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.gitlab-ci.yml
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.gitlab-ci.yml
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include:
- project: "epi2melabs/ci-templates"
file: "wf-containers.yaml"
variables:
# chunk_size here forces multiple chunks even for test data which better exercises some channels
NF_WORKFLOW_OPTS: "--fastq test_data/fastq --reference_based_assembly --reference test_data/ref/reference.subseq.fa.gz --threads 4 --chunk_size 100000"
NF_IGNORE_PROCESSES: "deNovo"
CI_FLAVOUR: "new"
docker-run:
parallel:
matrix:
- MATRIX_NAME: [de-novo, amr, barcode04, mixed-species, reference-iso, de-novo-advanced_options, de-novo-bam,
bacteria-medaka-model, no-reads]
TAG: [large_ram]
- MATRIX_NAME: [reference-based, check-model, sample-sheet]
TAG: [""]
tags:
- $TAG
rules:
# Reference-based assembly requires 16GB, de novo requires 32GB
- if: ($CI_COMMIT_BRANCH == null || $CI_COMMIT_BRANCH == "dev-template")
when: never
- if: $MATRIX_NAME == "de-novo"
variables:
NF_WORKFLOW_OPTS: "-executor.\\$$local.memory 32GB \
--fastq test_data/fastq --threads 3 --chunk_size 100000"
NF_IGNORE_PROCESSES: "medakaVariant,medakaVariantHdf,makePerSampleReports"
- if: $MATRIX_NAME == "de-novo-bam"
variables:
NF_WORKFLOW_OPTS: "-executor.\\$$local.memory 32GB \
--bam test_data/bam --threads 4 --chunk_size 100000 --override_basecaller_cfg [email protected]"
NF_IGNORE_PROCESSES: "medakaVariant,medakaVariantHdf,makePerSampleReports"
- if: $MATRIX_NAME == "de-novo-advanced_options"
variables:
NF_WORKFLOW_OPTS: "-executor.\\$$local.memory 32GB \
--fastq test_data/fastq --threads 3 --chunk_size 100000 --flye_opts '--genome-size 25k'"
NF_IGNORE_PROCESSES: "medakaVariant,medakaVariantHdf,makePerSampleReports"
- if: $MATRIX_NAME == "reference-based"
variables:
NF_WORKFLOW_OPTS: "-executor.\\$$local.memory 16GB \
--fastq test_data/fastq --reference_based_assembly --reference test_data/ref/reference.subseq.fa.gz --threads 4 --chunk_size 100000"
NF_IGNORE_PROCESSES: "deNovo,assemblyStats,runProkka,makePerSampleReports"
- if: $MATRIX_NAME == "check-model"
variables:
NF_WORKFLOW_OPTS: "-executor.\\$$local.memory 16GB \
--fastq test_data/fastq --reference_based_assembly --reference test_data/ref/reference.subseq.fa.gz --threads 4 --chunk_size 100000"
NF_IGNORE_PROCESSES: "deNovo,assemblyStats,runProkka,makePerSampleReports"
- if: $MATRIX_NAME == "amr"
variables:
NF_WORKFLOW_OPTS: "-executor.\\$$local.memory 32GB \
--fastq s3://ont-exd-int-s3-euwst1-epi2me-labs/wf-bacterial-genomes/test_data/isolates_fastq --sample_sheet test_data/isolates_sample_sheet.csv --threads 3 --chunk_size 100000 --isolates --client_fields test_data/client_fields.json --override_basecaller_cfg [email protected]"
NF_IGNORE_PROCESSES: "runProkka,medakaVariant,medakaVariantHdf,makePerSampleReports"
- if: $MATRIX_NAME == "sample-sheet"
variables:
NF_WORKFLOW_OPTS: "-executor.\\$$local.memory 16GB \
--fastq test_data/fastq --reference_based_assembly --reference test_data/ref/reference.subseq.fa.gz --threads 4 --chunk_size 100000 \
--sample_sheet test_data/sample_sheet.csv"
NF_IGNORE_PROCESSES: "deNovo,assemblyStats,runProkka,makePerSampleReports"
- if: $MATRIX_NAME == "barcode04"
# isolates barcode04 only has 4 reads and flye will fail due to low coverage
variables:
NF_WORKFLOW_OPTS: "-executor.\\$$local.memory 32GB \
--fastq s3://ont-exd-int-s3-euwst1-epi2me-labs/wf-bacterial-genomes/test_data/isolates_fastq/barcode04 \
--threads 3 --chunk_size 100000 --override_basecaller_cfg [email protected]"
NF_IGNORE_PROCESSES: "alignReads,readStats,coverStats,splitRegions,\
medakaConsensus,medakaNetwork,medakaVariant,medakaVariantHdf,makeReport,runProkka,makePerSampleReports"
- if: $MATRIX_NAME == "mixed-species"
variables:
NF_WORKFLOW_OPTS: "-executor.\\$$local.memory 32GB \
--fastq s3://ont-exd-int-s3-euwst1-epi2me-labs/wf-bacterial-genomes/test_data/isolates_fastq --sample_sheet test_data/isolates_mixed_sample_sheet.csv --threads 3 --chunk_size 100000 --isolates --override_basecaller_cfg [email protected]"
NF_IGNORE_PROCESSES: "runProkka,medakaVariant,medakaVariantHdf"
# serotyping
- if: $MATRIX_NAME == "reference-iso"
variables:
NF_WORKFLOW_OPTS: "-executor.\\$$local.memory 16GB \
--fastq s3://ont-exd-int-s3-euwst1-epi2me-labs/wf-bacterial-genomes/wf-bacterial-genomes-demo/isolates_fastq/barcode02 --reference_based_assembly --reference test_data/ref/salmonella_reference.fa.gz --threads 4 --chunk_size 100000 --isolates --override_basecaller_cfg [email protected]"
NF_IGNORE_PROCESSES: "deNovo,runProkka"
- if: $MATRIX_NAME == "bacteria-medaka-model"
variables:
NF_WORKFLOW_OPTS: "-executor.\\$$local.memory 32GB \
--bam test_data/bam --threads 4 --chunk_size 100000 --override_basecaller_cfg [email protected]"
NF_IGNORE_PROCESSES: "runProkka,makePerSampleReports"
- if: $MATRIX_NAME == "no-reads"
variables:
NF_WORKFLOW_OPTS: "-executor.\\$$local.memory 32GB \
--fastq test_data/no_data --sample_sheet test_data/sample_sheet_no_data.csv"
NF_IGNORE_PROCESSES: "alignReads,readStats,coverStats,splitRegions,\
medakaConsensus,medakaNetwork,medakaVariant,medakaVariantHdf,makeReport,runProkka,makePerSampleReports"
# reminder: update AUX_IMAGE_TAG if the aux container package versions are changed
release-prokka:
extends: .aux-container
variables:
AUX_IMAGE_NAME: "prokka"
AUX_IMAGE_ENVFILE: "environment_prokka.yaml"
AUX_IMAGE_TAG: "1.14.5"