Skip to content

Commit

Permalink
Merge pull request #72 from uclahs-cds/nwiltsie-mask-test-versions
Browse files Browse the repository at this point in the history
Mask version number in config tests
  • Loading branch information
nwiltsie authored Jun 11, 2024
2 parents 2515bf1 + 8b3fade commit 6fceff9
Showing 1 changed file with 16 additions and 7 deletions.
23 changes: 16 additions & 7 deletions test/configtest-F16.json
Original file line number Diff line number Diff line change
Expand Up @@ -22,6 +22,15 @@
"trace.file",
"params.date"
],
"version_fields": [
"manifest.version",
"params.log_output_dir",
"params.output_dir_base",
"params.workflow_output_dir",
"report.file",
"timeline.file",
"trace.file"
],
"expected_result": {
"docker": {
"all_group_ids": "$(for i in `id --real --groups`; do echo -n \"--group-add=$i \"; done)",
Expand All @@ -33,7 +42,7 @@
"author": "Nicole Zeltser",
"description": "Nextflow pipeline for calculating read-depth related statistics for targeted sequencing experiments",
"name": "calculate-targeted-coverage",
"version": "1.1.0"
"version": "VER.SI.ON"
},
"params": {
"bait_bed": "",
Expand All @@ -56,7 +65,7 @@
"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-1.1.0/TWGSAMIN000001-T002-S02-F/log-calculate-targeted-coverage-1.1.0-19970704T165655Z",
"log_output_dir": "/tmp/nf-config-test-outputs/calculate-targeted-coverage-VER.SI.ON/TWGSAMIN000001-T002-S02-F/log-calculate-targeted-coverage-VER.SI.ON-19970704T165655Z",
"max_cpus": "16",
"max_memory": "31 GB",
"merge_operation": "collapse",
Expand All @@ -69,7 +78,7 @@
"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-1.1.0/TWGSAMIN000001-T002-S02-F",
"output_dir_base": "/tmp/nf-config-test-outputs/calculate-targeted-coverage-VER.SI.ON/TWGSAMIN000001-T002-S02-F",
"output_enriched_target_file": true,
"patient": "null",
"picard_CollectHsMetrics_extra_args": "",
Expand All @@ -90,7 +99,7 @@
"target_interval_list": "",
"ucla_cds": true,
"work_dir": "/scratch/4674821",
"workflow_output_dir": "/tmp/nf-config-test-outputs/calculate-targeted-coverage-1.1.0/TWGSAMIN000001-T002-S02-F/SAMtools-1.16.1"
"workflow_output_dir": "/tmp/nf-config-test-outputs/calculate-targeted-coverage-VER.SI.ON/TWGSAMIN000001-T002-S02-F/SAMtools-1.16.1"
},
"process": {
"cache": true,
Expand Down Expand Up @@ -197,15 +206,15 @@
},
"report": {
"enabled": true,
"file": "/tmp/nf-config-test-outputs/calculate-targeted-coverage-1.1.0/TWGSAMIN000001-T002-S02-F/log-calculate-targeted-coverage-1.1.0-19970704T165655Z/nextflow-log/report.html"
"file": "/tmp/nf-config-test-outputs/calculate-targeted-coverage-VER.SI.ON/TWGSAMIN000001-T002-S02-F/log-calculate-targeted-coverage-VER.SI.ON-19970704T165655Z/nextflow-log/report.html"
},
"timeline": {
"enabled": true,
"file": "/tmp/nf-config-test-outputs/calculate-targeted-coverage-1.1.0/TWGSAMIN000001-T002-S02-F/log-calculate-targeted-coverage-1.1.0-19970704T165655Z/nextflow-log/timeline.html"
"file": "/tmp/nf-config-test-outputs/calculate-targeted-coverage-VER.SI.ON/TWGSAMIN000001-T002-S02-F/log-calculate-targeted-coverage-VER.SI.ON-19970704T165655Z/nextflow-log/timeline.html"
},
"trace": {
"enabled": true,
"file": "/tmp/nf-config-test-outputs/calculate-targeted-coverage-1.1.0/TWGSAMIN000001-T002-S02-F/log-calculate-targeted-coverage-1.1.0-19970704T165655Z/nextflow-log/trace.txt"
"file": "/tmp/nf-config-test-outputs/calculate-targeted-coverage-VER.SI.ON/TWGSAMIN000001-T002-S02-F/log-calculate-targeted-coverage-VER.SI.ON-19970704T165655Z/nextflow-log/trace.txt"
},
"tz": "sun.util.calendar.ZoneInfo[id=\"UTC\",offset=0,dstSavings=0,useDaylight=false,transitions=0,lastRule=null]",
"workDir": "/scratch/4674821"
Expand Down

0 comments on commit 6fceff9

Please sign in to comment.