Only run the annotation and the stats for analysis or the whole study #196
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| @@ -410,9 +416,8 @@ process calculate_statistics_vcf { | |||
| pipeline_parameters += " --spring.batch.job.names=calculate-statistics-job" | |||
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| pipeline_parameters += " --input.vcf.aggregation=" + aggregation.toString().toUpperCase() | |||
| pipeline_parameters += " --input.vcf=" + vcf_file.toRealPath().toString() | |||
| pipeline_parameters += " --input.vcf=" + file(vcf_files[0]).toRealPath().toString() // If there are multiple file only use the first | |||
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I'm not quite clear on the consequence of this choice yet.
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As far as I can tell, the code is using the file ID rather than the filename, so this is probably okay... I'm actually wondering, since the file ID is the analysis accession, whether we've been computing the same stats multiple times for the same analysis if it contains multiple files...
| @@ -410,9 +416,8 @@ process calculate_statistics_vcf { | |||
| pipeline_parameters += " --spring.batch.job.names=calculate-statistics-job" | |||
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| pipeline_parameters += " --input.vcf.aggregation=" + aggregation.toString().toUpperCase() | |||
| pipeline_parameters += " --input.vcf=" + vcf_file.toRealPath().toString() | |||
| pipeline_parameters += " --input.vcf=" + file(vcf_files[0]).toRealPath().toString() // If there are multiple file only use the first | |||
There was a problem hiding this comment.
As far as I can tell, the code is using the file ID rather than the filename, so this is probably okay... I'm actually wondering, since the file ID is the analysis accession, whether we've been computing the same stats multiple times for the same analysis if it contains multiple files...
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