SnakeMake workflow for the processing of EMseq data

public public 1yr ago Version: v0.1 0 bookmarks
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smk_emseq
smk_emseq
smk_emseq
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Code Snippets

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shell:
    """
    bismark_genome_preparation --genomic_composition {input.genome_dir}
    """
SnakeMake Bismark From line 20 of rules/bismark.smk 
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shell:
    """
    bismark -p {threads} --nucleotide_coverage {REF_GENOME_DIR} -1 {input.read1} -2 {input.read2} --basename {wildcards.sample}_mapped_{REF_SHORT}_trim_bismark --output_dir results/02_MAPPED 2> {log.log1}
    mv results/02_MAPPED/{wildcards.sample}_mapped_{REF_SHORT}_trim_bismark_PE_report.txt {log.log2}
    mv results/02_MAPPED/{wildcards.sample}_mapped_{REF_SHORT}_trim_bismark_pe.nucleotide_stats.txt {log.log3}
    """
SnakeMake Bismark From line 45 of rules/bismark.smk 
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shell:
    """
    deduplicate_bismark --paired --bam {input.bam} --output_dir results/02_MAPPED 2> {log}
    """
SnakeMake Bismark From line 67 of rules/bismark.smk 
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shell:
    """
    bismark_methylation_extractor {params.extra} --gzip --paired-end --multicore {threads} --genome_folder {params.ref} -s {input.bam} --output results/03_METHYL_EX 2> {log}
    """
SnakeMake Bismark From line 93 of rules/bismark.smk 
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shell:
    """
    bismark2bedGraph --CX --dir results/04_COVERAGE -o {params.bedGraph} {input.methylex} 2> {log}
    """
SnakeMake From line 116 of rules/bismark.smk 
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shell:
    """
    fastqc {input.read} -t {threads} -f fastq --outdir logs/fastqc/raw
    """
SnakeMake FastQC From line 24 of rules/qc.smk 
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shell:
    """
    bbduk.sh -Xmx8g in1={input.read1} in2={input.read2} out1={output.read1} out2={output.read2} stats={output.trim_stats} minlen=75 qtrim=rl trimq=20 ktrim=r k=25 mink=11 ref={params.adapter} hdist=1
    """
SnakeMake BBMap From line 46 of rules/qc.smk 
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shell:
    """
    fastqc {input.read} -t {threads} -f fastq --outdir logs/fastqc/trimmed
    """
SnakeMake FastQC From line 64 of rules/qc.smk 
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shell:
    """
    samtools sort {input.bam} > {output.sort}
    samtools index {output.sort}
    """
SnakeMake SAMtools From line 18 of rules/sort.smk
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Created: 1yr ago
Updated: 1yr ago
Maitainers: public
URL: https://github.com/wegnerce/smk_emseq
Name: smk_emseq
Version: v0.1
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Copyright: Public Domain
License: GNU General Public License v3.0
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