https://github.com/ccbr/ccbr_circrna_ampliconseq

Snakemake workflow to process circRNA AmpliconSeq datasets generated to study circRNAs in KSHV and human hosts using divergent primers.
https://github.com/ccbr/ccbr_circrna_ampliconseq

amplicon-pipeline amplicon-sequencing circrna circrna-pipeline snakemake-workflow

Last synced: 5 months ago
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Snakemake workflow to process circRNA AmpliconSeq datasets generated to study circRNAs in KSHV and human hosts using divergent primers.

• Host: GitHub
• URL: https://github.com/ccbr/ccbr_circrna_ampliconseq
• Owner: CCBR
• License: mit
• Created: 2021-03-09T18:32:49.000Z (over 5 years ago)
• Default Branch: main
• Last Pushed: 2025-01-21T15:27:21.000Z (over 1 year ago)
• Last Synced: 2025-09-09T23:29:57.030Z (9 months ago)
• Topics: amplicon-pipeline, amplicon-sequencing, circrna, circrna-pipeline, snakemake-workflow
• Language: Shell
• Homepage: https://ccbr.ccr.cancer.gov/
• Size: 480 KB
• Stars: 0
• Watchers: 4
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

          
# CCBR circRNA AmpliconSeq Snakemake Workflow

Process circRNA AmpliconSeq datasets generated to study circRNAs in KSHV and human hosts using divergent primers

![GitHub issues](https://img.shields.io/github/issues/CCBR/CCBR_circRNA_AmpliconSeq)![forks](https://img.shields.io/github/forks/CCBR/CCBR_circRNA_AmpliconSeq)![stars](https://img.shields.io/github/stars/CCBR/CCBR_circRNA_AmpliconSeq)![LICENSE](https://img.shields.io/github/license/CCBR/CCBR_circRNA_AmpliconSeq)

[![release](https://img.shields.io/github/v/release/CCBR/CCBR_circRNA_AmpliconSeq?color=blue&label=latest%20release)](https://github.com/CCBR/CCBR_circRNA_AmpliconSeq/releases/latest)

## Usage

```

USAGE:

  bash ./run_circRNA_AmpliconSeq -m/--runmode= -w/--workdir=

Required Arguments:

1.  RUNMODE: [Type: String] Valid options:

    *) init : initialize workdir

    *) run : run with slurm

    *) reset : DELETE workdir dir and re-init it

    *) dryrun : dry run snakemake to generate DAG

    *) unlock : unlock workdir if locked by snakemake

    *) runlocal : run without submitting to sbatch

2.  WORKDIR: [Type: String]: Absolute or relative path to the output folder with write permissions.

```