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.gitlab-ci.yml
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# Include shared CI
include:
- project: "epi2melabs/ci-templates"
file: "wf-containers.yaml"
variables:
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"
NF_IGNORE_PROCESSES: preprocess_reads,merge_transcriptomes
CI_FLAVOUR: "new"
macos-run:
# Let's avoid those ARM64 runners for now
tags:
- macos
- x86
docker-run:
artifacts:
when: always
paths:
- ${CI_PROJECT_NAME}
- .nextflow.log
exclude:
- ${CI_PROJECT_NAME}/**/*.gtf
- ${CI_PROJECT_NAME}/**/*.gtf.gz
- ${CI_PROJECT_NAME}/**/*.gff3
- ${CI_PROJECT_NAME}/**/*.gff3.gz
- ${CI_PROJECT_NAME}/**/*.gff
- ${CI_PROJECT_NAME}/**/*.gff.gz
- ${CI_PROJECT_NAME}/**/*.fna
- ${CI_PROJECT_NAME}/**/*.fasta
- ${CI_PROJECT_NAME}/**/*.mmi
# Define a 1D job matrix to inject a variable named MATRIX_NAME into
# the CI environment, we can use the value of MATRIX_NAME to determine
# which options to apply as part of the rules block below
# NOTE There is a slightly cleaner way to define this matrix to include
# the variables, but it is broken when using long strings! See CW-756
parallel:
matrix:
- MATRIX_NAME: [
"fusions", "differential_expression", "isoforms",
"only_differential_expression", "differential_expression_gff3",
"ncbi_gzip", "denovo", "ncbi_no_gene_id", "ensembl_with_versions"
]
rules:
# NOTE As we're overriding the rules block for the included docker-run
# we must redefine this CI_COMMIT_BRANCH rule to prevent docker-run
# being incorrectly scheduled for "detached merge request pipelines" etc.
- if: ($CI_COMMIT_BRANCH == null || $CI_COMMIT_BRANCH == "dev-template")
when: never
- if: $MATRIX_NAME == "isoforms"
variables:
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 --transcriptome-source reference-guided \
--ref_genome chr20/hg38_chr20.fa --ref_annotation chr20/gencode.v22.annotation.chr20.gtf"
NF_IGNORE_PROCESSES: preprocess_reads,merge_transcriptomes,decompress_annotation,decompress_ref
- if: $MATRIX_NAME == "denovo"
variables:
NF_WORKFLOW_OPTS: "--fastq test_data/fastq/SIRV_E0_PCS109_50.fq.gz --transcriptome_source denovo"
NF_IGNORE_PROCESSES: preprocess_reads,merge_transcriptomes,decompress_annotation,decompress_ref,build_minimap_index
- if: $MATRIX_NAME == "fusions"
variables:
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 --transcriptome-source reference-guided \
--ref_genome chr20/hg38_chr20.fa --ref_annotation chr20/gencode.v22.annotation.chr20.gtf \
--jaffal_refBase chr20/ --jaffal_genome hg38_chr20 --jaffal_annotation genCode22"
NF_IGNORE_PROCESSES: preprocess_reads,merge_transcriptomes,decompress_annotation,decompress_ref
- if: $MATRIX_NAME == "differential_expression"
variables:
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
NF_WORKFLOW_OPTS: "--fastq differential_expression/differential_expression_fastq \
--de_analysis \
--ref_genome differential_expression/hg38_chr20.fa --transcriptome-source reference-guided \
--ref_annotation differential_expression/gencode.v22.annotation.chr20.gtf \
--direct_rna --minimap_index_opts '-k 15' --sample_sheet test_data/sample_sheet.csv"
NF_IGNORE_PROCESSES: preprocess_reads,merge_transcriptomes,decompress_annotation,decompress_ref
- if: $MATRIX_NAME == "only_differential_expression"
variables:
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
NF_WORKFLOW_OPTS: "--fastq differential_expression/differential_expression_fastq \
--transcriptome-source precomputed \
--de_analysis \
--ref_genome differential_expression/hg38_chr20.fa \
--ref_annotation differential_expression/gencode.v22.annotation.chr20.gff \
--direct_rna --minimap_index_opts '-k 15' \
--ref_transcriptome differential_expression/ref_transcriptome.fasta \
--sample_sheet test_data/sample_sheet.csv"
NF_IGNORE_PROCESSES: >
preprocess_reads,merge_transcriptomes,assemble_transcripts,decompress_annotation,decompress_ref,
build_minimap_index,get_transcriptome,merge_gff_bundles,run_gffcompare,build_minimap_index,split_bam
- if: $MATRIX_NAME == "differential_expression_gff3"
variables:
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
NF_WORKFLOW_OPTS: "--fastq differential_expression/differential_expression_fastq \
--transcriptome-source precomputed \
--de_analysis \
--ref_genome differential_expression/hg38_chr20.fa \
--ref_annotation differential_expression/gencode.v22.annotation.chr20.gff3 \
--direct_rna --minimap_index_opts '-k 15' \
--ref_transcriptome differential_expression/ref_transcriptome.fasta \
--sample_sheet test_data/sample_sheet.csv"
NF_IGNORE_PROCESSES: >
preprocess_reads,merge_transcriptomes,assemble_transcripts,decompress_annotation,decompress_ref,
build_minimap_index,get_transcriptome,merge_gff_bundles,run_gffcompare,build_minimap_index,split_bam
- if: $MATRIX_NAME == "ncbi_gzip"
variables:
NF_BEFORE_SCRIPT: wget -O differential_expression_ncbi.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/differential_expression_ncbi.tar.gz && tar -xzvf differential_expression_ncbi.tar.gz
NF_WORKFLOW_OPTS: "-executor.\\$$local.memory 16GB \
--fastq differential_expression_ncbi/differential_expression_fastq \
--transcriptome-source precomputed \
--de_analysis \
--ref_genome differential_expression_ncbi/GRCh38.p14.NCBI_test.fna.gz \
--ref_annotation differential_expression_ncbi/GRCh38.p14_NCBI_test.gtf.gz \
--direct_rna --minimap_index_opts '-w 25' \
--sample_sheet test_data/sample_sheet.csv"
NF_IGNORE_PROCESSES: >
preprocess_reads,merge_transcriptomes,assemble_transcripts,
build_minimap_index,get_transcriptome,merge_gff_bundles,run_gffcompare,build_minimap_index,split_bam
- if: $MATRIX_NAME == "ncbi_no_gene_id"
variables:
NF_BEFORE_SCRIPT: wget -O differential_expression_ncbi.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/differential_expression_ncbi.tar.gz && tar -xzvf differential_expression_ncbi.tar.gz
NF_WORKFLOW_OPTS: "-executor.\\$$local.memory 16GB \
--fastq differential_expression_ncbi/differential_expression_fastq \
--transcriptome-source precomputed --de_analysis \
--ref_genome differential_expression_ncbi/GCF_000001405.40_GRCh38.p14_genomic.fna.gz \
--ref_annotation differential_expression_ncbi/GCF_000001405.40_GRCh38.p14_genomic.gff.gz \
--direct_rna --ref_transcriptome differential_expression_ncbi/GCF_000001405.40_GRCh38.p14_rna.fna.gz \
--transcriptome_assembly false --sample_sheet test_data/sample_sheet.csv"
NF_IGNORE_PROCESSES: >
preprocess_reads,merge_transcriptomes,assemble_transcripts,
build_minimap_index,get_transcriptome,merge_gff_bundles,run_gffcompare,build_minimap_index,split_bam
- if: $MATRIX_NAME == "ensembl_with_versions"
variables:
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
NF_WORKFLOW_OPTS: "-executor.\\$$local.memory 16GB \
--fastq differential_expression/differential_expression_fastq \
--transcriptome-source precomputed --de_analysis \
--ref_genome differential_expression/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz \
--ref_annotation differential_expression/Homo_sapiens.GRCh38.109.gtf.gz \
--direct_rna --ref_transcriptome differential_expression/Homo_sapiens.GRCh38.cdna.all.fa.gz \
--transcriptome_assembly false --sample_sheet test_data/sample_sheet.csv"
NF_IGNORE_PROCESSES: >
preprocess_reads,merge_transcriptomes,assemble_transcripts,
build_minimap_index,get_transcriptome,merge_gff_bundles,run_gffcompare,build_minimap_index,split_bam