Automated captcr-snakemake Pipeline: Barcode Extraction, MixCR, QC, and Clone Tracking

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cap-tcr
cap-tcr
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captcr-snakemake

Author: Arnavaz.Danesh@uhnresearch.ca Orginal repo: https://github.com/arnavaz/cap-tcr

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

Intallation requirements

  1. python-3.4.3 or higher

  2. Biopython (python package)

  3. pandas (python package)

  4. numpy (python package)

  5. matplotlib (python package)

  6. R/3.6 or higher

  7. ggplot2 (R-package)

  8. ggalluvial (R-package)

  9. randomcoloR (R-package)

Run with example data 

# clone the repo
salloc -c 1 -t 2:00:00 --mem=6G -p build
git clone https://github.com/LupienLab/cap-tcr.git
# Update config file
vi config.yaml
# Run Snakemake or submit a job
snakemake -s Snakefile --cores 1

Code Snippets

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shell:
   "python {params.extract_barcode} --read1 {input.R1} --read2 {input.R2} --outfile {params.outprefix} --blist {params.barcodes}"
SnakeMake From line 73 of main/Snakefile 
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shell:
   "{java_align} {input.R1} {input.R2} {output.vdjca}"
SnakeMake From line 82 of main/Snakefile 
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shell:
   "{assemble1} {input.vdjca} {output.vdjca_res1}"
SnakeMake From line 90 of main/Snakefile 
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shell:
    "{assemble1} {input.vdjca_res1} {output.vdjca_res2}"
SnakeMake From line 98 of main/Snakefile 
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shell:
    "{assembleEx} {input.vdjca_res2} {output.vdjca_ext}"
SnakeMake From line 106 of main/Snakefile 
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shell:
    "{assemble_f} {output.log} {input.vdjca_ext} {output.clns}"
SnakeMake From line 115 of main/Snakefile 
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shell:
    "{export} --chains TRA {input.cln}  {output.clones_A}"
SnakeMake From line 123 of main/Snakefile 
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shell:
    "{export} --chains TRB {input.clns} {output.clones_B}"
SnakeMake From line 131 of main/Snakefile 
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shell:
    "python {pars_log} -i  {logdir}  -o {logdir} -pm log_assemble_"
SnakeMake From line 137 of main/Snakefile 
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shell:
    "Rscript {mixcr_qc} {logdir}"
SnakeMake From line 143 of main/Snakefile 
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shell:
    "Rscript {clonetracker} {input.clones} {params.param1} {params.type}"
SnakeMake From line 155 of main/Snakefile
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Created: 1yr ago
Updated: 1yr ago
Maitainers: public
URL: https://github.com/LupienLab/cap-tcr
Name: cap-tcr
Version: 1
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Other Versions:
Version 2
Downloaded: 0
Copyright: Public Domain
License: None
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