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.gitlab-ci.yml
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.gitlab-ci.yml
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# Include shared CI
include:
- project: "epi2melabs/ci-templates"
file: "wf-containers.yaml"
# conda, mac, simg
variables:
NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -q -O ${CI_PROJECT_NAME}/data/demo_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-human-variation/snp_demo.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/demo_data.tar.gz -C ${CI_PROJECT_NAME}/data/"
NF_PROCESS_FILES: "modules/local/wf-human-snp.nf modules/local/wf-human-sv.nf"
NF_IGNORE_PROCESSES: "hap,lookup_clair3_model,phase_contig_haplotag,cat_haplotagged_contigs,makeAlignmentReport.\
get_genome,aggregate_all_variants,aggregate_full_align_variants,aggregate_pileup_variants,create_candidates,\
evaluate_candidates,get_qual_filter,makeReport,make_chunks,merge_pileup_and_full_vars,output_snp,phase_contig,\
pileup_variants,post_clair_phase_contig,select_het_snps,vcfStats,phase_gvcf"
NF_WORKFLOW_OPTS: "--snp --sv --bam ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.bam --bed ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.bed --ref ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.fasta --clair3_model_path ${CI_PROJECT_NAME}/data/snp_demo/ont_r104_e81_sup_g5015 --phased --annotation_threads 4"
CI_FLAVOUR: "new"
PYTEST_CONTAINER_CONFIG_KEY: "e2l_base_tag"
check-models:
extends: .preflight
script:
- !reference [.install, nextflow] # requires nextflow to read config
- bash util/update_models_schema.sh . docker
- >
if ! diff nextflow_schema.json nextflow_schema.json.new; then
echo "Model schema requires updating."
exit 1
fi
docker-run:
artifacts:
when: always
paths:
- ${CI_PROJECT_NAME}
- .nextflow.log
exclude:
- ${CI_PROJECT_NAME}/**/*.bam
- ${CI_PROJECT_NAME}/**/*.cram
- ${CI_PROJECT_NAME}/**/*.fa
- ${CI_PROJECT_NAME}/**/*.fna
- ${CI_PROJECT_NAME}/**/*.fasta
- ${CI_PROJECT_NAME}/**/ref_cache/**
- ${CI_PROJECT_NAME}/data/**/*
# Define a 1D job matrix to inject a variable named MATRIX_NAME into
# the CI environment, we can use the value of MATRIX_NAME to determine
# which options to apply as part of the rules block below
# NOTE There is a slightly cleaner way to define this matrix to include
# the variables, but it is broken when using long strings! See CW-756
parallel:
matrix:
- MATRIX_NAME: [
"haplocheck_mt",
"haplocheck_nomt",
"haplocheck_custommt_missing",
"run_all_no_report",
"gzref-bam-mod",
"gzref-bam-mod-hap",
"wf-human-snp_modelint",
"wf-human-snp_modelint_unphase",
"wf-human-snp_modelext",
"wf-human-snp_covblock",
"wf-human-snp_svrefine",
"wf-human-sv",
"wf-human-sv-phase",
"str-usersex",
"str-infersex",
"wf-human-cnv-spectre",
"wf-human-phase_all",
"wf-human-phase_all_lp",
"downsample",
"wf-human-snp_GVCF_unphased",
"wf-human-snp_GVCF_phased",
"wf-human-snp-gene-summary"
]
rules:
# NOTE As we're overriding the rules block for the included docker-run
# we must redefine this CI_COMMIT_BRANCH rule to prevent docker-run
# being incorrectly scheduled for "detached merge request pipelines" etc.
- if: ($CI_COMMIT_BRANCH == null || $CI_COMMIT_BRANCH == "dev-template")
when: never
# This uses the Spectre dataset, that contains the mt genome, and should therefore run
# haplocheck.
- if: $MATRIX_NAME == "haplocheck_mt"
variables:
NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -q -O ${CI_PROJECT_NAME}/data/demo_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-human-spectre/spectre_demo.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/demo_data.tar.gz -C ${CI_PROJECT_NAME}/data/"
NF_PROCESS_FILES: "modules/local/wf-human-snp.nf"
NF_IGNORE_PROCESSES: "post_clair_contig_haplotag,post_clair_phase_contig,phase_gvcf,hap,phase_contig_haplotag,cat_haplotagged_contigs,phase_contig,getGenome,get_coverage,getVersions,getParams,failedQCReport,refine_with_sv,makeAlignmentReport"
NF_WORKFLOW_OPTS: "--snp true --sv false --mod false --cnv false --str false --bam ${CI_PROJECT_NAME}/data/spectre_demo/demo.bam --ref ${CI_PROJECT_NAME}/data/spectre_demo/GCA_000001405.15_GRCh38_no_alt_analysis_set.fasta --bam_min_coverage 0 --haplocheck --annotation false"
# The SNP demo doesn't have the MT genome in the reference, and should fail with an expected error.
- if: $MATRIX_NAME == "haplocheck_nomt"
variables:
NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -q -O ${CI_PROJECT_NAME}/data/demo_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-human-variation/snp_demo.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/demo_data.tar.gz -C ${CI_PROJECT_NAME}/data/"
NF_PROCESS_FILES: "modules/local/wf-human-snp.nf"
NF_IGNORE_PROCESSES: "phase_gvcf,hap,phase_contig_haplotag,cat_haplotagged_contigs,phase_contig,getGenome,get_coverage,getVersions,getParams,failedQCReport,refine_with_sv,makeAlignmentReport"
NF_WORKFLOW_OPTS: "--snp --sv false --mod false --cnv false --str false --bam ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.bam --bed ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.bed --ref ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.fasta --basecaller_cfg dna_r10.4.1_e8.2_400bps_hac_prom --haplocheck --bam_min_coverage 0 --annotation false"
ASSERT_NEXTFLOW_FAILURE: "yes"
ASSERT_NEXTFLOW_FAILURE_REXP : "Unexpected number of mitochondrial chromosome found:"
# The SNP demo doesn't have the MT genome in the reference, and should fail with an expected error.
- if: $MATRIX_NAME == "haplocheck_custommt_missing"
variables:
NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -q -O ${CI_PROJECT_NAME}/data/demo_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-human-spectre/spectre_demo.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/demo_data.tar.gz -C ${CI_PROJECT_NAME}/data/"
NF_PROCESS_FILES: "modules/local/wf-human-snp.nf"
NF_IGNORE_PROCESSES: "post_clair_contig_haplotag,post_clair_phase_contig,phase_gvcf,hap,phase_contig_haplotag,cat_haplotagged_contigs,phase_contig,getGenome,get_coverage,getVersions,getParams,failedQCReport,refine_with_sv,makeAlignmentReport"
NF_WORKFLOW_OPTS: "--snp true --sv false --mod false --cnv false --str false --bam ${CI_PROJECT_NAME}/data/spectre_demo/demo.bam --ref ${CI_PROJECT_NAME}/data/spectre_demo/GCA_000001405.15_GRCh38_no_alt_analysis_set.fasta --bam_min_coverage 0 --haplocheck --mitogenome myVerySpecialMt --annotation false"
ASSERT_NEXTFLOW_FAILURE: "yes"
ASSERT_NEXTFLOW_FAILURE_REXP : "Mitochondrial genome myVerySpecialMt not present in the reference"
- if: $MATRIX_NAME == "wf-human-snp_modelint"
variables:
NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -q -O ${CI_PROJECT_NAME}/data/demo_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-human-variation/snp_demo.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/demo_data.tar.gz -C ${CI_PROJECT_NAME}/data/"
NF_PROCESS_FILES: "modules/local/wf-human-snp.nf"
NF_IGNORE_PROCESSES: "phase_gvcf,hap,phase_contig_haplotag,cat_haplotagged_contigs,phase_contig,getGenome,get_coverage,getVersions,getParams,failedQCReport,refine_with_sv,makeAlignmentReport"
NF_WORKFLOW_OPTS: "--snp --sv false --mod false --cnv false --str false --bam ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.bam --bed ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.bed --ref ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.fasta --basecaller_cfg dna_r10.4.1_e8.2_400bps_hac_prom --phased --bam_min_coverage 0.00001 --annotation_threads 4"
- if: $MATRIX_NAME == "wf-human-snp_modelint_unphase"
variables:
NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -q -O ${CI_PROJECT_NAME}/data/demo_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-human-variation/snp_demo.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/demo_data.tar.gz -C ${CI_PROJECT_NAME}/data/"
NF_PROCESS_FILES: "modules/local/wf-human-snp.nf"
NF_IGNORE_PROCESSES: "hap,phase_contig_haplotag,post_clair_phase_contig,cat_haplotagged_contigs,phase_contig,getGenome,get_coverage,
getVersions,getParams,failedQCReport,refine_with_sv,makeAlignmentReport,post_clair_contig_haplotag,phase_gvcf"
NF_WORKFLOW_OPTS: "--snp --sv false --mod false --cnv false --str false --bam ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.bam --bed ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.bed --ref ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.fasta --basecaller_cfg dna_r10.4.1_e8.2_400bps_hac_prom --bam_min_coverage 0.00001 --annotation_threads 4"
- if: $MATRIX_NAME == "wf-human-snp_modelext"
variables:
NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -q -O ${CI_PROJECT_NAME}/data/demo_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-human-variation/snp_demo.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/demo_data.tar.gz -C ${CI_PROJECT_NAME}/data/"
NF_PROCESS_FILES: "modules/local/wf-human-snp.nf"
NF_IGNORE_PROCESSES: "phase_gvcf,hap,lookup_clair3_model,phase_contig,phase_contig_haplotag,cat_haplotagged_contigs,getGenome,get_coverage,getVersions,getParams,failedQCReport,refine_with_sv,makeAlignmentReport"
NF_WORKFLOW_OPTS: "--snp --sv false --mod false --cnv false --str false --bam ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.bam --bed ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.bed --ref ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.fasta --clair3_model_path ${CI_PROJECT_NAME}/data/snp_demo/ont_r104_e81_sup_g5015 --phased --bam_min_coverage 0.00001 --annotation_threads 4"
- if: $MATRIX_NAME == "wf-human-snp_covblock"
variables:
NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -q -O ${CI_PROJECT_NAME}/data/demo_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-human-variation/snp_demo.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/demo_data.tar.gz -C ${CI_PROJECT_NAME}/data/"
NF_PROCESS_FILES: "modules/local/wf-human-snp.nf"
NF_IGNORE_PROCESSES: "hap,lookup_clair3_model,phase_contig_haplotag,cat_haplotagged_contigs,post_clair_contig_haplotag,\
getGenome,aggregate_all_variants,aggregate_full_align_variants,aggregate_pileup_variants,create_candidates,\
evaluate_candidates,get_qual_filter,makeReport,make_chunks,merge_pileup_and_full_vars,output_snp,phase_contig,\
pileup_variants,post_clair_phase_contig,select_het_snps,vcfStats,refine_with_sv,annotate_vcf,bed_filter,phase_gvcf"
NF_WORKFLOW_OPTS: "--snp --sv false --mod false --cnv false --str false --bam ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.bam --bed ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.bed --ref ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.fasta --clair3_model_path ${CI_PROJECT_NAME}/data/snp_demo/ont_r104_e81_sup_g5015 --phased --bam_min_coverage 100"
- if: $MATRIX_NAME == "wf-human-snp_svrefine"
variables:
NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -q -O ${CI_PROJECT_NAME}/data/demo_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-human-variation/snp_demo.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/demo_data.tar.gz -C ${CI_PROJECT_NAME}/data/"
NF_PROCESS_FILES: "modules/local/wf-human-snp.nf"
NF_IGNORE_PROCESSES: "hap,lookup_clair3_model,phase_contig_haplotag,cat_haplotagged_contigs,makeAlignmentReport.\
get_genome,aggregate_all_variants,aggregate_full_align_variants,aggregate_pileup_variants,create_candidates,\
evaluate_candidates,get_qual_filter,makeReport,make_chunks,merge_pileup_and_full_vars,output_snp,phase_contig,\
pileup_variants,post_clair_phase_contig,select_het_snps,vcfStats,phase_gvcf"
NF_WORKFLOW_OPTS: "--snp --sv --mod false --cnv false --str false --bam ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.bam --bed ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.bed --ref ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.fasta --clair3_model_path ${CI_PROJECT_NAME}/data/snp_demo/ont_r104_e81_sup_g5015 --phased --annotation_threads 4"
- if: $MATRIX_NAME == "wf-human-sv"
variables:
NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -q -O ${CI_PROJECT_NAME}/data/demo_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-human-sv/demo_data.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/demo_data.tar.gz -C ${CI_PROJECT_NAME}/data/"
NF_PROCESS_FILES: "modules/local/wf-human-sv.nf"
NF_IGNORE_PROCESSES: "getAllChromosomesBed,minimap2_alignment,get_coverage,getVersions,getParams,failedQCReport,makeAlignmentReport,annotate_vcf"
NF_WORKFLOW_OPTS: "--snp false --sv --mod false --cnv false --str false --bam ${CI_PROJECT_NAME}/data/demo_data/test.bam --ref ${CI_PROJECT_NAME}/data/demo_data/chr20_human_g1k_v37_part.fasta.gz --bed ${CI_PROJECT_NAME}/data/demo_data/target.bed --tr_bed ${CI_PROJECT_NAME}/data/demo_data/human_hs37d5.trf.bed --bam_min_coverage 0.00001 --annotation_threads 4"
- if: $MATRIX_NAME == "wf-human-sv-phase"
variables:
NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -q -O ${CI_PROJECT_NAME}/data/demo_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-human-variation/snp_demo.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/demo_data.tar.gz -C ${CI_PROJECT_NAME}/data/"
NF_PROCESS_FILES: "modules/local/wf-human-sv.nf"
NF_IGNORE_PROCESSES: "getAllChromosomesBed,minimap2_alignment,get_coverage,getVersions,getParams,failedQCReport,makeAlignmentReport,annotate_vcf"
NF_WORKFLOW_OPTS: "--mod false --cnv false --str false --sv true --snp true --bam ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.bam --bed ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.bed --ref ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.fasta --clair3_model_path ${CI_PROJECT_NAME}/data/snp_demo/ont_r104_e81_sup_g5015 --annotation_threads 4 --phased"
- if: $MATRIX_NAME == "wf-human-cnv-spectre"
variables:
NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -q -O ${CI_PROJECT_NAME}/data/demo_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-human-spectre/spectre_demo.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/demo_data.tar.gz -C ${CI_PROJECT_NAME}/data/"
NF_PROCESS_FILES: "modules/local/wf-human-cnv.nf"
NF_IGNORE_PROCESSES: "get_coverage,getVersions,getParams,failedQCReport,makeAlignmentReport,phase_gvcf"
NF_WORKFLOW_OPTS: "--snp false --sv false --mod false --cnv --str false --bam ${CI_PROJECT_NAME}/data/spectre_demo/demo.bam --ref ${CI_PROJECT_NAME}/data/spectre_demo/GCA_000001405.15_GRCh38_no_alt_analysis_set.fasta --bam_min_coverage 0.00001"
- if: $MATRIX_NAME == "gzref-bam-mod-hap"
variables:
NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -q -O ${CI_PROJECT_NAME}/data/demo_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-somatic-variation/wf-somatic-variation-demo.tar.gz && \
tar -xzvf ${CI_PROJECT_NAME}/data/demo_data.tar.gz -C ${CI_PROJECT_NAME}/data/ && \
wget -q -O ${CI_PROJECT_NAME}/data/wf-somatic-variation-demo/GCA_000001405.15_GRCh38_no_alt_analysis_set.fa.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-human-reference/GCA_000001405.15_GRCh38_no_alt_analysis_set.fa.gz"
NF_PROCESS_FILES: "workflows/methyl.nf"
NF_IGNORE_PROCESSES: "minimap2_ubam,index_ref_gzi,get_coverage,getVersions,getParams,failedQCReport,makeAlignmentReport,annotate_vcf,eval_downsampling,downsampling,modkit"
NF_WORKFLOW_OPTS: "--snp false --sv false --mod --cnv false --str false --bed ${CI_PROJECT_NAME}/data/wf-somatic-variation-demo/demo.bed --bam ${CI_PROJECT_NAME}/data/wf-somatic-variation-demo/demo_normal.bam --ref ${CI_PROJECT_NAME}/data/wf-somatic-variation-demo/GCA_000001405.15_GRCh38_no_alt_analysis_set.fa.gz --sample_name HOOT --ubam_map_threads 2 --ubam_sort_threads 1 --ubam_bam2fq_threads 1 --bam_min_coverage 0.00001 --phased --annotation false --modkit_threads 4"
- if: $MATRIX_NAME == "gzref-bam-mod"
variables:
NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -q -O ${CI_PROJECT_NAME}/data/demo_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-somatic-variation/wf-somatic-variation-demo.tar.gz && \
tar -xzvf ${CI_PROJECT_NAME}/data/demo_data.tar.gz -C ${CI_PROJECT_NAME}/data/ && \
wget -q -O ${CI_PROJECT_NAME}/data/wf-somatic-variation-demo/GCA_000001405.15_GRCh38_no_alt_analysis_set.fa.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-human-reference/GCA_000001405.15_GRCh38_no_alt_analysis_set.fa.gz"
NF_PROCESS_FILES: "workflows/methyl.nf"
NF_IGNORE_PROCESSES: "minimap2_ubam,index_ref_gzi,get_coverage,getVersions,getParams,failedQCReport,makeAlignmentReport,annotate_vcf,eval_downsampling,downsampling,modkit_phase"
NF_WORKFLOW_OPTS: "--snp false --sv false --mod --cnv false --str false --bed ${CI_PROJECT_NAME}/data/wf-somatic-variation-demo/demo.bed --bam ${CI_PROJECT_NAME}/data/wf-somatic-variation-demo/demo_normal.bam --ref ${CI_PROJECT_NAME}/data/wf-somatic-variation-demo/GCA_000001405.15_GRCh38_no_alt_analysis_set.fa.gz --sample_name HOOT --ubam_map_threads 2 --ubam_sort_threads 1 --ubam_bam2fq_threads 1 --bam_min_coverage 0.00001 --annotation false --modkit_threads 4"
- if: $MATRIX_NAME == "downsample"
variables:
NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -qO ${CI_PROJECT_NAME}/data/demo_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-human-str/demo_data.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/demo_data.tar.gz -C ${CI_PROJECT_NAME}/data/"
NF_PROCESS_FILES: "workflows/methyl.nf"
NF_IGNORE_PROCESSES: "minimap2_ubam,index_ref_gzi,getGenome,get_coverage,getVersions,getParams,failedQCReport,makeAlignmentReport,eval_downsampling,downsampling,compress_bed,modkit_phase,annotate_vcf"
NF_WORKFLOW_OPTS: "--snp false --sv false --mod --annotation false --bam ${CI_PROJECT_NAME}/data/demo_data/demo.bam --ref ${CI_PROJECT_NAME}/data/demo_data/GCA_000001405.15_GRCh38_no_alt_analysis_set.fa.gz \
--sample_name HOOT --ubam_map_threads 2 --ubam_sort_threads 1 \
--ubam_bam2fq_threads 1 --bam_min_coverage 0 --skip_annotation \
--downsample_coverage --downsample_coverage_target 10 --modkit_threads 4"
- if: $MATRIX_NAME == "str-usersex"
variables:
NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -qO ${CI_PROJECT_NAME}/data/demo_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-human-str/demo_data.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/demo_data.tar.gz -C ${CI_PROJECT_NAME}/data/ && wget -qO ${CI_PROJECT_NAME}/data/r1041_e82_400bps_sup_g615.tar.gz https://cdn.oxfordnanoportal.com/software/analysis/models/clair3/r1041_e82_400bps_sup_g615.tar.gz && tar -xvf ${CI_PROJECT_NAME}/data/r1041_e82_400bps_sup_g615.tar.gz -C ${CI_PROJECT_NAME}/data"
NF_PROCESS_FILES: "modules/local/wf-human-str.nf"
NF_IGNORE_PROCESSES: "get_coverage,getVersions,getParams,failedQCReport,makeAlignmentReport"
NF_WORKFLOW_OPTS: "--snp false --sv false --mod false --cnv false --str --bam ${CI_PROJECT_NAME}/data/demo_data/demo.bam --ref ${CI_PROJECT_NAME}/data/demo_data/GCA_000001405.15_GRCh38_no_alt_analysis_set.fa.gz --sample_name demo --sex XX --bam_min_coverage 0.00001 --annotation false --clair3_model_path ${CI_PROJECT_NAME}/data/r1041_e82_400bps_sup_g615"
- if: $MATRIX_NAME == "str-infersex"
variables:
NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -qO ${CI_PROJECT_NAME}/data/demo_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-human-str/demo_data.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/demo_data.tar.gz -C ${CI_PROJECT_NAME}/data/ && wget -qO ${CI_PROJECT_NAME}/data/r1041_e82_400bps_sup_g615.tar.gz https://cdn.oxfordnanoportal.com/software/analysis/models/clair3/r1041_e82_400bps_sup_g615.tar.gz && tar -xvf ${CI_PROJECT_NAME}/data/r1041_e82_400bps_sup_g615.tar.gz -C ${CI_PROJECT_NAME}/data"
NF_PROCESS_FILES: "modules/local/wf-human-str.nf"
NF_IGNORE_PROCESSES: "get_coverage,getVersions,getParams,failedQCReport,makeAlignmentReport"
NF_WORKFLOW_OPTS: "--snp false --sv false --mod false --cnv false --str --bam ${CI_PROJECT_NAME}/data/demo_data/demo.bam --ref ${CI_PROJECT_NAME}/data/demo_data/GCA_000001405.15_GRCh38_no_alt_analysis_set.fa.gz --sample_name demo --bam_min_coverage 0.00001 --annotation false --clair3_model_path ${CI_PROJECT_NAME}/data/r1041_e82_400bps_sup_g615"
- if: $MATRIX_NAME == "run_all_no_report"
variables:
NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -qO ${CI_PROJECT_NAME}/data/demo_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-human-str/demo_data.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/demo_data.tar.gz -C ${CI_PROJECT_NAME}/data/ && wget -qO ${CI_PROJECT_NAME}/data/r1041_e82_400bps_sup_g615.tar.gz https://cdn.oxfordnanoportal.com/software/analysis/models/clair3/r1041_e82_400bps_sup_g615.tar.gz && tar -xvf ${CI_PROJECT_NAME}/data/r1041_e82_400bps_sup_g615.tar.gz -C ${CI_PROJECT_NAME}/data"
NF_PROCESS_FILES: "modules/local/wf-human-str.nf"
NF_IGNORE_PROCESSES: "get_coverage,getVersions,getParams,failedQCReport,makeAlignmentReport,make_report"
NF_WORKFLOW_OPTS: "--snp --sv --cnv --str --phased --output_report false --bam ${CI_PROJECT_NAME}/data/demo_data/demo.bam --ref ${CI_PROJECT_NAME}/data/demo_data/GCA_000001405.15_GRCh38_no_alt_analysis_set.fa.gz --sample_name demo --bam_min_coverage 0 --annotation false --clair3_model_path ${CI_PROJECT_NAME}/data/r1041_e82_400bps_sup_g615"
- if: $MATRIX_NAME == "wf-human-phase_all"
variables:
NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -q -O ${CI_PROJECT_NAME}/data/demo_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-human-variation/snp_demo.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/demo_data.tar.gz -C ${CI_PROJECT_NAME}/data/"
NF_PROCESS_FILES: "modules/local/wf-human-sv.nf modules/local/wf-human-snp.nf"
NF_IGNORE_PROCESSES: "get_coverage,getVersions,getParams,failedQCReport,makeAlignmentReport,hap,phase_contig,post_clair_phase_contig,bed_filter,phase_gvcf"
NF_WORKFLOW_OPTS: "--mod false --cnv false --str false --sv --snp --phased --bam ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.bam --bed ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.bed --ref ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.fasta --sample_name demo --sex XX --bam_min_coverage 0.00001 --annotation false"
- if: $MATRIX_NAME == "wf-human-phase_all_lp"
variables:
NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -q -O ${CI_PROJECT_NAME}/data/demo_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-human-variation/snp_demo.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/demo_data.tar.gz -C ${CI_PROJECT_NAME}/data/"
NF_PROCESS_FILES: "modules/local/wf-human-sv.nf modules/local/wf-human-snp.nf"
NF_IGNORE_PROCESSES: "get_coverage,getVersions,getParams,failedQCReport,makeAlignmentReport,hap,phase_contig,post_clair_phase_contig,bed_filter,phase_gvcf"
NF_WORKFLOW_OPTS: "--mod false --cnv false --str false --sv --snp --phased --use_longphase true --bam ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.bam --bed ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.bed --ref ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.fasta --sample_name demo --sex XX --bam_min_coverage 0.00001 --annotation false"
- if: $MATRIX_NAME == "wf-human-snp_GVCF_unphased"
variables:
NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -q -O ${CI_PROJECT_NAME}/data/demo_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-human-variation/snp_demo.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/demo_data.tar.gz -C ${CI_PROJECT_NAME}/data/"
NF_PROCESS_FILES: "modules/local/wf-human-snp.nf"
NF_IGNORE_PROCESSES: "get_coverage,getVersions,getParams,failedQCReport,makeAlignmentReport,hap,phase_contig,post_clair_phase_contig,bed_filter,phase_gvcf,cat_haplotagged_contigs,post_clair_contig_haplotag,refine_with_sv"
NF_WORKFLOW_OPTS: "--mod false --cnv false --str false --sv false --snp --phased false --GVCF --use_longphase false --bam ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.bam --bed ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.bed --ref ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.fasta --sample_name demo --sex XX --bam_min_coverage 0.00001 --annotation false"
- if: $MATRIX_NAME == "wf-human-snp_GVCF_phased"
variables:
NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -q -O ${CI_PROJECT_NAME}/data/demo_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-human-variation/snp_demo.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/demo_data.tar.gz -C ${CI_PROJECT_NAME}/data/"
NF_PROCESS_FILES: "modules/local/wf-human-snp.nf"
NF_IGNORE_PROCESSES: "get_coverage,getVersions,getParams,failedQCReport,makeAlignmentReport,hap,phase_contig,post_clair_phase_contig,bed_filter,phase_gvcf,refine_with_sv"
NF_WORKFLOW_OPTS: "--mod false --cnv false --str false --sv false --snp --phased true --GVCF --use_longphase false --bam ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.bam --bed ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.bed --ref ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.fasta --sample_name demo --sex XX --bam_min_coverage 0.00001 --annotation false"
- if: $MATRIX_NAME == "wf-human-snp-gene-summary"
variables:
NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -q -O ${CI_PROJECT_NAME}/data/demo_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/snp_demo_new/snp_demo.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/demo_data.tar.gz -C ${CI_PROJECT_NAME}/data/"
NF_PROCESS_FILES: "modules/local/wf-human-snp.nf"
NF_IGNORE_PROCESSES: "phase_gvcf,hap,phase_contig_haplotag,cat_haplotagged_contigs,phase_contig,getGenome,get_coverage,getVersions,getParams,failedQCReport,refine_with_sv,makeAlignmentReport"
NF_WORKFLOW_OPTS: "--snp --sv false --mod false --cnv false --str false --bam ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.bam --bed ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20_with_gene.bed --ref ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.fasta --phased --bam_min_coverage 0.00001 --output_gene_summary --annotation false"
aws-run:
stage: test
artifacts:
when: always
paths:
- ${CI_PROJECT_NAME}
- .nextflow.log
exclude:
- ${CI_PROJECT_NAME}/**/*.bam
- ${CI_PROJECT_NAME}/**/*.cram
- ${CI_PROJECT_NAME}/**/*.fa
- ${CI_PROJECT_NAME}/**/*.fna
- ${CI_PROJECT_NAME}/**/*.fasta
- ${CI_PROJECT_NAME}/**/ref_cache/**
variables:
CWG_AWS_ENV_NAME: "stack"
# Define a 1D job matrix to inject a variable named MATRIX_NAME into
# the CI environment, we can use the value of MATRIX_NAME to determine
# which options to apply as part of the rules block below
# NOTE There is a slightly cleaner way to define this matrix to include
# the variables, but it is broken when using long strings! See CW-756
parallel:
matrix:
- MATRIX_NAME: [
"wf-human-cnv-ubam-to-bam",
"wf-human-cnv-downsample",
"wf-human-cnv-skip-downsample",
]
rules:
# NOTE As we're overriding the rules block for the included docker-run
# we must redefine this CI_COMMIT_BRANCH rule to prevent docker-run
# being incorrectly scheduled for "detached merge request pipelines" etc.
- if: ($CI_COMMIT_BRANCH == null || $CI_COMMIT_BRANCH == "dev-template")
when: never
- if: $MATRIX_NAME == "wf-human-cnv-downsample"
variables:
NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -q -O ${CI_PROJECT_NAME}/data/demo_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/snp_demo/snp_demo.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/demo_data.tar.gz -C ${CI_PROJECT_NAME}/data/"
NF_PROCESS_FILES: "modules/local/wf-human-cnv-qdnaseq.nf"
NF_IGNORE_PROCESSES: "get_coverage,getVersions,getParams,failedQCReport,makeAlignmentReport"
NF_WORKFLOW_OPTS: "--snp false --sv false --mod false --cnv --use_qdnaseq --str false --bam ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.bam --bed ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.bed --ref ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.fasta --bin_size 500 --bam_min_coverage 0.00001 --downsample_coverage --downsample_coverage_target 20"
- if: $MATRIX_NAME == "wf-human-cnv-skip-downsample"
variables:
NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -q -O ${CI_PROJECT_NAME}/data/demo_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/snp_demo/snp_demo.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/demo_data.tar.gz -C ${CI_PROJECT_NAME}/data/"
NF_PROCESS_FILES: "modules/local/wf-human-cnv-qdnaseq.nf"
NF_IGNORE_PROCESSES: "get_coverage,getVersions,getParams,failedQCReport,makeAlignmentReport"
NF_WORKFLOW_OPTS: "--snp false --sv false --mod false --cnv --use_qdnaseq --str false --bam ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.bam --bed ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.bed --ref ${CI_PROJECT_NAME}/data/snp_demo/chr6_chr20.fasta --bin_size 500 --bam_min_coverage 0.00001 --downsample_coverage --downsample_coverage_target 1000"
- if: $MATRIX_NAME == "wf-human-cnv-ubam-to-bam"
variables:
NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -q -O ${CI_PROJECT_NAME}/data/demo_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-human-cnv/demo_data.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/demo_data.tar.gz -C ${CI_PROJECT_NAME}/data/"
NF_PROCESS_FILES: "modules/local/wf-human-cnv-qdnaseq.nf"
NF_IGNORE_PROCESSES: "get_coverage,getVersions,getParams,failedQCReport,makeAlignmentReport"
NF_WORKFLOW_OPTS: "--snp false --sv false --mod false --cnv --use_qdnaseq --str false --bam ${CI_PROJECT_NAME}/data/demo_data/test.ubam --ref ${CI_PROJECT_NAME}/data/demo_data/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz --bin_size 500 --bam_min_coverage 0.00001"
macos-run:
# Let's avoid those ARM64 runners for now
tags:
- macos
- x86