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.gitlab-ci.yml
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# Include shared CI
include:
- project: "epi2melabs/ci-templates"
file: "wf-containers.yaml"
variables:
# We'll use the single-file case for these runs
NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/wf-aav-test-data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-aav-qc/test_data && tar -xzvf ${CI_PROJECT_NAME}/data/wf-aav-test-data.tar.gz -C ${CI_PROJECT_NAME}/data/"
NF_WORKFLOW_OPTS: "-executor.\\$$local.memory 16GB --fastq ${CI_PROJECT_NAME}/data/test_data/fastq --ref_host ${CI_PROJECT_NAME}/data/test_data/cell_line.fasta.gz --ref_helper ${CI_PROJECT_NAME}/data/test_data/helper.fasta --ref_rep_cap ${CI_PROJECT_NAME}/data/test_data/repcap.fasta --itr1_start 11 --itr1_end 156 --itr2_start 2156 --itr2_end 2286 --ref_transgene_plasmid ${CI_PROJECT_NAME}/data/test_data/transgene.fasta --threads 4 "
CI_FLAVOUR: "new" # set to "classic" for old-style CI
# Remove this block in downstream templates
singularity-run:
tags: [] # no need for big ram
# end
docker-run:
# Remove this directive in downstream templates
tags:
- large_ram
# Define a 1D job matrix to inject a variable named MATRIX_NAME into
# the CI environment, we can use the value of MATRIX_NAME to determine
# which options to apply as part of the rules block below
# NOTE There is a slightly cleaner way to define this matrix to include
# the variables, but it is broken when using long strings! See CW-756
parallel:
matrix:
- MATRIX_NAME: [
"fastq_input", "ubam_input", "fastq_input_splitbam",
"no-basecall-model", "no-basecall-model-basecaller-cfg",
"itrs_from_bed", "host_files_in_dir"
]
rules:
# NOTE As we're overriding the rules block for the included docker-run
# we must redefine this CI_COMMIT_BRANCH rule to prevent docker-run
# being incorrectly scheduled for "detached merge request pipelines" etc.
- if: ($CI_COMMIT_BRANCH == null || $CI_COMMIT_BRANCH == "dev-template")
when: never
- if: $MATRIX_NAME == "fastq_input"
variables:
NF_IGNORE_PROCESSES: "split_bams_by_structure"
# use default `NF_WORKFLOW_OPTS` defined above
- if: $MATRIX_NAME == "ubam_input"
variables:
NF_WORKFLOW_OPTS: "-executor.\\$$local.memory 16GB --bam ${CI_PROJECT_NAME}/data/test_data/ubam --ref_host ${CI_PROJECT_NAME}/data/test_data/cell_line.fasta.gz --ref_helper ${CI_PROJECT_NAME}/data/test_data/helper.fasta --ref_rep_cap ${CI_PROJECT_NAME}/data/test_data/repcap.fasta --itr1_start 11 --itr1_end 156 --itr2_start 2156 --itr2_end 2286 --ref_transgene_plasmid ${CI_PROJECT_NAME}/data/test_data/transgene.fasta --threads 4"
NF_IGNORE_PROCESSES: "split_bams_by_structure"
- if: $MATRIX_NAME == "fastq_input_splitbam"
variables:
NF_WORKFLOW_OPTS: "-executor.\\$$local.memory 16GB --fastq ${CI_PROJECT_NAME}/data/test_data/fastq --ref_host ${CI_PROJECT_NAME}/data/test_data/cell_line.fasta.gz --ref_helper ${CI_PROJECT_NAME}/data/test_data/helper.fasta --ref_rep_cap ${CI_PROJECT_NAME}/data/test_data/repcap.fasta --itr1_start 11 --itr1_end 156 --itr2_start 2156 --itr2_end 2286 --ref_transgene_plasmid ${CI_PROJECT_NAME}/data/test_data/transgene.fasta --output_genometype_bams --threads 4"
- if: $MATRIX_NAME == "no-basecall-model"
variables:
NF_WORKFLOW_OPTS: "-executor.\\$$local.memory 16GB --fastq ${CI_PROJECT_NAME}/data/test_data/fastq-no-basecall-model --ref_host ${CI_PROJECT_NAME}/data/test_data/cell_line.fasta.gz --ref_helper ${CI_PROJECT_NAME}/data/test_data/helper.fasta --ref_rep_cap ${CI_PROJECT_NAME}/data/test_data/repcap.fasta --itr1_start 11 --itr1_end 156 --itr2_start 2156 --itr2_end 2286 --ref_transgene_plasmid ${CI_PROJECT_NAME}/data/test_data/transgene.fasta --threads 4"
ASSERT_NEXTFLOW_FAILURE: 1
ASSERT_NEXTFLOW_FAILURE_REXP: Found no basecall model information in the input data for sample .*\. Please provide it with the `--override_basecaller_cfg` parameter.
- if: $MATRIX_NAME == "no-basecall-model-basecaller-cfg"
variables:
NF_WORKFLOW_OPTS: "-executor.\\$$local.memory 16GB --fastq ${CI_PROJECT_NAME}/data/test_data/fastq-no-basecall-model --override_basecaller_cfg [email protected] --ref_host ${CI_PROJECT_NAME}/data/test_data/cell_line.fasta.gz --ref_helper ${CI_PROJECT_NAME}/data/test_data/helper.fasta --ref_rep_cap ${CI_PROJECT_NAME}/data/test_data/repcap.fasta --itr1_start 11 --itr1_end 156 --itr2_start 2156 --itr2_end 2286 --ref_transgene_plasmid ${CI_PROJECT_NAME}/data/test_data/transgene.fasta --threads 4"
- if: $MATRIX_NAME == "itrs_from_bed"
variables:
NF_WORKFLOW_OPTS: "-executor.\\$$local.memory 16GB --fastq ${CI_PROJECT_NAME}/data/test_data/fastq --transgene_bed ${CI_PROJECT_NAME}/data/test_data/sim.bed --ref_host ${CI_PROJECT_NAME}/data/test_data/cell_line.fasta.gz --ref_helper ${CI_PROJECT_NAME}/data/test_data/helper.fasta --ref_rep_cap ${CI_PROJECT_NAME}/data/test_data/repcap.fasta --ref_transgene_plasmid ${CI_PROJECT_NAME}/data/test_data/transgene.fasta --threads 4"
- if: $MATRIX_NAME == "host_files_in_dir"
variables:
NF_WORKFLOW_OPTS: "-executor.\\$$local.memory 16GB --bam ${CI_PROJECT_NAME}/data/test_data/ubam --non_transgene_refs ${CI_PROJECT_NAME}/data/test_data/non_transgene_refs/ --itr1_start 11 --itr1_end 156 --itr2_start 2156 --itr2_end 2286 --ref_transgene_plasmid ${CI_PROJECT_NAME}/data/test_data/transgene.fasta --threads 4"