16 lines
764 B
YAML
16 lines
764 B
YAML
# Include shared CI
|
|
include:
|
|
- project: "epi2melabs/ci-templates"
|
|
file: "wf-containers.yaml"
|
|
|
|
variables:
|
|
# Workflow inputs given to nextflow.
|
|
# The workflow should define `--out_dir`, the CI template sets this.
|
|
# Only common file inputs and option values need to be given here
|
|
# (not things such as -profile)
|
|
NF_BEFORE_SCRIPT: |
|
|
wget -O test_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/wf-isoforms_test_data.tar.gz && tar -xzvf test_data.tar.gz
|
|
NF_WORKFLOW_OPTS: "--fastq ERR6053095_chr20.fastq \
|
|
--ref_genome chr20/hg38_chr20.fa --ref_annotation chr20/gencode.v22.annotation.chr20.gtf \
|
|
--jaffal_refBase chr20/ --jaffal_genome hg38_chr20 --jaffal_annotation genCode22"
|