GitHub - INSaFLU/insaflu_snakemake: A snakemake implementation of a subset of INSaFLU functionality (original) (raw)

Install some system dependencies

sudo apt install git build-essential zlib1g-dev

Create Environment

Install Mamba Forge:

curl -L https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh -o Mambaforge-Linux-x86_64.sh

bash Mambaforge-Linux-x86_64.sh

Activate Conda:

Create Environment:

git clone https://github.com/INSaFLU/insaflu_snakemake.git cd insaflu_snakemake mamba env create --name insaflu --file config/insaflu.yaml

Activate Environment

Setup the folder to run

Change directory to user, create reads directory and move your reads to this directory

cd user mkdir reads cp path/to/your/files/your_files.fastq.gz path/user/reads/ cd ..

Edit the csv in the folder user called project_metadata.csv

• This csv has to have the following format:
  sample_name,fastq1,fastq2,tech
  sample_01,sample_01_R1_001,sample_02_R2_002,illumina
  sample_02,samle_02,,ont
• All samples much be in fastq.gz format (do not append .fastq.gz in the fastq1 and fastq2 fields)

Go to user/project.yaml and fill the following fields

• only_samples (Run the sample only pipeline or run like a project)
• project_name (your project name)
• fasta_reference (mandatory for project)
• gb_reference (mandatory for project)
• primers (mandatory for iVar project)
• consensus_assembler (mandatory for project -> between "snippy" and "iVar")
• abricate (soon will change to classification)

Change the parameters in the run in user/parameters.yaml

• Here is possible to change the parameters in some softwares, change at your own responsability. A copy of the default parameters are in config/default_parameters.yaml
• Each project will recive a copy of this file inside projects/project_name_folder/

The references are in user/references folder

To add new ones just copy your fasta and genbank file.

You must keep the fasta identifier equal to the GenBank Locus

">ON563414" == "LOCUS ON563414"

To change the names of the project.yaml, samples.csv and parameters.yaml it is in config/constants.yaml

It is possible to change the following entries:

• sample_yaml
• sample_csv
• software_parameters You should give the absolute path or the relative path starting in the results folder.

Running the workflow

Run your project or analyze your samples with the following command:

snakemake -c {threads} --use-conda