diff --git a/mutant/modules/generic_reporter.py b/mutant/modules/generic_reporter.py index 63852f6..9090cff 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", @@ -279,28 +277,6 @@ def create_delivery_metrics(self, fastq_dir: str) -> None: else: if not record["sequencing_qc_pass"]: continue - # Concat reads forwards - deliverables["files"].append( - { - "format": "fastq", - "id": sampleID, - "path": f"{fastq_dir}/{base_sample}_1.fastq.gz", - "path_index": "~", - "step": "concatination", - "tag": "forward-reads", - } - ) - # Concat reads reverse - deliverables["files"].append( - { - "format": "fastq", - "id": sampleID, - "path": f"{fastq_dir}/{base_sample}_2.fastq.gz", - "path_index": "~", - "step": "concatination", - "tag": "reverse-reads", - } - ) # Variants (vcf) deliverables["files"].append( {