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.gitlab-ci.yml
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# Include shared CI
include:
- project: "epi2melabs/ci-templates"
file: "wf-containers.yaml"
variables:
# Workflow inputs given to nextflow.
# The workflow should define `--out_dir`, the CI template sets this.
# Only common file inputs and option values need to be given here
# (not things such as -profile)
NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/wf-pore-c-demo.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-pore-c/wf-pore-c-demo.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/wf-pore-c-demo.tar.gz -C ${CI_PROJECT_NAME}/data/"
NF_WORKFLOW_OPTS: "-executor.\\$$local.memory 32GB \
--bam ${CI_PROJECT_NAME}/data/wf-pore-c-demo/porec_test.concatemers.bam --chunk_size 100 --ref \
${CI_PROJECT_NAME}/data/wf-pore-c-demo/porec_test.fasta \
--cutter NlaIII \
--vcf ${CI_PROJECT_NAME}/data/wf-pore-c-demo/porec_test.phased_variants.vcf.gz \
--paired_end_minimum_distance 100 --paired_end_maximum_distance 200 --hi_c --mcool --paired_end"
CI_FLAVOUR: "new"
macos-run:
tags:
- macos
- x86
docker-run:
parallel:
matrix:
- MATRIX_NAME: [
"no-sample-sheet-chunk", "sample-sheet", "sample-sheet-cutter",
"fastq", "chromunity", "input-dir-hic", "demo",
"sample-sheet-and-chunk-size", "vcf-no-tbi",
"sample-sheet-no-vcf", "sample-sheet-vcf-no-tbi"]
rules:
- if: ($CI_COMMIT_BRANCH == null || $CI_COMMIT_BRANCH == "dev-template")
when: never
- if: $MATRIX_NAME == "no-sample-sheet-chunk"
variables:
NF_WORKFLOW_OPTS: "-executor.\\$$local.memory 32GB \
--bam test_data/porec_test.concatemers.bam --chunk_size 100 --ref \
test_data/porec_test.fasta \
--cutter NlaIII \
--vcf test_data/porec_test.phased_variants.vcf.gz --pairs \
--chromunity --paired_end --filter_pairs --paired_end_minimum_distance 100 \
--paired_end_maximum_distance 200 --bed"
- if: $MATRIX_NAME == "sample-sheet"
variables:
NF_WORKFLOW_OPTS: "-executor.\\$$local.memory 32GB \
--bam test_data/bams --ref \
test_data/porec_test.fasta \
--pairs --chunk_size 0 \
--chromunity --paired_end --filter_pairs --paired_end_minimum_distance 100 \
--paired_end_maximum_distance 200 --sample_sheet test_data/sample_sheet.csv \
--max_monomers 8"
NF_IGNORE_PROCESSES: "index_bam"
- if: $MATRIX_NAME == "sample-sheet-cutter"
variables:
NF_WORKFLOW_OPTS: "-executor.\\$$local.memory 32GB \
--bam test_data/bams --ref \
test_data/porec_test.fasta \
--pairs --chunk_size 0 \
--chromunity --paired_end --filter_pairs --paired_end_minimum_distance 100 \
--paired_end_maximum_distance 200 --sample_sheet test_data/sample_sheet_cutter.csv \
--max_monomers 8"
NF_IGNORE_PROCESSES: "index_bam"
- if: $MATRIX_NAME == "input-dir-hic"
variables:
NF_WORKFLOW_OPTS: "-executor.\\$$local.memory 32GB \
--bam test_data/bams_dir --chunk_size 500 --ref \
test_data/porec_test.fasta \
--cutter NlaIII \
--vcf test_data/porec_test.phased_variants.vcf.gz \
--chromunity --paired_end --filter_pairs --paired_end_minimum_distance 100 \
--paired_end_maximum_distance 200 --hi_c"
- if: $MATRIX_NAME == "fastq"
variables:
NF_WORKFLOW_OPTS: "-executor.\\$$local.memory 32GB \
--fastq test_data/porec_test.concatemers.fastq --ref \
test_data/porec_test.fasta \
--cutter NlaIII \
--vcf test_data/porec_test.phased_variants.vcf.gz --pairs \
--chromunity --paired_end --filter_pairs --paired_end_minimum_distance 100 \
--paired_end_maximum_distance 200"
NF_IGNORE_PROCESSES: "index_bam"
- if: $MATRIX_NAME == "chromunity"
variables:
NF_WORKFLOW_OPTS: "-executor.\\$$local.memory 32GB \
--fastq test_data/porec_test.concatemers.fastq --ref \
test_data/porec_test.fasta \
--mcool_resolutions 1000,2000,3000 --cutter NlaIII \
--vcf test_data/porec_test.phased_variants.vcf.gz --pairs \
--chromunity --paired_end --filter_pairs --paired_end_minimum_distance 100 \
--paired_end_maximum_distance 200 --chromunity --chromunity_merge_distance 5 --mcool"
NF_IGNORE_PROCESSES: "index_bam"
- if: $MATRIX_NAME == "demo"
variables:
NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/wf-pore-c-demo.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-pore-c/wf-pore-c-demo.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/wf-pore-c-demo.tar.gz -C ${CI_PROJECT_NAME}/data/"
NF_WORKFLOW_OPTS: "-executor.\\$$local.memory 32GB \
--bam ${CI_PROJECT_NAME}/data/wf-pore-c-demo/porec_test.concatemers.bam --chunk_size 100 --ref \
${CI_PROJECT_NAME}/data/wf-pore-c-demo/porec_test.fasta \
--cutter NlaIII \
--vcf ${CI_PROJECT_NAME}/data/wf-pore-c-demo/porec_test.phased_variants.vcf.gz \
--paired_end_minimum_distance 100 --paired_end_maximum_distance 200 --hi_c --mcool --paired_end"
- if: $MATRIX_NAME == "sample-sheet-and-chunk-size"
variables:
NF_WORKFLOW_OPTS: "-executor.\\$$local.memory 32GB \
--bam test_data/bams --ref \
test_data/porec_test.fasta \
--pairs --chunk_size 100 \
--chromunity --paired_end --filter_pairs --paired_end_minimum_distance 100 \
--paired_end_maximum_distance 200 --sample_sheet test_data/sample_sheet.csv"
- if: $MATRIX_NAME == "vcf-no-tbi"
variables:
NF_WORKFLOW_OPTS: "-executor.\\$$local.memory 32GB \
--fastq test_data/porec_test.concatemers.fastq --ref \
test_data/porec_test.fasta \
--cutter NlaIII \
--vcf test_data/porec_test_no_index.phased_variants.vcf.gz --pairs \
--chromunity --paired_end --filter_pairs --paired_end_minimum_distance 100 \
--paired_end_maximum_distance 20"
- if: $MATRIX_NAME == "sample-sheet-no-vcf"
variables:
NF_WORKFLOW_OPTS: "-executor.\\$$local.memory 32GB \
--bam test_data/bams --ref \
test_data/porec_test.fasta \
--pairs --chunk_size 100 \
--chromunity --paired_end --filter_pairs --paired_end_minimum_distance 100 \
--paired_end_maximum_distance 200 --sample_sheet test_data/sample_sheet_no_vcf.csv"
- if: $MATRIX_NAME == "sample-sheet-vcf-no-tbi"
variables:
NF_WORKFLOW_OPTS: "-executor.\\$$local.memory 32GB \
--bam test_data/bams --ref \
test_data/porec_test.fasta \
--pairs --chunk_size 100 \
--chromunity --paired_end --filter_pairs --paired_end_minimum_distance 100 \
--paired_end_maximum_distance 200 \
--sample_sheet test_data/sample_sheet_no_tbi.csv"