From f4fdf64bf846aa79c4de63a6b98d7123a93756d3 Mon Sep 17 00:00:00 2001 From: Diane Trout Date: Thu, 3 Dec 2015 14:26:36 -0800 Subject: [PATCH] report if a flowcell was single or paired ended as a file property --- htsworkflow/submission/aws_submission.py | 6 ++++++ htsworkflow/templates/aws_metadata.sparql | 3 ++- 2 files changed, 8 insertions(+), 1 deletion(-) diff --git a/htsworkflow/submission/aws_submission.py b/htsworkflow/submission/aws_submission.py index 17abcbb..23ba81a 100644 --- a/htsworkflow/submission/aws_submission.py +++ b/htsworkflow/submission/aws_submission.py @@ -136,6 +136,10 @@ class AWSSubmission(Submission): platform_alias = { 'Illumina HiSeq 2500': 'ENCODE:HiSeq2500' } + run_type_alias = { + 'Single': 'single-ended', + 'Paired': 'paired-ended', + } query_template = loader.get_template('aws_metadata.sparql') context = Context({ @@ -152,6 +156,8 @@ class AWSSubmission(Submission): row['platform'] = platform_alias[row['platform']] if 'read_length' in row: row['read_length'] = int(row['read_length']) + if 'run_type' in row: + row['run_type'] = run_type_alias[str(row['run_type'])] flowcell_details = {} for term in ['machine', 'flowcell', 'lane', 'barcode']: if term in row: diff --git a/htsworkflow/templates/aws_metadata.sparql b/htsworkflow/templates/aws_metadata.sparql index dc2ae32..0468a23 100644 --- a/htsworkflow/templates/aws_metadata.sparql +++ b/htsworkflow/templates/aws_metadata.sparql @@ -27,7 +27,8 @@ WHERE { a ?fileClass . ?flowcell_url htswlib:sequenced_by ?machine ; - htswlib:flowcell_id ?flowcell . + htswlib:flowcell_id ?flowcell ; + htswlib:flowcell_type ?run_type . ?library htswlib:multiplex_index ?barcode . ?machine htswlib:sequencer_model ?platform . -- 2.30.2