Running Snakemake Workflows in Binder for RNA-Seq Analysis

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2020-ggg-201b-rnaseq
2020-ggg-201b-rnaseq
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To run in binder --

  1. start the binder

  2. at the command line, run 

snakemake -j 4 --use-conda

  1. open rnaseq-workflow.Rmd

  2. knit to HTML

Code Snippets

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args = commandArgs(trailingOnly=TRUE)


output_format = "html_document"
if (length(args)==1) {
  output_format = args[1]
}

rmarkdown::render("rnaseq-workflow.Rmd", output_format=output_format)
R From line 2 of latest/knit-Rmd.R 
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shell:
    "./knit-Rmd.R {wildcards.format}_document"
SnakeMake From line 31 of latest/Snakefile 
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shell:
    """
    curl -L {params.download_link} -o {output}
    """
SnakeMake From line 39 of latest/Snakefile 
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shell:
    """
    fastqc {input} --outdir {params.outdir}
    """
SnakeMake FastQC From line 50 of latest/Snakefile 
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shell:
    """
    curl -L https://raw.githubusercontent.com/timflutre/trimmomatic/master/adapters/TruSeq2-SE.fa -o {output}
    """
SnakeMake From line 58 of latest/Snakefile 
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shell:
    """
    trimmomatic SE {input.reads} {output} ILLUMINACLIP:{input.adapters}:2:0:15 LEADING:2 TRAILING:2 SLIDINGWINDOW:4:2 MINLEN:25    
    """
SnakeMake Trimmomatic From line 69 of latest/Snakefile 
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shell:
    """
    fastqc {input} --outdir {params.outdir}
    """
SnakeMake FastQC From line 80 of latest/Snakefile 
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shell:
    """
    multiqc -f {params.raw_dir} {params.trimmed_dir} --filename {output}
    """
SnakeMake MultiQC From line 94 of latest/Snakefile 
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shell:
    """
    curl -L ftp://ftp.ensembl.org/pub/release-99/fasta/saccharomyces_cerevisiae/cdna/Saccharomyces_cerevisiae.R64-1-1.cdna.all.fa.gz -o {output}
    """
SnakeMake From line 102 of latest/Snakefile 
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shell:
    """
    salmon index --index {output} --transcripts {input} # --type quasi
    """
SnakeMake Salmon From line 111 of latest/Snakefile 
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shell:
    """
    salmon quant -i {input.index_dir} --libType A -r {input.reads} -o {params.outdir} --seqBias --gcBias --validateMappings
    """
SnakeMake Quant Salmon From line 125 of latest/Snakefile
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Created: 1yr ago
Updated: 1yr ago
Maitainers: public
URL: https://github.com/ngs-docs/2020-ggg-201b-rnaseq
Name: 2020-ggg-201b-rnaseq
Version: 1
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Copyright: Public Domain
License: None
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