Pughlab CaptCR Pipeline Automation with Snakemake

public 1yr ago Version: 2 0 bookmarks

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This repository is to automate the pughlab captcr pipeline using a snakemake workflow The pipeline consists of barcode extraction, running mixcr, running QC, and clonetracking

Code Snippets

shell:
   "python {params.extract_barcode} --read1 {input.R1} --read2 {input.R2} --outfile {params.outprefix} --blist {params.barcodes}"

SnakeMake From line 74 of main/Snakefile

shell:
   "{java_align} {input.R1} {input.R2} {output.vdjca}"

SnakeMake From line 83 of main/Snakefile

shell:
   "{assemble1} {input.vdjca} {output.vdjca_res1}"

SnakeMake From line 91 of main/Snakefile

shell:
    "{assemble1} {input.vdjca_res1} {output.vdjca_res2}"

SnakeMake From line 99 of main/Snakefile

shell:
    "{assembleEx} {input.vdjca_res2} {output.vdjca_ext}"

SnakeMake From line 107 of main/Snakefile

shell:
    "{assemble_f} {output.log} {input.vdjca_ext} {output.clns}"

SnakeMake From line 116 of main/Snakefile

shell:
    "{export} --chains TRA {input.cln}  {output.clones_A}"

SnakeMake From line 124 of main/Snakefile

shell:
    "{export} --chains TRB {input.clns} {output.clones_B}"

SnakeMake From line 132 of main/Snakefile

shell:
    "python {pars_log} -i  {logdir}  -o {logdir} -pm log_assemble_"

SnakeMake From line 138 of main/Snakefile

shell:
    "Rscript {mixcr_qc} {logdir}"

SnakeMake From line 144 of main/Snakefile

shell:
    "Rscript {clonetracker} {input.clones} {params.param1} {params.type}"

SnakeMake From line 156 of main/Snakefile

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Created: 1yr ago

Updated: 1yr ago

Maitainers: public

URL: https://github.com/arnavaz/cap-tcr

Name: cap-tcr

Version: 2

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License: None

Keywords:

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