sra-download-wf

bit sra-download workflow

This is a snakemake workflow for downloading reads from NCBI's SRA in fastq format. For all workflows available with bit, see here.

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• Overview
• Usage
  • Retrieving the workflow
  • Creating the input file and modifying the config.yaml
  • Running the workflow
  • Combining SRRs if needed
• Version info

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Overview

This workflow will download reads from SRA based on input run accessions (i.e., the accessions starting with ERR..., SRR, or DRR) using prefetch and fasterq-dump.

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Usage

bit should be installed via conda as described here.

Retrieving the worklfow

bit-get-workflow sra-download

Creating the input file and modifying the config.yaml

Before running it, you first need to make a file holding the target run accessions, one per line in a single-column.

The path to that file needs to be set for the "target_sra_accessions_file" variable in the config.yaml.

Running the workflow

After the target run accessions file has been created and set in the config.yaml, here's an example of how it could be run (note that it should still be run inside the bit conda environment):

snakemake --use-conda --conda-prefix ${CONDA_PREFIX}/envs -j 4 -p

• --use-conda – this specifies to use the conda environments included in the workflow
• --conda-prefix – this allows us to point to where the needed conda environments should be stored. Including this means if we use the workflow on a different dataset somewhere else in the future, it will re-use the same conda environments rather than make new ones. The value listed here, ${CONDA_PREFIX}/envs, is the default location for conda environments (the variable ${CONDA_PREFIX} will be expanded to the appropriate location on whichever system it is run on).
• -j – this lets us set how many jobs Snakemake should run concurrently (keep in mind that many of the thread and cpu parameters set in the config.yaml file will be multiplied by this)
• -p – specifies to print out each command being run to the screen

See snakemake -h for more options and details.

Combining SRRs if needed

Sometimes multiple "runs" belong to the same sample, but we still need to download the runs independently from SRA. A helper script is included with the workflow to facilitate combining those multiple read files into one forward and one reverse for a given sample. We first need to prepare a tab-delimited mapping file with 2 columns that lists:

1. The ultimate sample name we want to have
2. The SRR accessions that belong with each sample name

Here is an example:

cat map.tsv

Sample-1    SRR123456
Sample-1    SRR123457
Sample-2    SRR123458
Sample-3    SRR123459
Sample-3    SRR123460

For example, SRR123456 and SRR123457 read files would be combined (via cat) into one forward and one reverse read file called "Sample-1_R1.fastq.gz" and "Sample-1_R2.fastq.gz". Since Sample-2 only has one input, those files would just be renamed.

The helper script takes two positional arguments: the first being the tsv mapping file; and the second being the path to the directory holding all the starting fastq files.

Example usage:

bash scripts/combine-sra-accessions.sh -i map.tsv -d fastq-files/

Note that by default the original files will be removed after they are combined or renamed. If you want to keep them, provide the -k flag also. See bash scripts/combine-sra-accessions.sh -h for more info.

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Version info

Note that the workflows are version independently of the bit package. When you pull one with bit-get-workflow, the directory name will have the version, and it is also listed at the top of the Snakefile.

All versions of programs used can be found in their corresponding conda yaml file in the envs/ directory.