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MorrellLAB / sequence_handling

A series of scripts to automate sequence workflows
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sequence handling workflow numbers #42

Closed pmorrell closed 4 years ago

pmorrell commented 4 years ago

The usage message for the primary sequence_handling script does not list the handlers by the correct number for each option. For example, NP_Quality_Assessment is listed as "17" but it is option 15 in script, so option 17 starts read mapping. Other handlers at the bottom of the list are also off by 2 values.

Usage: sequence_handling Where: is one of: Recommended workflow: 1 | Quality_Assessment 2 | Adapter_Trimming 3 | Read_Mapping 4 | SAM_Processing 5 | Coverage_Mapping 6 | Haplotype_Caller 7 | Genomics_DB_Import 8 | Genotype_GVCFs 9 | Create_HC_Subset 10 | Variant_Recalibrator 11 | Variant_Filtering 12 | Variant_Analysis Other handlers: 13 | GBS_Demultiplex (in progress) 14 | Quality_Trimming 15 | Realigner_Target_Creator 16 | Indel_Realigner Nanopore workflow: 17 | NP_Quality_Assessment (in progress) 18 | NP_Adapter_Trimming (in progress) 19 | NP_Read_Mapping (in progress) 20 | NP_SAM_Processing (in progress)

ChaochihL commented 4 years ago

Hi @pmorrell, the commit 1ec3c27f57add6b23dfaf730a39ed217bf01ba72 fixes this issue. Thanks for reporting!