From 35c6eb8e6bc0f38a7db21ea7f72831e22a378c77 Mon Sep 17 00:00:00 2001 From: karlnyr Date: Mon, 27 May 2024 09:30:06 +0200 Subject: [PATCH] Store vcfs on a case level --- mutant/modules/generic_reporter.py | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/mutant/modules/generic_reporter.py b/mutant/modules/generic_reporter.py index 63852f6..49b88de 100644 --- a/mutant/modules/generic_reporter.py +++ b/mutant/modules/generic_reporter.py @@ -226,9 +226,7 @@ def create_delivery_metrics(self, fastq_dir: str) -> None: { "format": "csv", "id": self.case, - "path": os.path.join( - self.indir, f"{self.ticket}_komplettering.csv" - ), + "path": os.path.join(self.indir, f"{self.ticket}_komplettering.csv"), "path_index": "~", "step": "report", "tag": "SARS-CoV-2-info", @@ -258,7 +256,7 @@ def create_delivery_metrics(self, fastq_dir: str) -> None: deliverables["files"].append( { "format": "vcf", - "id": sampleID, + "id": self.case, "path": f"{self.indir}/articNcovNanopore_Genotyping_typeVariants/vcf/{base_sample}.vcf", "path_index": "~", "step": "genotyping", @@ -305,7 +303,7 @@ def create_delivery_metrics(self, fastq_dir: str) -> None: deliverables["files"].append( { "format": "vcf", - "id": sampleID, + "id": self.case, "path": f"{self.indir}/ncovIllumina_Genotyping_typeVariants/vcf/{base_sample}.vcf", "path_index": "~", "step": "genotyping",