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Nextflow related documentation

Installation

If you do not have an installed environment or you don't have nextflow itself, here is one of the ways to install it.

Define NXF_HOME env variable to use a nextflow home location instead of the default one ($HOME/.nextflow). Everything else is unchanged from the default Nextflow installation instructions on https://www.nextflow.io/index.html#GetStarted.

# add NXF_HOME env
export NXF_HOME=$(pwd)/dot.nextflow # or whatever

# get nextflow and install almost like here: https://www.nextflow.io/index.html#GetStarted
wget -O - https://get.nextflow.io  > nextflow.install.bash

# review and run
cat nextflow.install.bash | bash -i 2>&1 | tee nextflow.install.log

# run test, see https://www.nextflow.io/index.html#GetStarted
./nextflow run hello

Configure the environment you are using if you have not done so yet. Don't forget to add NXF_HOME, patch PATH and export them.

# fix env variables, i.e.:
export NXF_HOME=$(pwd)/dot.nextflow
export PATH=$(pwd):$PATH

If you wish, you can set NXF_WORK env to be used by nextflow.

export NXF_WORK=...

Or use nextflow -e.NXF_WORK=... approach. Ideally, should be overridable by the -work-dir (-w) option of nextflow run

Running a pipeline

Once you have production (and nextflow) env ready, you can run pipelines. I.e.

CMD=<dba_alias>

mkdir -p data
pushd data
  data_dir=$(pwd)
  nextflow run \
    -w ${data_dir}/nextflow_work \
    ${ENSEMBL_ROOT_DIR}/ensembl-genomio/pipelines/nextflow/workflows/dumper_pipeline/main.nf \
    -profile lsf \
    $(${CMD} details script) \
    --dbname_re '^drosophila_melanogaster_\w+_57_.*$' \
    --output_dir ${data_dir}/dumper_output
popd

Try to invoke pipelines with --help option to get insight on how to run them.

Strange things we met

Channel is not forked, only one operation on stream is allowed

Symptoms:

When running a stage or a subworkflow on a channel with a single element we expect stream to be forked, allowing us to seed several task at a time.

// create that channel with a single element
//   calls read_json(...) in turn, see below
dbs = from_read_json(...)

DUMP_SQL(..., dbs, ...)
DUMP_METADATA(..., dbs, ...)

Instead pipeline dies with

Caused by: Cannot load from object array because "this.keys" is null

and when printing this object (dbs in this case, with println "db: ${db}"), we see it dict surrounded by the curly brackets like this

{..., "db_name":"some_db_name", ...}

instead of this (with square brackets)

[..., "db_name":"some_db_name", ...]

Reason / solution

In our case we used the read_json function similar to this one:

def read_json(json_path) {
    slurp = new JsonSlurper()
    json_file = file(json_path)
    text = json_file.text
    return slurp.parseText(text) // <-- problem here
}

that returned some kind of a lazy evaluator/iterator/whatever(not sure).

Replacing return slurp.parseText(text) with

    not_a_lazy_val = slurp.parseText(text)
    return not_a_lazy_val

did help.