Snakemake workflow for SM-PATseq

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sm-patseq
sm-patseq
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Description

A simple Snakemake file using a conda environment built from requirements.txt and helper scripts. This takes subread data resulting from a Poly-A tail reading experiment from the PacBio Sequel platform, assigns gene identities to t

Code Snippets

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shell:
    "ccs -j {threads} --report-file PacBio{wildcards.r}/{wildcards.cell}/ccs_report.txt PacBio{wildcards.r}/{wildcards.cell}/*.subreads.bam {output.xml}"
SnakeMake From line 62 of main/Snakefile 
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shell:
    "lima --peek-guess --split-bam-named -s -j {threads} {input.ccs} {input.bcs} PacBio{wildcards.r}/{wildcards.cell}/split.bam;"
SnakeMake MLM From line 73 of main/Snakefile 
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shell:
    "mkdir -p cell_reports/PacBio{wildcards.r}/{wildcards.cell}; runqc-reports -o cell_reports/PacBio{wildcards.r}/{wildcards.cell} {input.xml}"
SnakeMake From line 82 of main/Snakefile 
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shell:
    "mkdir -p merged_bams;"
    "samtools merge -f -@ {threads} {output} PacBio*/*/split.lbc{params.value}--lbc{params.value}.bam"
SnakeMake SAMtools From line 93 of main/Snakefile 
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shell:
    "mkdir -p reads;"
    "samtools fastq {input} | gzip - > {output.fq};"
    "samtools fasta {input} | gzip - > {output.fa};"
SnakeMake SAMtools From line 104 of main/Snakefile 
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shell:
    "mkdir -p {wildcards.id};"
    "perl {input.pl} {input.fa} {params.fadapter} {params.radapter} 2>{log} | gzip - > {output};"
SnakeMake From line 120 of main/Snakefile 
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shell:
    "mkdir -p {wildcards.id};"
    "minimap2 -a {transcripts} {input.read} | samtools sort -O BAM - > {output};"
    "samtools index {output}"
SnakeMake SAMtools Minimap2 From line 130 of main/Snakefile 
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shell:
    "perl {input.pl} {input.minimap} {input.len} {params.gencode} | gzip - > {output}"
SnakeMake From line 144 of main/Snakefile 
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shell:
    "perl {input.pl} {input.minimap} {input.len} {params.gencode} 2>{log} >{output}"
SnakeMake From line 157 of main/Snakefile
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Created: 1yr ago
Updated: 1yr ago
Maitainers: public
URL: https://github.com/ibenjame/SM-PATseq
Name: sm-patseq
Version: 1
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Copyright: Public Domain
License: MIT License
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