From e9660e0b349abf42ba650705aa1eab6f5fc28817 Mon Sep 17 00:00:00 2001 From: Diane Trout Date: Sat, 26 Sep 2009 01:35:25 +0000 Subject: [PATCH] The config file should also set the SEQUENCE_FORMAT (also I forgot to change a .getcode() to .code --- htsworkflow/pipelines/retrieve_config.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/htsworkflow/pipelines/retrieve_config.py b/htsworkflow/pipelines/retrieve_config.py index 3b6ba3e..dbd3e69 100644 --- a/htsworkflow/pipelines/retrieve_config.py +++ b/htsworkflow/pipelines/retrieve_config.py @@ -49,7 +49,7 @@ def retrieve_flowcell_info(base_host_url, flowcell): contents = web.read() headers = web.info() - + if web.code == 403: msg = "403 - Forbbidden, probably need api key" raise FlowCellNotFound(msg) @@ -106,6 +106,8 @@ def format_gerald_header(flowcell_info): lane_info = flowcell_info['lane_set'][lane_number] config += ['Lane%s: %s | %s' % (lane_number, lane_info['library_id'], lane_info['library_name'])] + + config += ['SEQUENCE_FORMAT --fastq'] config += [''] return "\n# ".join(config) -- 2.30.2