Genotype concordance workflows #414
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| { | ||
| "JoinRawCalls.gatk_docker":{{ dockers.gatk_docker | tojson }}, | ||
| "JoinRawCalls.sv_base_mini_docker": {{ dockers.sv_base_mini_docker | tojson }}, | ||
| "JoinRawCalls.sv_pipeline_docker": {{ dockers.sv_pipeline_docker | tojson }}, | ||
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| "JoinRawCalls.clustered_depth_vcfs" : [{{ test_batch.merged_depth_vcf | tojson }}], | ||
| "JoinRawCalls.clustered_manta_vcfs" : [{{ test_batch.merged_manta_vcf | tojson }}], | ||
| "JoinRawCalls.clustered_wham_vcfs" : [{{ test_batch.merged_wham_vcf | tojson }}], | ||
| "JoinRawCalls.clustered_melt_vcfs" : [{{ test_batch.merged_melt_vcf | tojson }}], | ||
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| "JoinRawCalls.ploidy_table": {{ test_batch.ploidy_table | tojson }}, | ||
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| "JoinRawCalls.contig_list": {{ reference_resources.primary_contigs_list | tojson }}, | ||
| "JoinRawCalls.reference_fasta": {{ reference_resources.reference_fasta | tojson }}, | ||
| "JoinRawCalls.reference_fasta_fai": {{ reference_resources.reference_index | tojson }}, | ||
| "JoinRawCalls.reference_dict": {{ reference_resources.reference_dict | tojson }}, | ||
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| "JoinRawCalls.cohort": {{ test_batch.name | tojson }} | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,22 @@ | ||
| { | ||
| "SVConcordance.gatk_docker":{{ dockers.gatk_docker_concordance | tojson }}, | ||
| "SVConcordance.sv_base_mini_docker": {{ dockers.sv_base_mini_docker | tojson }}, | ||
| "SVConcordance.sv_pipeline_docker": {{ dockers.sv_pipeline_docker | tojson }}, | ||
| "SVConcordance.sv_utils_docker": {{ dockers.sv_utils_docker | tojson }}, | ||
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| "SVConcordance.eval_vcf" : {{ test_batch.clean_vcf | tojson }}, | ||
| "SVConcordance.truth_vcf" : {{ test_batch.joined_raw_calls_vcf | tojson }}, | ||
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| "SVConcordance.ploidy_table": {{ test_batch.ploidy_table | tojson }}, | ||
| "SVConcordance.cohort": {{ test_batch.name | tojson }}, | ||
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| "SVConcordance.run_svutils_truth_vcf": "false", | ||
| "SVConcordance.run_formatter_truth_vcf": "false", | ||
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| "SVConcordance.run_svutils_eval_vcf": "true", | ||
| "SVConcordance.run_formatter_eval_vcf": "true", | ||
| "SVConcordance.formatter_eval_args": "--only-add-cn-fields --replace-ev-format --filter-unsupported-types", | ||
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| "SVConcordance.contig_list": {{ reference_resources.primary_contigs_list | tojson }}, | ||
| "SVConcordance.reference_dict": {{ reference_resources.reference_dict | tojson }} | ||
| } |
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I suppose this PR is not related to EH, if so, I wonder how
build_docker.pyended up incorrectly updating this, while it worked correctly when invoked by the bot.There was a problem hiding this comment.
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Had to do with the way I invoked build_docker.py - my master branch was out of date on the machine where I did the build but my working branch was rebased on the latest master, which contained your recent changes to some str code. I used "master" as the current commit - so it saw the str updates relative to the outdated master and rebuilt the docker.
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That explains it, thanks!