How to install

Please install nextflow Nextflow and either Singularity or Docker before.

For installing Nextflow you need a POSIX compatible system (Linux, OS X, etc). It requires Bash 3.2 (or later) and Java 8 (or later, up to 17). Windows system is supported through WSL. For the installation of Nextflow just run:

curl -s https://get.nextflow.io | bash

For installing the pipeline you need to download the repo:

git clone --depth 1 --recurse-submodules https://github.com/biocorecrg/MOP2.git

You can use INSTALL.sh to download the guppy 3.4.5 or you can download the version you prefer by adding an extra parameter.

Note

Please consider that the support of VBZ compression of fast5 started with version 3.4.X.

cd MoP2; bash INSTALL.sh

or

cd MoP2; bash INSTALL.sh 4.0.15

Testing

cd mop_preprocess

nextflow run mop_preprocess.nf -with-singularity -bg -profile local > log

Tip

You can replace `-with-singularity` with `-with-docker` if you want to use the docker engine.

Apple M1 processor

Use the profile m1mac for running on machines with Apple M1 processor.

cd mop_preprocess

nextflow run mop_preprocess.nf -with-singularity -bg -profile m1mac > log