diff --git a/CHANGELOG.md b/CHANGELOG.md index 5ad38af..0150f52 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -13,6 +13,7 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm - Add workflow to build and deploy documentation to GitHub Pages - Add workflow to run Nextflow configuration regression tests - Add NFTest infrastructure and test cases +- Add one Nextflow regression test ### Changed - Update CI/CD workflow to use current image diff --git a/test/configtest-F16.json b/test/configtest-F16.json new file mode 100644 index 0000000..5bd74ee --- /dev/null +++ b/test/configtest-F16.json @@ -0,0 +1,215 @@ +{ + "nextflow_version": "23.10.0", + "config": [ + "test/nftest.config" + ], + "params_file": "test/single.yaml", + "cpus": 16, + "memory_gb": 31, + "nf_params": { + "output_dir": "/tmp/nf-config-test-outputs" + }, + "envvars": { + "SLURM_JOB_ID": "4674821" + }, + "mocks": { + "check_path": "" + }, + "dated_fields": [ + "params.log_output_dir", + "report.file", + "timeline.file", + "trace.file", + "params.date" + ], + "expected_result": { + "docker": { + "all_group_ids": "$(for i in `id --real --groups`; do echo -n \"--group-add=$i \"; done)", + "enabled": true, + "runOptions": "-u $(id -u):$(id -g) $(for i in `id --real --groups`; do echo -n \"--group-add=$i \"; done)", + "uid_and_gid": "-u $(id -u):$(id -g)" + }, + "manifest": { + "author": "Nicole Zeltser", + "description": "Nextflow pipeline for calculating read-depth related statistics for targeted sequencing experiments", + "name": "calculate-targeted-coverage", + "version": "1.0.0-rc.2" + }, + "params": { + "bait_bed": "", + "bait_interval_list": "", + "bedr_version": "1.1.0", + "bedtools_version": "2.29.2", + "blcds_registered_dataset": false, + "collect_metrics": true, + "coverage_cap": "3000", + "dataset_id": "TWGSAMIN000001-T002-S02-F", + "dataset_registry_prefix": "/hot/data", + "date": "19970704T165655Z", + "dbSNP_slop": "150", + "docker_container_registry": "ghcr.io/uclahs-cds", + "docker_image_bedops": "ghcr.io/uclahs-cds/bedr:1.1.0", + "docker_image_bedtools": "ghcr.io/uclahs-cds/bedtools:2.29.2", + "docker_image_picard": "ghcr.io/uclahs-cds/picard:3.0.0", + "docker_image_samtools": "ghcr.io/uclahs-cds/samtools:1.16.1", + "docker_image_validate": "ghcr.io/uclahs-cds/pipeval:4.0.0-rc.2", + "gatk_command_mem_diff": "2 GB", + "genome_sizes": "/hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta.fai", + "input": { + "bam": "/hot/resource/SMC-HET/tumours/A-mini/bams/n1/output/S2.T-n1.bam" + }, + "log_output_dir": "/tmp/nf-config-test-outputs/calculate-targeted-coverage-1.0.0-rc.2/TWGSAMIN000001-T002-S02-F/log-calculate-targeted-coverage-1.0.0-rc.2-19970704T165655Z", + "max_cpus": "16", + "max_memory": "31 GB", + "merge_operation": "collapse", + "min_base_quality": "20", + "min_cpus": "1", + "min_mapping_quality": "20", + "min_memory": "1 MB", + "min_read_depth": "30", + "near_distance": "250", + "off_target_depth": true, + "off_target_slop": "500", + "output_dir": "/tmp/nf-config-test-outputs", + "output_dir_base": "/tmp/nf-config-test-outputs/calculate-targeted-coverage-1.0.0-rc.2/TWGSAMIN000001-T002-S02-F", + "output_enriched_target_file": true, + "patient": "null", + "picard_CollectHsMetrics_extra_args": "", + "picard_version": "3.0.0", + "pipeval_version": "4.0.0-rc.2", + "reference_dbSNP": "/hot/ref/database/dbSNP-155/thinned/GRCh38/dbSNP-155_thinned_hg38.vcf.gz", + "reference_dict": "/hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.dict", + "sample": "null", + "sample_id": "TWGSAMIN000001-T002-S02-F", + "samtools_depth_extra_args": "", + "samtools_version": "1.16.1", + "save_all_dbSNP": false, + "save_intermediate_files": false, + "save_interval_list": false, + "save_raw_target_bed": false, + "target_bed": "/hot/software/pipeline/pipeline-calculate-targeted-coverage/Nextflow/development/input/GRch38-small.bed", + "target_depth": true, + "target_interval_list": "", + "ucla_cds": true, + 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"memory": { + "1": "3 GB", + "2": "6 GB", + "3": "9 GB", + "closure": "closure()" + } + }, + "withLabel:process_medium": { + "cpus": { + "1": "6", + "2": "12", + "3": "16", + "closure": "closure()" + }, + "memory": { + "1": "31 GB", + "2": "31 GB", + "3": "31 GB", + "closure": "closure()" + } + }, + "withName:convert_depth_to_bed": { + "cpus": "1", + "memory": "1 GB" + }, + "withName:merge_bedfiles_BEDtools": { + "cpus": "1", + "memory": "1 GB" + }, + "withName:run_BedToIntervalList_picard": { + "cpus": "1", + "memory": "3 GB" + }, + "withName:run_CollectHsMetrics_picard": { + "cpus": "1", + "memory": "25 GB" + }, + "withName:run_depth_SAMtools": { + "cpus": "1", + "memory": "1 GB" + }, + "withName:run_depth_filter": { + "cpus": "1", + "memory": "1 GB" + }, + "withName:run_intersect_BEDtools": { + "cpus": "1", + "memory": "1 GB" + }, + "withName:run_merge_BEDtools": { + "cpus": "1", + "memory": "1 GB" + }, + "withName:run_slop_BEDtools": { + "cpus": "1", + "memory": "1 GB" + } + }, + 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