/DIDA-Seq

Primary LanguagePython

DIDA

Organization

This snakemake workflow includes two workflows, which are linked together. The first takes 1 or more "run" files (R1 and R2), which is then demultiplexed into multiple files using a metadata file which links each sample ID to it's unique barcode. Once the files have been demultiplexed, these individual files are processed in parallel through a sequence of processing steps.

  • The first workflow is executed by the Snakefile demultiplex_Snakefile, and defines it's sample IDs by parsing through the metadata file provided, which includes the one-to-one mapping of sample ID to barcode.
  • The second workflow defines the first as it's "sub-workflow" and requires that it is completed prior to launching any of the downstream processing steps. This workflow is defined by Snakefile and defines the demultiplexing as it's "sub-workflow"

Software requirements

To launch this workflow properly, you must:

  • Have miniconda3 installed. If this is not installed, you can install with the following commands.
$ cd ~
$ wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
$ bash Miniconda3-latest-Linux-x86_64.sh
  • Install snakemake through conda into your base environment.
$ conda install -c bioconda -c conda-forge snakemake

Setup

Clone this repository into your preferred location.

$ git clone https://github.com/ohsu-cedar-comp-hub/DIDA.git
$ cd DIDA

Once in the directory DIDA, you must upload the necessary files for demultiplexing to be run properly. Please upload a tab-delimited text file following this format:
sample1 gtcaNNNNgtcaNNNN
sample2 aagtNNNNaagtNNNN
sample3 aaccNNNNaaccNNNN
... ...

Important to note is that snakemake defines the samples to run in parallel by parsing through this file, so please only include the sample IDs & barcodes which were run.

Once this file is uploaded, you can write the absolute path to it under the barcodes header in the file omic_config.yaml. The omic_config.yaml file is also where you can alter the following variables which may change depending on your run:

  1. barcodes - Metadata file which links sample ID to barcode
  2. ref_genome - Reference genome fasta file
  3. num_pcr - Number of processors
  4. gd_cutoff
  5. gd_Ncutoff

Once you have uploaded your metadata and edited the omic_config.yaml to your liking, please symbolically link / copy your raw sequencing files to the directory samples/raw within your working directory.

$ ln -s /path/to/data/* samples/raw

OR

$ cp /path/to/data/* samples/raw

Launch workflow

To test that your workflow is set up correctly, you can do a "dry-run" of your snakemake workflow, which will create a Directed Acyclic Graph (DAG) of every job that will be launched in the workflow. If there are any syntactical errors, they will be reported here.

$ snakemake -np --verbose

If the dry-run looks good, then you can launch the workflow with this command:

$ sbatch submit_snakemake.sh