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vidboda / autofastq

script to automate Illumina bcl2fastq utility
GNU General Public License v3.0
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[bug] special characters #2

Open Char-Al opened 5 years ago

Char-Al commented 5 years ago

Special characters need to be escaped in the samples names.

example

BCL to FASTQ file converter
bcl2fastq v2.18.0.12
Copyright (c) 2007-2015 Illumina, Inc.

2019-07-18 09:40:03 [1a90880] Command-line invocation: bcl2fastq -R /path/to/runs/190716_NB******_****_************* --stats-dir /path/to/runs/190716_NB******_****_*************/bcl2fastq --reports-dir /path/to/runs/190716_NB******_****_*************/bcl2fastq --barcode-mismatches 0 --no-lane-splitting --sample-sheet /path/to/runs/samplesheets/190716.csv --ignore-missing-bcls --ignore-missing-filter --ignore-missing-positions -o /path/to/runs/190716_NB******_****_*************/FastQs 
2019-07-18 09:40:03 [1a90880] INFO: Minimum log level: INFO
2019-07-18 09:40:03 [1a90880] INFO: Sample sheet: '/path/to/runs/samplesheets/190716.csv'
2019-07-18 09:40:03 [1a90880] ERROR: bcl2fastq::common::Exception: 2019-Jul-18 09:40:03: Inappropriate ioctl for device (25): /TeamCityBuildAgent/work/ca410b6b30c4ffb6/src/cxx/include/common/CsvGrammar.
hpp(92): Throw in function bcl2fastq::common::CsvGrammarAttribute bcl2fastq::common::parseCsvData(Iterator, Iterator) [with Iterator = __gnu_cxx::__normal_iterator<char*, std::vector<char> >; bcl2fastq:
:common::CsvGrammarAttribute = std::vector<std::vector<std::basic_string<char> > >]
Dynamic exception type: boost::exception_detail::clone_impl<bcl2fastq::common::InputDataError>
std::exception::what: Could not parse the CSV stream text:
vidboda commented 5 years ago

Who would put a special character in a sample name? :) Ok on the TODO list