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phac-nml / sistr_cmd

SISTR (Salmonella In Silico Typing Resource) command-line tool
Apache License 2.0
25 stars 9 forks source link

Galaxy workflow for SISTR v1.1.1 supporting batch processing from raw reads to reports #47

Closed kbessonov1984 closed 3 years ago

kbessonov1984 commented 3 years ago

The Galaxy workflow is a nice practical addition to SISTR v1.1.1 allowing to automate processing of sequenced samples. It uses shovill assembler to assemble draft genomes, followed by SISTR v1.1.1 serotyping and report aggregation using tp_cat tool. This workflow is also deployed at Galaxy EU instance. Contrary to previous recipe version, now the sample ids are preserved and are reported in the genome field of the final aggregated sample report. This workflow was successfully tested on galaxy.cscscience.ca

kbessonov1984 commented 3 years ago

Added changes to readme. please check section Galaxy workflows

apetkau commented 3 years ago

Looks great to me. Thanks so much @kbessonov1984