Nextflow template for non-nf-core pipelines

This repository contains a configuration file and parameters template for running Nextflow pipelines on Sasquatch. If you are using an nf-core pipeline, you should not use the instructions in this repository, but should instead use -profile seattlechildrens. (See nf-core_vetted_pipelines for some specific information on individual pipelines that we have tested on Sasquatch.) Otherwise, if you are building your own pipeline or using one that you found on GitHub, you can use the files from this repository to get it running on Sasquatch.

1. Copy conf/sasquatch.config to the conf folder in your workflow. You might consider modifying the workDir or cacheDir directories if you want to have pipeline-specific directories.

2. Edit nextflow.config to add the line includeConfig "./conf/sasquatch.config"

3. If using a params file to pass in parameters (highly recommended so you don't have to further edit nextflow.config) you can use params/params.yml as a starting point. Alternatively you can define the assoc parameter in your own params or config file.

4. The code below can be modified for running your pipeline.

mamba activate nextflow

DATE=$(date +%F)
PREFIX="pipelinereport_${DATE}"

nextflow -log "reports/${PREFIX}_nextflow.log" \
    -c nextflow.config \
    run main.nf \
    -profile sasquatch \
    -params-file params/<PARAMS.yml> \
    -work-dir <WORKDIR> \
    -resume