {input.forward_} \
        --in2 {input.reverse_} \
        --out1 {output.forward_} \
        --out2 {output.reverse_} \
        --unpaired1 {output.unpaired1} \
        --unpaired2 {output.unpaired2} \
        --html {output.html} \
        --json {output.json} \
        --compression 1 \
        --verbose \
        --trim_poly_g \
        --trim_poly_x \
        --adapter_sequence {params.adapter_forward} \
        --adapter_sequence_r2 {params.adapter_reverse} \
        --thread {threads} \
        {params.extra} \
    2> {log} 1>&2
    """
SnakeMake fastp From line 27 of rules/fastp.smk 
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shell:
    """
    multiqc \
        --title fastp \
        --force \
        --filename fastp \
        --outdir {params.dir} \
        --config {input.config} \
        {input} \
    2> {log} 1>&2
    """
SnakeMake MultiQC fastp From line 58 of rules/report_step.smk

Snakemake workflow: Bioinfo_Macro_Microbial_Metatranscriptomics 

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shell:
    """
    fastp \
        --in1 {input.forward_} \
        --in2 {input.reverse_} \
        --out1 {output.forward_} \
        --out2 {output.reverse_} \
        --unpaired1 {output.unpaired1} \
        --unpaired2 {output.unpaired2} \
        --html {output.html} \
        --json {output.json} \
        --compression 1 \
        --verbose \
        --adapter_sequence {params.adapter_forward} \
        --adapter_sequence_r2 {params.adapter_reverse} \
        --thread {threads} \
        {params.extra} \
    2> {log} 1>&2
    """
SnakeMake fastp From line 25 of rules/fastp.smk 
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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

Snakemake workflow: Bioinfo_Macro_Microbial_Metatranscriptomics 

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shell:
    """
    fastp \
        --in1 {input.forward_} \
        --in2 {input.reverse_} \
        --out1 {output.forward_} \
        --out2 {output.reverse_} \
        --unpaired1 {output.unpaired1} \
        --unpaired2 {output.unpaired2} \
        --html {output.html} \
        --json {output.json} \
        --compression 1 \
        --verbose \
        --adapter_sequence {params.adapter_forward} \
        --adapter_sequence_r2 {params.adapter_reverse} \
        --thread {threads} \
        {params.extra} \
    2> {log} 1>&2
    """
SnakeMake fastp From line 25 of rules/fastp.smk 
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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
tool / biotools

fastp

fastp

A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance.

biotools fastp
edam operation_3192
edam operation_3187
GitHub OpenGene/fastp
doi 10.1093/bioinformatics/bty560
topic: Probes and primers
toolType: Command-line tool
operation: Sequence contamination filtering
signature: fastp
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