Open eudesbarbosa opened 2 years ago
@ericblanc20 and @messersc, for future references - this issue.
Extracted from #156 :
Based on commit c46917387b3552c08113b6fab9e88e88c18c6ebf
cbioportal_export
default config.snappy_wrappers/wrappers/cbioportal/case_lists/wrapper.py
..snappy_wrappers/wrappers/cbioportal/meta_files/wrapper.py
.snappy_wrappers/wrappers/vcf2maf/vcf2maf/wrapper.py
.
Suggested changes
[ ] Method
cbioportalExportStepPart.iterate_over_biomedsheets
should be broken up to follow single-responsibility principle:iterate_over_biomedsheets()
: Responsible for yielding biomedsheets contentscbioportalCnaFilesStepPart._get_input_file_gistic()
: Responsible for input files for action 'gistic'cbioportalCnaFilesStepPart._get_input_file_log2()
: Responsible for input files for action 'log2'cbioportalCnaFilesStepPart._get_input_file_segments()
: Responsible for input files for action 'segments'cbioportalZscoresStepPart._get_input_file_zscores_input()
: Responsible for input files for action 'zscores_input'Alternatively,
iterate_over_biomedsheets
could be run once in the workflow constructor, the information could be stored in a dictionary for instance. Examples fromVariantExportWorkflow._build_ngs_library_to_kit()
: codecbioportalExportStepPart.iterate_over_biomedsheets
, both{mapper}
and{tools}
should be extracted from config instead of being hardcoded.cbioportal_export_CNA_log2
andcbioportal_export_CNA_calls
.cbioportal_export_concatenate_maf
.