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Use GBCMS directly instead of genotype variants
enhancementNew feature or requestNew feature or requestStatus: Open.#24 In mskcc-omics-workflows/access_data_analysis_nf;Docker / Singularity Option
enhancementNew feature or requestNew feature or requestStatus: Open.#23 In mskcc-omics-workflows/access_data_analysis_nf;- Status: Open.#22 In mskcc-omics-workflows/access_data_analysis_nf;
Defining Input Parameters
enhancementNew feature or requestNew feature or requestStatus: Open.#21 In mskcc-omics-workflows/access_data_analysis_nf;Main file should handle initialization, pipeline and completion
enhancementNew feature or requestNew feature or requestStatus: Open.#20 In mskcc-omics-workflows/access_data_analysis_nf;GetBaseCountsMultiSample path hardcoded in GENOTYPE_VARIANTS/main.nf
bugSomething isn't workingSomething isn't workingStatus: Open.#19 In mskcc-omics-workflows/access_data_analysis_nf;MSI score selection for clinical ACCESS when multiple values present
questionFurther information is requestedFurther information is requestedStatus: Open.#18 In mskcc-omics-workflows/access_data_analysis_nf;Missing/incorrect columns in SNV/indel final output files
bugSomething isn't workingSomething isn't workingStatus: Open.#17 In mskcc-omics-workflows/access_data_analysis_nf;ACCESS CNA call is "RESCUE" even though fold change >2
questionFurther information is requestedFurther information is requestedStatus: Open.#16 In mskcc-omics-workflows/access_data_analysis_nf;Create utils.py for common functions across multiple python scripts
enhancementNew feature or requestNew feature or requestStatus: Open.#15 In mskcc-omics-workflows/access_data_analysis_nf;None tuple output in filter_calls step
bugSomething isn't workingSomething isn't workingStatus: Open.#14 In mskcc-omics-workflows/access_data_analysis_nf;Include and Exclude optional inputs not handled properly
bugSomething isn't workingSomething isn't workingStatus: Open.#13 In mskcc-omics-workflows/access_data_analysis_nf;