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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 pipeline uses both custom and public images. All images can be downloaded on the fly, automatically by nextflow, and this is the recommended way to do it.

If you want to download it yourself, you can find all the images used in the pipeline described in the file docker.config (for docker) and singularity.config (for singularity).

The images are defined like the following:

withLabel: 'db_download|db_tools|misc' {
    container = 'fmalmeida/bacannot@sha256:bdb31637cacf99736656ab3b69f1f01ba1b5eb026771d5c266b4c84e96153057'

And could be downloaded like this:

docker pull fmalmeida/bacannot@sha256:bdb31637cacf99736656ab3b69f1f01ba1b5eb026771d5c266b4c84e96153057

You would need to do it for each image.

If 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 reusable 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:v3.3_misc becomes fmalmeida-bacannot-v3.3_misc.img
# for singularity --> prepare env variables
# remember to properly set NXF_SINGULARITY_LIBRARYDIR
#
export NXF_SINGULARITY_LIBRARYDIR=<path in your machine>    # Set a path to your singularity storage dir
export NXF_SINGULARITY_CACHEDIR=<path in your machine>      # Set a path to your singularity cache dir
export SINGULARITY_CACHEDIR=<path in your machine>          # Set a path to your singularity cache dir

singularity pull \
    fmalmeida-bacannot-v3.3_misc.img docker://fmalmeida/bacannot:v3.3_misc

Bacannot databases

Bacannot databases are not inside the docker images anymore to avoid huge images and problems with connections and limit rates with dockerhub.


Users can directly download pre-formatted databases from Zenodo:

Useful for standardization and also overcoming known issues that may arise when formatting databases with singularity profile.

A module to download the latest pre-formatted database has also been made available:

# Download pipeline pre-built databases
nextflow run fmalmeida/bacannot \
    --get_zenodo_db \
    --output ./ \
    -profile <docker/singularity>

I want to generate a new formatted database

# Download pipeline databases
nextflow run fmalmeida/bacannot \
    --get_dbs \
    --output bacannot_dbs \
    -profile <docker/singularity>

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 --bacannot_db ./bacannot_dbs
  2. Singularity
    • nextflow run fmalmeida/mpgap -profile singularity,test --bacannot_db ./bacannot_dbs

About NF profiles

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