In order to use this module, the following dependencies are required:
Input data should be added to samples.tsv
and units.tsv.
The following information need to be added to these files:
| Column Id | Description |
|---|---|
samples.tsv |
|
| sample | unique sample/patient id, one per row |
units.tsv |
|
| sample | same sample/patient id as in samples.tsv |
| type | data type identifier (one letter), can be one of Tumor, Normal, RNA |
| platform | type of sequencing platform, e.g. NovaSeq |
| machine | specific machine id, e.g. NovaSeq instruments have @Axxxxx |
| flowcell | identifer of flowcell used |
| lane | flowcell lane number |
| barcode | sequence library barcode/index, connect forward and reverse indices by +, e.g. ATGC+ATGC |
| fastq1/2 | absolute path to forward and reverse reads |
| adapter | adapter sequences to be trimmed, separated by comma |
The workflow repository contains a small test dataset .tests/integration which can be run like so:
$ cd .tests/integration
$ snakemake -s ../../Snakefile -j1 --use-singularityTo use this run this pipeline the requirements in requirements.txt must be installed. It is most straightforward to install the requirements inside a python virtual environment created with the python venv module. The sample.tsv, units.tsv, resources.yaml, and config.yaml files need to be available in the config directory (or otherwise specified in config.yaml). You always need to specify the config-file either in the profile yaml file or in the snakemake command. To run the pipeline:
Running the pipeline on CPU:
module load slurm-drmaa
module load singularity/3.11.0
python3.9 -m venv venv
source venv/bin/acfivate
pip install -r requirements.txt
pipeline_path=/path/to/pipeline
snakemake --profile ${pipeline_path}/profiles/slurm/ -s ${pipeline_path}/workflow/Snakefile --prioritize prealignment_fastp_pe \
-p --configfile config/config.yaml --config aligner=bwa_cpu snp_caller=deepvariant_cpu
To create a reference for exomedepth based on the samples in the samples_ref.tsv and units_ref.tsv a config_reference.yaml must be specified in the command:
snakemake --profile ${pipeline_path}/profiles/slurm/ -s ${pipeline_path}/workflow/Snakefile --prioritize prealignment_fastp_pe \
-p --configfiles config/config.yaml config/config_reference.yaml --config aligner=bwa_cpu snp_caller=deepvariant_cpu --notemp -nThis pipeline is created to run on Illumina whole genome sequence data to call germline variants.
The workflow repository contains a dry run test of the pipeline in .tests/integration which can be run like so:
$ cd .tests/integration
$ snakemake -n -s ../../workflow/Snakefile --configfile config/config.yaml