Update to sample sheet preparation addressing some issues arising fro… #22
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…m the generate_sample_sheets function from the mip_functions module. That function is removed now and generating the final sample sheet from the various input files (capture plates, legacy sample sheets etc.) is handled by the sample_sheet_prep.py script. demux app is also updated to reflect this change. demux app now takes the samplesheet.csv files generated by the sample_sheet_prep.py script, and do not run the old generate_sampe_sheets function from within the mip_functions module. demux app also does not need the sequencing platform anymore. This commit also moves the barcode dictionary file from the base_resources root directory to sample_prep subdirectory for a more cohesive organization. The update changes how the sample sheets are generated so that the error arising when the first or last column of a sample file was empty (when sample_name was not the first column, for example). This update also changes the behaviour of sample_sheet_prep.py script so that when the inputs contain invalid samples, fields etc. an error is raised. The old behaviour was to print a warning message which could lead to missing samples if these warning messages are overlooked. The input files should not contain any invalid information so the new behaviour makes sure that the input information is good.
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…m the generate_sample_sheets function from the mip_functions module. That function is removed now and generating the final sample sheet from the various input files (capture plates, legacy sample sheets etc.) is handled by the sample_sheet_prep.py script. demux app is also updated to reflect this change. demux app now takes the samplesheet.csv files generated by the sample_sheet_prep.py script, and do not run the old generate_sampe_sheets function from within the mip_functions module. demux app also does not need the sequencing platform anymore. This commit also moves the barcode dictionary file from the base_resources root directory to sample_prep subdirectory for a more cohesive organization. The update changes how the sample sheets are generated so that the error arising when the first or last column of a sample file was empty (when sample_name was not the first column, for example). This update also changes the behaviour of sample_sheet_prep.py script so that when the inputs contain invalid samples, fields etc. an error is raised. The old behaviour was to print a warning message which could lead to missing samples if these warning messages are overlooked. The input files should not contain any invalid information so the new behaviour makes sure that the input information is good.