This repo contains some example code for building a Nextflow pipeline. The example shows some csv defining the filepath for paired-end mates across a set of 5 samples. There are three scripts which iteratively build a pipeline which creates a channel to parse the csv, append the paired-end mates, then run fastqc in a container on the merged reads for each sample.
which nextflow && which docker
should produce something like:
/usr/local/bin/nextflow
/usr/bin/docker
Clone the repo
git clone [email protected]:jgallowa07/Nextflow-Example.git && cd Nextflow-Example
running hello-channel:
nextflow run hello-channel.nf
running hello-process:
nextflow run hello-process.nf
running hello-container:
nextflow run -c compute_config/nextflow.local.config hello-container.nf
To run on a SLURM cluster, set up for gizmo: First, log onto to the cluster and clone the repo
git clone [email protected]:jgallowa07/Nextflow-Example.git && cd Nextflow-Example
Next, grab an interactive node
(base) rhino03 ~ » kinit
Password for [email protected]:
(base) rhino03 ~ » grabnode
How many CPUs/cores would you like to grab on the node? [1-36] 12
How much memory (GB) would you like to grab? [240] 12
Please enter the max number of days you would like to grab this node: [1-7] 1
Do you need a GPU ? [y/N]N
Finally, run the script
./run_gizmo
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