RASflow: RNA-Seq Analysis Snakemake Workflow

public public 1yr ago Version: v2.0 0 bookmarks
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rasflow-rna-seq-analysis-snakemake-workflow
rasflow-rna-seq-analysis-snakemake-workflow
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RASflow is a modular, flexible, and user-friendly RNA-Seq analysis workflow. RASflow can be applied to both model and non-model organisms. It supports mapping RNA-Seq raw reads to both genome and transcriptome (downloaded from a public database or homemade by users), and it can do both transcript- and gene-level Differential Expression Analysis (DEA) when transcriptome is used as a mapping reference. It requires little programming skills for basic use.

Code Snippets

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awk -F'"' '{print $2"\t"$6}' $1 > $2
Shell From line 9 of scripts/formatCount.sh 
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shell:
    "hisat2-build -p {config[NCORE]} {input.trans} {params.index}"
SnakeMake HISAT2 From line 18 of workflow/align_count_cod_oldTrans.rules 
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run:
    shell("scp -i {input.key} {config[NELSIN]}/{wildcards.sample}_*_R1_001.fastq.gz {output.forward}")
    shell("scp -i {input.key} {config[NELSIN]}/{wildcards.sample}_*_R2_001.fastq.gz {output.reverse}")
SnakeMake scp From line 27 of workflow/align_count_cod_oldTrans.rules 
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shell:
    "hisat2 -p {config[NCORE]} -x {params.index} -1 {input.forward} -2 {input.reverse} -S {output.sam}"
    " && samtools view -b -S {output.sam} > {output.bam}"
SnakeMake SAMtools HISAT2 From line 43 of workflow/align_count_cod_oldTrans.rules 
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shell:
    "samtools sort {input.bam} -o {output.sort} && samtools index {output.sort}"
SnakeMake SAMtools From line 52 of workflow/align_count_cod_oldTrans.rules 
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shell:
    "samtools idxstats {input.sort} > {output.count}"
SnakeMake SAMtools From line 60 of workflow/align_count_cod_oldTrans.rules 
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shell:
    "cd ../scripts && javac -cp opencsv-1.8.jar:. sumgenescod.java && java -cp opencsv-1.8.jar:. sumgenescod codgenelist.csv {input}"
SnakeMake From line 68 of workflow/align_count_cod_oldTrans.rules 
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shell:
    "sh ../scripts/formatCount.sh {input.geneCount} {output.formatCount}"
SnakeMake From line 76 of workflow/align_count_cod_oldTrans.rules 
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run:
    shell("scp -i {params.key} {params.input_path}/{wildcards.sample}_*R1*.f*q.gz {output.forward}"),
    shell("scp -i {params.key} {params.input_path}/{wildcards.sample}_*R2*.f*q.gz {output.reverse}")
SnakeMake scp From line 28 of workflow/align_count_genome.rules 
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shell:
    """
    shopt -s extglob
    scp -i {params.key} {params.input_path}/{wildcards.sample}?(_*)?(.*).f*q.gz {output.read}
    """
SnakeMake scp extglob From line 39 of workflow/align_count_genome.rules 
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shell:
    "mkdir {output.indexes} && hisat2-build -p {config[NCORE]} {input.genome} {params.index}"
    "&& hisat2_extract_splice_sites.py {config[ANNOTATION]} > {output.splicesites}"
SnakeMake HISAT2 From line 53 of workflow/align_count_genome.rules 
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run:
    shell("hisat2 -p {config[NCORE]} --known-splicesite-infile {input.splicesites} -x {params.index} -1 {input.forward} -2 {input.reverse} -S {output.sam}")
    shell("samtools view -@ {config[NCORE]} -b -S {output.sam} > {output.bam}")
SnakeMake SAMtools HISAT2 From line 71 of workflow/align_count_genome.rules 
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run:
    shell("hisat2 -p {config[NCORE]} --known-splicesite-infile {input.splicesites} -x {params.index} -U {input.forward} -S {output.sam}")
    shell("samtools view -@ {config[NCORE]} -b -S {output.sam} > {output.bam}")
SnakeMake SAMtools HISAT2 From line 87 of workflow/align_count_genome.rules 
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shell:
    "samtools sort -@ {config[NCORE]} {input.bam} -o {output.sort}"
SnakeMake SAMtools From line 96 of workflow/align_count_genome.rules 
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run:
    if config["COUNTER"]=="featureCounts":
        if config["END"]=="pair":
            shell("featureCounts -p -T {config[NCORE]} -t exon -g {config[ATTRIBUTE]} -a {input.annotation} -o {output.count} {input.sort} && tail -n +3 {output.count} | cut -f1,7 > temp.{wildcards.sample} && mv temp.{wildcards.sample} {output.count}")
        else:
            shell("featureCounts -T {config[NCORE]} -t exon -g {config[ATTRIBUTE]} -a {input.annotation} -o {output.count} {input.sort} && tail -n +3 {output.count} | cut -f1,7 > temp.{wildcards.sample} && mv temp.{wildcards.sample} {output.count}")
    elif config["COUNTER"]=="htseq-count":
        shell("htseq-count -f bam -i {config[ATTRIBUTE]} -s no -t exon {input.sort} {input.annotation} | sed '/^__/ d' > {output.count}")
SnakeMake FeatureCounts htseqcount From line 106 of workflow/align_count_genome.rules 
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shell:
    "qualimap bamqc -bam {input.sort} -nt {config[NCORE]} --java-mem-size=6G -outdir {output.bamqc}"
SnakeMake QualiMap From line 121 of workflow/align_count_genome.rules 
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shell:
    "multiqc {input.bamqc} {input.count_summary} --filename {output.report}"
SnakeMake MultiQC From line 130 of workflow/align_count_genome.rules 
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shell:
    "multiqc {input.count_summary} --filename {output.report}"
SnakeMake MultiQC From line 138 of workflow/align_count_genome.rules 
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run:
    shell("scp -i {params.key} {params.input_path}/{wildcards.sample}_*R1*.f*q.gz {output.forward}"),
    shell("scp -i {params.key} {params.input_path}/{wildcards.sample}_*R2*.f*q.gz {output.reverse}")
SnakeMake scp From line 23 of workflow/quality_control.rules 
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shell:
    "fastqc -t $(({config[NCORE]}+0)) -o {params.outputpath} {input.forward} && "
    "fastqc -t $(({config[NCORE]}+0)) -o {params.outputpath} {input.reverse}"
SnakeMake FastQC From line 36 of workflow/quality_control.rules 
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shell:
    "multiqc {params.path} --filename {output.report}"
SnakeMake MultiQC From line 48 of workflow/quality_control.rules 
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shell:
    """
    shopt -s extglob
    scp -i {params.key} {params.input_path}/{wildcards.sample}?(_*)?(.*).f*q.gz {output.read}
    """
SnakeMake scp extglob From line 58 of workflow/quality_control.rules 
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shell:
    "fastqc -t $(({config[NCORE]}+0)) -o {params.outputpath} {input.read}"
SnakeMake FastQC From line 71 of workflow/quality_control.rules 
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shell:
    "multiqc {params.path} --filename {output.report}"
SnakeMake MultiQC From line 81 of workflow/quality_control.rules 
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run:
    shell("scp -i {params.key} {params.input_path}/{wildcards.sample}_*R1*.f*q.gz {output.forward_read}"),
    shell("scp -i {params.key} {params.input_path}/{wildcards.sample}_*R2*.f*q.gz {output.reverse_read}")
SnakeMake scp From line 27 of workflow/quantify_trans.rules 
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shell:
    """
    shopt -s extglob
    scp -i {params.key} {params.input_path}/{wildcards.sample}?(_*)?(.*).f*q.gz {output.read}
    """
SnakeMake scp extglob From line 38 of workflow/quantify_trans.rules 
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shell:
    "salmon index -t {input} -i {output} --type quasi -k 31 -p {config[NCORE]}"
SnakeMake Salmon From line 49 of workflow/quantify_trans.rules 
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shell:
    """
    salmon quant -i {input.index} -l A -1 {input.forward_read} -2 {input.reverse_read} -o {output.quant_dir} -p {config[NCORE]} --seqBias --useVBOpt --validateMappings
    awk 'NR==1{{next}}{{print $1"\\t"$4}}' {output.quant_dir}/quant.sf > {output.tpm}
    """
SnakeMake Quant Salmon From line 61 of workflow/quantify_trans.rules 
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shell:
    """
    salmon quant -i {input.index} -l A -r {input.read} -o {output.quant_dir} -p {config[NCORE]} --seqBias --useVBOpt --validateMappings
    awk 'NR==1{{next}}{{print $1"\\t"$4}}' {output.quant_dir}/quant.sf > {output.tpm}
    """
SnakeMake Quant Salmon From line 74 of workflow/quantify_trans.rules 
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shell:
    "multiqc {input} --filename {output}"
SnakeMake MultiQC From line 85 of workflow/quantify_trans.rules 
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run:
    shell("scp -i {params.key} {params.input_path}/{wildcards.sample}_*R1*.f*q.gz {output.forward}"),
    shell("scp -i {params.key} {params.input_path}/{wildcards.sample}_*R2*.f*q.gz {output.reverse}")
SnakeMake scp From line 31 of workflow/trim.rules 
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shell:
    "trim_galore --fastqc -j 4 --paired --basename {wildcards.sample} -o {params.outputpath} {input.forward} {input.reverse}"
SnakeMake Trim_Galore From line 44 of workflow/trim.rules 
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shell:
    """
    shopt -s extglob
    scp -i {params.key} {params.input_path}/{wildcards.sample}?(_*)?(.*).f*q.gz {output.read}
    """
SnakeMake scp extglob From line 54 of workflow/trim.rules 
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shell:
    "trim_galore --fastqc -j 4 --basename {wildcards.sample} -o {params.outputpath} {input.read}"
SnakeMake Trim_Galore From line 67 of workflow/trim.rules 
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shell:
    "multiqc {params.path} --filename {output.report}"
SnakeMake MultiQC From line 77 of workflow/trim.rules
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Created: 1yr ago
Updated: 1yr ago
Maitainers: public
URL: https://github.com/zhxiaokang/RASflow
Name: rasflow-rna-seq-analysis-snakemake-workflow
Version: v2.0
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Copyright: Public Domain
License: Creative Commons Zero v1.0 Universal
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