Skip to content

Latest commit

 

History

History
95 lines (73 loc) · 3.45 KB

README.md

File metadata and controls

95 lines (73 loc) · 3.45 KB
Raw

MetaRiboSeq Workflows

This directory contains the workflow for the MetaRiboSeq method. It uses nextflow as the workflow manager and combination of Docker and Singularity to build containers.

Building Images

The singularity images for this workflow are built using both docker and singularity. Docker is used since it is much more performant and flexible than singularity especially when used with buildkit. Two docker images are used, one that is a base image intend for broad use and a second that is specific to metariboseq. The singularity image packages the metariboseq docker image for use on a local cluster, such as Stanford's SCG, however, there is nothing specific to SCG in this workflow and it can run on a single node or even a laptop, albeit slowly.

See the ./docker and ./singularity directories for build scripts etc.

Nextflow Workflows

Nextflow version 20.07.1.5412 is used to implement the actual workflow. Note that this is installed in /labs/asbhatt/tools/swtools/bin.

Some common conventions:

  1. All nextflow scripts have the suffix .nf
  2. A shell script, run-nextflow.sh is used to run nextflow with appropriate parameters. The samples are specified via a parameter file, as are common workflow options.
  3. Nextflow configuration files are specified by these scripts as appropriate for runing locally or using slurm. These are in the nextflow-configs directory.

The parameters file is in yaml format and is structured as follows:

option1: some options
option2: some options
sampleSpecs:
    - name: <name>
      metagenomic: <metogenomic-data>
      metariboseq: <metariboseq-data>

The options are used to configure various command line arguments passed to the various commands used, e.g. number of threads for spades, or arguments to trim_galore. The sampleSpecs simple enumerate all of the samples to be processed by giving each a name and the file name component (without .fq.gz) for each paired set of sequencing files. Here is a complete example.

trimGaloreOptions: "--cores 4 -q 30 --illumina"
spadesOptions: "--threads=4 --memory=96"
alignmentMemory: "96 GB"
assemblyMemory: "96 GB"
bowtieIndexOptions: "--threads 4"
bowtieAlignmentOptions: "--threads 4"
sampleSpecs:
    - name: sampleA
      metagenomic: SampleADNA
      metariboseq: BrayonRibo_1_S7_R1_001

All workflows are in the workflows directory:

  1. subsample: generates sub-sampled input data for testing/development.
  2. metariboseq: the actual metariboseq workflow.

Testing and Development

A nextflow script is provided for subsampling a given set of samples to create a small 'test' sample for development purposes. The full samples take on the order of 24-48 hours to assemble and hence are cumbersome to work with. See the subsample directory for details. The run-nextflow.sh script runs nextflow with appropriate parameter files and configuration to generate the subsampled data.

Metariboseq and Analysis Workflows

The run-nextflow.sh scripts accepts one of the following parameters:

  • test: runs with subsampled test data
  • scg-sampleA: runs on scg for sampleA
  • scg-all: runs all samples on scg

Making changes to the parameter files should be fairly self-evident.

Metariboseq Nextflow Workflow

The nextflow execution graph is complicated by the need to create assemblies for the metagenomic files, but not for the metariboseq files and to then build indices and aligments using the metagenomic assembly.