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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: 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"
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
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/demo.nextflow.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
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"
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
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"
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
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"
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
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"
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
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"
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
NF_WORKFLOW_OPTS: "-executor.\\$$local.memory 16GB \
--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"
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
NF_WORKFLOW_OPTS: "-executor.\\$$local.memory 16GB \
--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"
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
NF_WORKFLOW_OPTS: "-executor.\\$$local.memory 16GB \
--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"
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
NF_WORKFLOW_OPTS: "-executor.\\$$local.memory 16GB \
--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"
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
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"
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
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"
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
NF_WORKFLOW_OPTS: "-executor.\\$$local.memory 16GB \
--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"
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