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AusARG / pipesnake

ausarg/pipesnake is a bioinformatics best-practice analysis pipeline for phylogenomic reconstruction starting from short-read 'second-generation' sequencing data.
MIT License
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Pipeline Flexibility - Running from PRG Stage #6

Closed IanGBrennan closed 8 months ago

IanGBrennan commented 8 months ago

Description of feature

Without making too many changes, it'd be good to have the flexibility to pick up the pipeline at a given stage, e.g. from the PRG stage and proceeding to the end.

As an example: I have PRG fasta files from two different projects, but want to do a new project with some samples from each. I could put the sample specific PRG/fasta files of interest into a directory, with a sample info csv file that specifies the lineages and the full path to the files and the pipeline picks up from there. modules: phylogeny_make_alignments --> iqtree --> aster

We could add a parameter to tell the pipeline to jump to a specific step...

ziadbkh commented 8 months ago

@IanGBrennan: Please test by passing the input sample sheet in csv format (sample_id, prg_file) and the parameter --stage from-prg

IanGBrennan commented 8 months ago

tested and works brilliantly.

Note: it still requires --blat_db even though it doesn't use it, but that's not really a problem. Note2: the prg_file column must give the full path to the PRG file