Workflow Steps and Code Snippets

142 tagged steps and code snippets that match keyword Trim_Galore

cfMeDIP-seq Circulating Methylome Data Post-processing Pipeline 

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shell:
    'trim_galore --cores 4 --dont_gzip --paired {params.trimgalore_settings} --output_dir {params.outdir} {input.R1} {input.R2} && cp ' + path_to_data + '/{wildcards.cohort}/tmp/trim_fastq/{wildcards.sample}_lib{wildcards.lib}_extract_barcode_R*.fastq_trimming_report.txt ' + path_to_data + '/{wildcards.cohort}/results/qc/trim_report/'
SnakeMake Trim_Galore From line 294 of Master/Snakefile 
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shell:
    'trim_galore --cores 4 --dont_gzip {params.trimgalore_settings} --output_dir {params.outdir} {input.R1}  && cp ' + path_to_data + '/{wildcards.cohort}/tmp/trim_fastq/{wildcards.sample}_lib{wildcards.lib}_R1.fastq_trimming_report.txt ' + path_to_data + '/{wildcards.cohort}/results/qc/trim_report/'
SnakeMake Trim_Galore From line 309 of Master/Snakefile

Assembly pipeline for 10X chromium genomes of Mytilus species (v1.0) 

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shell: 
    """
    trim_galore --cores {threads} \
    --phred33 \
    --quality 20 \
    --stringency 1 \
    -e 0.1 \
    --length 70 \
    --output_dir {params.outdir} \
    --basename {params.basename} \
    --dont_gzip \
    --paired \
    {input} \
    > {log} 2>&1
    """
SnakeMake Trim_Galore From line 94 of rules/agouti.smk

Fosmid assembly annotation 

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shell:
    "trim_galore --paired {input} --basename {wildcards.id} --output_dir {params.dirname}"
SnakeMake Trim_Galore From line 34 of workflow/Snakefile

Phaeocystis Viral Elements Extraction Workflow for Polinton-like Virus Study 

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shell:
    "trim_galore -a ' {params.truseq} -a {params.nextera} -n 3' --cores {threads} --trim-n --paired --retain_unpaired --output_dir {params.outdir} --length {params.min_read} {input.r1} {input.r2}"
SnakeMake Trim_Galore From line 47 of workflow/Snakefile 
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shell:
    "trim_galore -a ' {params.truseq} -a {params.nextera} -n 3' --cores {threads} --trim-n --length {params.min_read} --output_dir {params.outdir} {input.reads}"
SnakeMake Trim_Galore From line 64 of workflow/Snakefile 
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shell:
    "trim_galore -a ' {params.truseq} -a {params.nextera} -n 3' --cores {threads} --trim-n --paired --retain_unpaired --output_dir {params.outdir} --length {params.min_read} {input.r1} {input.r2}"
SnakeMake Trim_Galore From line 225 of workflow/Snakefile 
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shell:
    "trim_galore -a ' {params.truseq} -a {params.nextera} -n 3' --cores {threads} --trim-n --output_dir {params.outdir} --length {params.min_read} {input}"
SnakeMake Trim_Galore From line 244 of workflow/Snakefile

RNA-seq Pipeline for the PI3K Project 

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shell:
    "trim_galore --cores {threads} --gzip --fastqc --paired -o {params.outdir} {input} &> {log} && "
    "mv trimmed_fq/{wildcards.sample}_1_val_1.fq.gz {output.fq1} &>> {log} && "
    "mv trimmed_fq/{wildcards.sample}_2_val_2.fq.gz {output.fq2} &>> {log}"
SnakeMake Trim_Galore From line 16 of rules/trim_galore.smk

Demonstrating an RNA-seq workflow in Snakemake. 

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shell:
    """
    trim_galore \
    -q {params.quality} \
    --length {params.length} \
    --basename {params.base} \
    -o {params.out_dir} \
    --dont_gzip \
    --paired {input.r1} {input.r2}
    """
SnakeMake Trim_Galore From line 113 of workflow/Snakefile
tool

Trim_Galore

Trim Galore! is a wrapper script to automate quality and adapter trimming as well as quality control, with some added functionality to remove biased methylation positions for RRBS sequence files (for directional, non-directional (or paired-end) sequencing).

URL https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/
signature: trim_galore|trimgalore.py
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