226 lines
22 KiB
YAML
226 lines
22 KiB
YAML
# Include shared CI
|
|
include:
|
|
- project: "epi2melabs/ci-templates"
|
|
file: "wf-containers.yaml"
|
|
|
|
variables:
|
|
NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/differential_expression.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/differential_expression.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/differential_expression.tar.gz -C ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/demo.nextflow.config https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/demo.nextflow.config"
|
|
NF_WORKFLOW_OPTS: "--fastq ${CI_PROJECT_NAME}/data/differential_expression/differential_expression_fastq \
|
|
--de_analysis --ref_genome ${CI_PROJECT_NAME}/data/differential_expression/hg38_chr20.fa \
|
|
--transcriptome_source reference-guided \
|
|
--ref_annotation ${CI_PROJECT_NAME}/data/differential_expression/gencode.v22.annotation.chr20.gtf \
|
|
--direct_rna --minimap2_index_opts '-k 15' --sample_sheet ${CI_PROJECT_NAME}/data/differential_expression/sample_sheet.csv \
|
|
-c ${CI_PROJECT_NAME}/data/demo.nextflow.config"
|
|
CI_FLAVOUR: "new"
|
|
PYTEST_CONTAINER_NAME: "wf-common"
|
|
PYTEST_CONTAINER_CONFIG_KEY: "common_sha"
|
|
MEM_CFG: "echo 'process { withName:build_minimap_index { memory = '16.GB' }; withName:build_minimap_index_transcriptome { memory = '16.GB' } }' > ${CI_PROJECT_NAME}/data/mm2.config"
|
|
|
|
macos-run:
|
|
# Let's avoid those ARM64 runners for now
|
|
tags:
|
|
- macos
|
|
- x86
|
|
|
|
aws-run:
|
|
artifacts:
|
|
when: always
|
|
|
|
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
|
|
- ${CI_PROJECT_NAME}/**/*.mmi
|
|
|
|
# Define a 1D job matrix to inject a variable named MATRIX_NAME into
|
|
# the CI environment, we can use the value of MATRIX_NAME to determine
|
|
# which options to apply as part of the rules block below
|
|
# NOTE There is a slightly cleaner way to define this matrix to include
|
|
# the variables, but it is broken when using long strings! See CW-756
|
|
parallel:
|
|
matrix:
|
|
- MATRIX_NAME: [
|
|
"differential_expression", "isoforms", "isoforms_bam",
|
|
"only_differential_expression", "differential_expression_gff3",
|
|
"ncbi_gzip", "ncbi_no_gene_id", "ensembl_with_versions",
|
|
"differential_expression_mouse", "no_ref_annotation",
|
|
"unstranded_annotation_error", "igv", "igv_fai_gz"
|
|
]
|
|
rules:
|
|
# NOTE As we're overriding the rules block for the included docker-run
|
|
# we must redefine this CI_COMMIT_BRANCH rule to prevent docker-run
|
|
# being incorrectly scheduled for "detached merge request pipelines" etc.
|
|
- if: ($CI_COMMIT_BRANCH == null || $CI_COMMIT_BRANCH == "dev-template")
|
|
when: never
|
|
- if: $MATRIX_NAME == "isoforms"
|
|
variables:
|
|
NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/wf-isoforms_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 ${CI_PROJECT_NAME}/data/wf-isoforms_test_data.tar.gz -C ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/demo.nextflow.config https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/demo.nextflow.config; ${MEM_CFG}"
|
|
NF_WORKFLOW_OPTS: "--fastq ${CI_PROJECT_NAME}/data/ERR6053095_chr20.fastq --transcriptome_source reference-guided \
|
|
--ref_genome ${CI_PROJECT_NAME}/data/chr20/hg38_chr20.fa --ref_annotation ${CI_PROJECT_NAME}/data/chr20/gencode.v22.annotation.chr20.gtf --pychopper_backend phmm \
|
|
-c ${CI_PROJECT_NAME}/data/mm2.config"
|
|
NF_IGNORE_PROCESSES: preprocess_reads,faidx,gz_faidx,check_annotation_strand,merge_transcriptomes,decompress_annotation,decompress_ref,decompress_transcriptome,preprocess_ref_transcriptome
|
|
- if: $MATRIX_NAME == "isoforms_bam"
|
|
variables:
|
|
NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/wf-isoforms_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 ${CI_PROJECT_NAME}/data/wf-isoforms_test_data.tar.gz -C ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/demo.nextflow.config https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/demo.nextflow.config; ${MEM_CFG}"
|
|
NF_WORKFLOW_OPTS: "--bam ${CI_PROJECT_NAME}/data/ERR6053095_chr20.bam --transcriptome_source reference-guided \
|
|
--ref_genome ${CI_PROJECT_NAME}/data/chr20/hg38_chr20.fa --ref_annotation ${CI_PROJECT_NAME}/data/chr20/gencode.v22.annotation.chr20.gtf --pychopper_backend phmm \
|
|
-c ${CI_PROJECT_NAME}/data/demo.nextflow.config -c ${CI_PROJECT_NAME}/data/mm2.config"
|
|
NF_IGNORE_PROCESSES: preprocess_reads,faidx,gz_faidx,check_annotation_strand,merge_transcriptomes,decompress_annotation,decompress_ref,decompress_transcriptome,preprocess_ref_transcriptome
|
|
- if: $MATRIX_NAME == "no_ref_annotation"
|
|
variables:
|
|
NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/wf-isoforms_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 ${CI_PROJECT_NAME}/data/wf-isoforms_test_data.tar.gz -C ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/demo.nextflow.config https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/demo.nextflow.config; ${MEM_CFG}"
|
|
NF_WORKFLOW_OPTS: "--fastq ${CI_PROJECT_NAME}/data/ERR6053095_chr20.fastq --transcriptome_source reference-guided \
|
|
--ref_genome ${CI_PROJECT_NAME}/data/chr20/hg38_chr20.fa \
|
|
-c ${CI_PROJECT_NAME}/data/demo.nextflow.config -c ${CI_PROJECT_NAME}/data/mm2.config"
|
|
NF_IGNORE_PROCESSES: run_gffcompare,check_annotation_strand,preprocess_reads,faidx,gz_faidx,merge_transcriptomes,decompress_annotation,decompress_ref,decompress_transcriptome,preprocess_ref_transcriptome
|
|
- if: $MATRIX_NAME == "differential_expression"
|
|
variables:
|
|
NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/differential_expression.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/differential_expression.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/differential_expression.tar.gz -C ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/demo.nextflow.config https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/demo.nextflow.config; ${MEM_CFG}"
|
|
NF_WORKFLOW_OPTS: "--fastq ${CI_PROJECT_NAME}/data/differential_expression/differential_expression_fastq \
|
|
--de_analysis \
|
|
--ref_genome ${CI_PROJECT_NAME}/data/differential_expression/hg38_chr20.fa --transcriptome_source reference-guided \
|
|
--ref_annotation ${CI_PROJECT_NAME}/data/differential_expression/gencode.v22.annotation.chr20.gtf \
|
|
--direct_rna --minimap2_index_opts '-k 15' --sample_sheet ${CI_PROJECT_NAME}/data/differential_expression/sample_sheet.csv \
|
|
-c ${CI_PROJECT_NAME}/data/demo.nextflow.config -c ${CI_PROJECT_NAME}/data/mm2.config"
|
|
NF_IGNORE_PROCESSES: preprocess_reads,faidx,gz_faidx,merge_transcriptomes,decompress_annotation,decompress_ref,decompress_transcriptome,preprocess_ref_transcriptome
|
|
- if: $MATRIX_NAME == "only_differential_expression"
|
|
variables:
|
|
NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/differential_expression.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/differential_expression.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/differential_expression.tar.gz -C ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/demo.nextflow.config https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/demo.nextflow.config; ${MEM_CFG}"
|
|
NF_WORKFLOW_OPTS: "--fastq ${CI_PROJECT_NAME}/data/differential_expression/differential_expression_fastq \
|
|
--transcriptome_source precomputed \
|
|
--de_analysis \
|
|
--ref_genome ${CI_PROJECT_NAME}/data/differential_expression/hg38_chr20.fa \
|
|
--ref_annotation ${CI_PROJECT_NAME}/data/differential_expression/gencode.v22.annotation.chr20.gff \
|
|
--direct_rna --minimap2_index_opts '-k 15' \
|
|
--ref_transcriptome ${CI_PROJECT_NAME}/data/differential_expression/ref_transcriptome.fasta \
|
|
--sample_sheet test_data/sample_sheet.csv \
|
|
-c ${CI_PROJECT_NAME}/data/demo.nextflow.config -c ${CI_PROJECT_NAME}/data/mm2.config"
|
|
NF_IGNORE_PROCESSES: >
|
|
preprocess_reads,faidx,gz_faidx,merge_transcriptomes,merge_gff_bundles,assemble_transcripts,decompress_annotation,decompress_ref,
|
|
build_minimap_index,get_transcriptome,run_gffcompare,build_minimap_index,split_bam,decompress_transcriptome,preprocess_ref_transcriptome
|
|
- if: $MATRIX_NAME == "differential_expression_gff3"
|
|
variables:
|
|
NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/differential_expression.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/differential_expression.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/differential_expression.tar.gz -C ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/demo.nextflow.config https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/demo.nextflow.config; ${MEM_CFG}"
|
|
NF_WORKFLOW_OPTS: "--fastq ${CI_PROJECT_NAME}/data/differential_expression/differential_expression_fastq \
|
|
--transcriptome_source precomputed \
|
|
--de_analysis \
|
|
--ref_genome ${CI_PROJECT_NAME}/data/differential_expression/hg38_chr20.fa \
|
|
--ref_annotation ${CI_PROJECT_NAME}/data/differential_expression/gencode.v22.annotation.chr20.gff3 \
|
|
--direct_rna --minimap2_index_opts '-k 15' \
|
|
--ref_transcriptome ${CI_PROJECT_NAME}/data/differential_expression/ref_transcriptome.fasta \
|
|
--sample_sheet test_data/sample_sheet.csv \
|
|
-c ${CI_PROJECT_NAME}/data/demo.nextflow.config -c ${CI_PROJECT_NAME}/data/mm2.config"
|
|
NF_IGNORE_PROCESSES: >
|
|
preprocess_reads,faidx,gz_faidx,merge_transcriptomes,assemble_transcripts,decompress_annotation,decompress_ref,
|
|
build_minimap_index,get_transcriptome,merge_gff_bundles,run_gffcompare,build_minimap_index,split_bam,decompress_transcriptome,preprocess_ref_transcriptome
|
|
- if: $MATRIX_NAME == "ncbi_gzip"
|
|
variables:
|
|
NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/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 ${CI_PROJECT_NAME}/data/differential_expression_ncbi.tar.gz -C ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/demo.nextflow.config https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/demo.nextflow.config; ${MEM_CFG}"
|
|
NF_WORKFLOW_OPTS:
|
|
"--fastq ${CI_PROJECT_NAME}/data/differential_expression_ncbi/differential_expression_fastq \
|
|
--de_analysis \
|
|
--ref_genome ${CI_PROJECT_NAME}/data/differential_expression_ncbi/GRCh38.p14.NCBI_test.fna.gz \
|
|
--ref_annotation ${CI_PROJECT_NAME}/data/differential_expression_ncbi/GRCh38.p14_NCBI_test.gtf.gz \
|
|
--direct_rna --minimap2_index_opts '-w 25' \
|
|
--sample_sheet test_data/sample_sheet.csv \
|
|
-c ${CI_PROJECT_NAME}/data/demo.nextflow.config -c ${CI_PROJECT_NAME}/data/mm2.config"
|
|
NF_IGNORE_PROCESSES: >
|
|
preprocess_reads,faidx,gz_faidx,merge_transcriptomes,assemble_transcripts,
|
|
build_minimap_index,get_transcriptome,merge_gff_bundles,run_gffcompare,build_minimap_index,split_bam,decompress_transcriptome,preprocess_ref_transcriptome
|
|
- if: $MATRIX_NAME == "ncbi_no_gene_id"
|
|
variables:
|
|
NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/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 ${CI_PROJECT_NAME}/data/differential_expression_ncbi.tar.gz -C ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/demo.nextflow.config https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/demo.nextflow.config; ${MEM_CFG}"
|
|
NF_WORKFLOW_OPTS:
|
|
"--fastq ${CI_PROJECT_NAME}/data/differential_expression_ncbi/differential_expression_fastq \
|
|
--transcriptome_source precomputed --de_analysis \
|
|
--ref_genome ${CI_PROJECT_NAME}/data/differential_expression_ncbi/GCF_000001405.40_GRCh38.p14_genomic.fna.gz \
|
|
--ref_annotation ${CI_PROJECT_NAME}/data/differential_expression_ncbi/GCF_000001405.40_GRCh38.p14_genomic.gff.gz \
|
|
--direct_rna --ref_transcriptome ${CI_PROJECT_NAME}/data/differential_expression_ncbi/GCF_000001405.40_GRCh38.p14_rna.fna.gz \
|
|
--sample_sheet test_data/sample_sheet.csv \
|
|
-c ${CI_PROJECT_NAME}/data/demo.nextflow.config -c ${CI_PROJECT_NAME}/data/mm2.config"
|
|
NF_IGNORE_PROCESSES: >
|
|
preprocess_reads,faidx,gz_faidx,merge_transcriptomes,assemble_transcripts,
|
|
build_minimap_index,get_transcriptome,merge_gff_bundles,run_gffcompare,build_minimap_index,split_bam,decompress_transcriptome,preprocess_ref_transcriptome
|
|
- if: $MATRIX_NAME == "ensembl_with_versions"
|
|
variables:
|
|
NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/differential_expression.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/differential_expression.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/differential_expression.tar.gz -C ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/demo.nextflow.config https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/demo.nextflow.config; ${MEM_CFG}"
|
|
NF_WORKFLOW_OPTS:
|
|
"--fastq ${CI_PROJECT_NAME}/data/differential_expression/differential_expression_fastq \
|
|
--de_analysis \
|
|
--ref_genome ${CI_PROJECT_NAME}/data/differential_expression/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz \
|
|
--ref_annotation ${CI_PROJECT_NAME}/data/differential_expression/Homo_sapiens.GRCh38.109.gtf.gz \
|
|
--direct_rna --ref_transcriptome ${CI_PROJECT_NAME}/data/differential_expression/Homo_sapiens.GRCh38.cdna.all.fa.gz \
|
|
--sample_sheet test_data/sample_sheet.csv \
|
|
-c ${CI_PROJECT_NAME}/data/demo.nextflow.config -c ${CI_PROJECT_NAME}/data/mm2.config"
|
|
NF_IGNORE_PROCESSES: >
|
|
preprocess_reads,faidx,gz_faidx,merge_transcriptomes,assemble_transcripts,
|
|
build_minimap_index,get_transcriptome,merge_gff_bundles,run_gffcompare,build_minimap_index,split_bam,decompress_transcriptome,preprocess_ref_transcriptome
|
|
- if: $MATRIX_NAME == "differential_expression_mouse"
|
|
variables:
|
|
NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/differential_expression_mouse.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/differential_expression_mouse.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/differential_expression_mouse.tar.gz -C ${CI_PROJECT_NAME}/data/&& wget -O ${CI_PROJECT_NAME}/data/demo.nextflow.config https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/demo.nextflow.config; ${MEM_CFG}"
|
|
NF_WORKFLOW_OPTS:
|
|
"--fastq ${CI_PROJECT_NAME}/data/differential_expression_mouse/differential_expression_fastq \
|
|
--transcriptome_source precomputed --de_analysis \
|
|
--ref_genome ${CI_PROJECT_NAME}/data/differential_expression_mouse/GRCm39.genome.fa.gz \
|
|
--ref_annotation ${CI_PROJECT_NAME}/data/differential_expression_mouse/gencode.vM33.annotation.gtf \
|
|
--direct_rna --ref_transcriptome ${CI_PROJECT_NAME}/data/differential_expression_mouse/gencode.vM33.transcripts.fa.gz \
|
|
--sample_sheet ${CI_PROJECT_NAME}/data/differential_expression_mouse/sample_sheet.csv \
|
|
-c ${CI_PROJECT_NAME}/data/demo.nextflow.config -c ${CI_PROJECT_NAME}/data/mm2.config"
|
|
NF_IGNORE_PROCESSES: >
|
|
preprocess_reads,faidx,gz_faidx,merge_transcriptomes,assemble_transcripts,decompress_annotation,
|
|
build_minimap_index,get_transcriptome,merge_gff_bundles,run_gffcompare,build_minimap_index,split_bam
|
|
- if: $MATRIX_NAME == "unstranded_annotation_error"
|
|
variables:
|
|
NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/differential_expression.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-transcriptomes/differential_expression.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/differential_expression.tar.gz -C ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/demo.nextflow.config https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/demo.nextflow.config; ${MEM_CFG}"
|
|
NF_WORKFLOW_OPTS: "--fastq ${CI_PROJECT_NAME}/data/differential_expression/differential_expression_fastq \
|
|
--de_analysis \
|
|
--ref_genome ${CI_PROJECT_NAME}/data/differential_expression/hg38_chr20.fa --transcriptome_source reference-guided \
|
|
--ref_annotation ${CI_PROJECT_NAME}/data/differential_expression/unstranded_annotation.gtf \
|
|
--direct_rna --minimap2_index_opts '-k 15' --sample_sheet ${CI_PROJECT_NAME}/data/differential_expression/sample_sheet.csv \
|
|
-c ${CI_PROJECT_NAME}/data/demo.nextflow.config -c ${CI_PROJECT_NAME}/data/mm2.config"
|
|
NF_IGNORE_PROCESSES: preprocess_reads,faidx,gz_faidx,merge_transcriptomes,decompress_annotation,decompress_ref,decompress_transcriptome,preprocess_ref_transcriptome
|
|
ASSERT_NEXTFLOW_FAILURE: "test_fail" # set to any non-zero length str to allow the nextflow CMD to fail
|
|
ASSERT_NEXTFLOW_FAILURE_REXP: "In ref_annotation, transcript features must have a strand of either '+' or '-'"
|
|
- if: $MATRIX_NAME == "igv"
|
|
variables:
|
|
NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/differential_expression.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/differential_expression.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/differential_expression.tar.gz -C ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/demo.nextflow.config https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/demo.nextflow.config; ${MEM_CFG}"
|
|
NF_WORKFLOW_OPTS: "--fastq ${CI_PROJECT_NAME}/data/differential_expression/differential_expression_fastq \
|
|
--de_analysis \
|
|
--ref_genome ${CI_PROJECT_NAME}/data/differential_expression/hg38_chr20.fa \
|
|
--ref_annotation ${CI_PROJECT_NAME}/data/differential_expression/gencode.v22.annotation.chr20.gff \
|
|
--direct_rna --minimap2_index_opts '-k 15' \
|
|
--ref_transcriptome ${CI_PROJECT_NAME}/data/differential_expression/ref_transcriptome.fasta \
|
|
--sample_sheet test_data/sample_sheet.csv \
|
|
--igv \
|
|
-c ${CI_PROJECT_NAME}/data/demo.nextflow.config -c ${CI_PROJECT_NAME}/data/mm2.config"
|
|
NF_IGNORE_PROCESSES: >
|
|
preprocess_reads,gz_faidx,merge_transcriptomes,assemble_transcripts,decompress_annotation,decompress_ref,
|
|
build_minimap_index,get_transcriptome,merge_gff_bundles,run_gffcompare,build_minimap_index,split_bam,decompress_transcriptome,preprocess_ref_transcriptome
|
|
- if: $MATRIX_NAME == "igv_fai_gz"
|
|
variables:
|
|
NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/differential_expression_ncbi.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-transcriptomes/differential_expression_ncbi.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/differential_expression_ncbi.tar.gz -C ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/demo.nextflow.config https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/demo.nextflow.config; ${MEM_CFG}"
|
|
NF_WORKFLOW_OPTS:
|
|
"--fastq ${CI_PROJECT_NAME}/data/differential_expression_ncbi/differential_expression_fastq \
|
|
--transcriptome_source precomputed --de_analysis \
|
|
--ref_genome ${CI_PROJECT_NAME}/data/differential_expression_ncbi/GCF_000001405.40_GRCh38.p14_genomic.fna.gz \
|
|
--ref_annotation ${CI_PROJECT_NAME}/data/differential_expression_ncbi/GCF_000001405.40_GRCh38.p14_genomic.gff.gz \
|
|
--direct_rna --ref_transcriptome ${CI_PROJECT_NAME}/data/differential_expression_ncbi/GCF_000001405.40_GRCh38.p14_rna.fna.gz \
|
|
--sample_sheet test_data/sample_sheet.csv \
|
|
--igv \
|
|
-c ${CI_PROJECT_NAME}/data/demo.nextflow.config -c ${CI_PROJECT_NAME}/data/mm2.config"
|
|
NF_IGNORE_PROCESSES: >
|
|
preprocess_reads,merge_transcriptomes,assemble_transcripts,
|
|
build_minimap_index,get_transcriptome,merge_gff_bundles,run_gffcompare,build_minimap_index,split_bam,decompress_transcriptome,preprocess_ref_transcriptome,faidx,gz_faidx
|
|
|