74 lines
4.6 KiB
YAML
74 lines
4.6 KiB
YAML
# Include shared CI
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include:
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- project: "epi2melabs/ci-templates"
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file: "wf-containers.yaml"
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variables:
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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
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NF_WORKFLOW_OPTS: "--fastq ERR6053095_chr20.fastq \
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--ref_genome chr20/hg38_chr20.fa --ref_annotation chr20/gencode.v22.annotation.chr20.gtf \
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--jaffal_refBase chr20/ --jaffal_genome hg38_chr20 --jaffal_annotation genCode22"
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NF_IGNORE_PROCESSES: preprocess_reads,merge_transcriptomes
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CI_FLAVOUR: "new"
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macos-run:
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# Let's avoid those ARM64 runners for now
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tags:
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- macos
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- x86
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docker-run:
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# Define a 1D job matrix to inject a variable named MATRIX_NAME into
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# the CI environment, we can use the value of MATRIX_NAME to determine
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# which options to apply as part of the rules block below
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# NOTE There is a slightly cleaner way to define this matrix to include
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# the variables, but it is broken when using long strings! See CW-756
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parallel:
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matrix:
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- MATRIX_NAME: [
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"fusions", "differential_expression", "only_differential_expression", "isoforms"
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]
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rules:
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# NOTE As we're overriding the rules block for the included docker-run
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# we must redefine this CI_COMMIT_BRANCH rule to prevent docker-run
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# being incorrectly scheduled for "detached merge request pipelines" etc.
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- if: ($CI_COMMIT_BRANCH == null || $CI_COMMIT_BRANCH == "dev-template")
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when: never
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- if: $MATRIX_NAME == "isoforms"
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variables:
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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
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NF_WORKFLOW_OPTS: "--fastq ERR6053095_chr20.fastq --transcriptome-source reference-guided \
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--ref_genome chr20/hg38_chr20.fa --ref_annotation chr20/gencode.v22.annotation.chr20.gtf"
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NF_IGNORE_PROCESSES: preprocess_reads,merge_transcriptomes
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- if: $MATRIX_NAME == "fusions"
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variables:
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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
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NF_WORKFLOW_OPTS: "--fastq ERR6053095_chr20.fastq --transcriptome-source reference-guided \
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--ref_genome chr20/hg38_chr20.fa --ref_annotation chr20/gencode.v22.annotation.chr20.gtf \
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--jaffal_refBase chr20/ --jaffal_genome hg38_chr20 --jaffal_annotation genCode22"
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NF_IGNORE_PROCESSES: preprocess_reads,merge_transcriptomes
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- if: $MATRIX_NAME == "differential_expression"
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variables:
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NF_BEFORE_SCRIPT: wget -O differential_expression.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/differential_expression.tar.gz && tar -xzvf differential_expression.tar.gz
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NF_WORKFLOW_OPTS: "--fastq differential_expression/differential_expression_fastq \
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--de_analysis \
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--ref_genome differential_expression/hg38_chr20.fa --transcriptome-source reference-guided \
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--ref_annotation differential_expression/gencode.v22.annotation.chr20.gtf \
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--direct_rna --minimap_index_opts \\-k15"
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NF_IGNORE_PROCESSES: preprocess_reads,merge_transcriptomes
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- if: $MATRIX_NAME == "only_differential_expression"
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variables:
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NF_BEFORE_SCRIPT: wget -O differential_expression.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/differential_expression.tar.gz && tar -xzvf differential_expression.tar.gz
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NF_WORKFLOW_OPTS: "--fastq differential_expression/differential_expression_fastq \
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--transcriptome-source precomputed \
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--de_analysis \
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--ref_genome differential_expression/hg38_chr20.fa \
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--ref_annotation differential_expression/gencode.v22.annotation.chr20.gtf \
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--direct_rna --minimap_index_opts \\-k15 \
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--ref_transcriptome differential_expression/ref_transcriptome.fasta \
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--transcriptome_assembly false"
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NF_IGNORE_PROCESSES: >
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preprocess_reads,merge_transcriptomes,assemble_transcripts,
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build_minimap_index,get_transcriptome,merge_gff_bundles,run_gffcompare,build_minimap_index,split_bam
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