pytest2nf-test

Converts a Nextflow component pytest to nf-test. The Antlr grammar and associated Java classes are taken from the nextflow/language-server. The converter code is written in Kotlin which is compiled into Java byte code for execution on Java Runtime.

Assumptions

1. OpenJDK 17
2. The component main.nf file contains a single process or workflow
3. The component main.nf and pytest main.nf both adhere to nextflow/language-server grammar

Build

./gradlew installDist

The built executable is placed at ./build/install/pytest2nf-test/bin/pytest2nf-test directory. It can also be moved to a directory which on PATH. It is preferable to move the executable to a directory which is on PATH or add the ./build/install/pytest2nf-test/bin directory to PATH.

Another alternative is to create an alias in your shell configuration file.

alias pytest2nf-test=${PWD}/build/install/pytest2nf-test/bin/pytest2nf-test

Test

General module

pytest2nf-test \
    --main test/cadd/main.nf \
    --test test/cadd/tests/pytest/main.nf \
    --output test/cadd/tests/main.nf.test \
    --data-dict test/test_data.config

pytest2nf-test \
    --main test/amps/main.nf \
    --test test/amps/tests/pytest/main.nf \
    --output test/amps/tests/main.nf.test \
    --data-dict test/test_data.config

pytest2nf-test \
    --main test/vcf_phase_shapeit5/main.nf \
    --test test/vcf_phase_shapeit5/tests/pytest/main.nf \
    --output test/vcf_phase_shapeit5/tests/main.nf.test \
    --data-dict test/test_data.config

nf-core module or sub-workflow

From the nf-core/modules directory,

pytest2nf-test \
    --nf-core-module canu

pytest2nf-test \
    --nf-core-sbwf vcf_phase_shapeit5

Nextflow Antlr Grammar

• Source: https://github.com/nextflow-io/language-server
• Version: dff88b5
• License: Apache License 2.0