Skip to content



The pipeline require only a UNIX system, Nextflow and either Docker or Singularity. Please, for installing these tools refer to their manual.

Downloading the pipeline

You can easily get a copy of the pipeline with:

# nextflow pull
nextflow pull fmalmeida/bacannot


The pipeline requires a UNIX system, therefore, Windows users may successfully use this pipeline via the Linux subsystem for window. Nextflow team has made available a nice tutorial about this issue.

Downloading docker images

The docker images used by the pipeline are:

docker pull fmalmeida/bacannot:v3.2_misc    ;
docker pull fmalmeida/bacannot:v3.2_perlenv ;
docker pull fmalmeida/bacannot:v3.2_pyenv   ;
docker pull fmalmeida/bacannot:v3.2_renv    ;
docker pull fmalmeida/bacannot:jbrowse      ;

Using singularity

Docker and singularity images are downloaded on the fly. Be sure to properly set NXF_SINGULARITY_LIBRARYDIR env variable to a writable directory if using Singularity. This will make that the downloaded images are resuable through different executions. Read more at:

For example, to download the images for docker you may:

# apply this command to each image
# just change the "/" and ":" for "-".
# E.g. Image fmalmeida/bacannot:v3.2_misc becomes fmalmeida-bacannot-v3.2_misc.img
singularity pull --dir $NXF_SINGULARITY_LIBRARYDIR fmalmeida-bacannot-v3.2_misc.img docker://fmalmeida/bacannot:v3.2_misc

Testing your installation

After that, you can run the pipeline with a testing dataset by selecting one of the available profiles:

  1. Docker
    • nextflow run fmalmeida/mpgap -profile docker,test
  2. Singularity
    • nextflow run fmalmeida/mpgap -profile singularity,test

About NF profiles

Please read more about how to proper select NF profiles to better understand it.

Last update: 2022-12-19