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Processes
Young edited this page Feb 23, 2024
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Processes
The Grandeur workflow is broken into several subworkflows and each subworkflow calls multiple processes to analyze samples. Each process in Grandeur is intended to be beneficial to the end user in some way.
There are many processes, and each has either been given its own wiki page with examples or is listed in the subworkflow that it functions inside.
- amrfinderplus
- bbduk
- blastn
- blobtools_create
- blobtools_plot
- blobtools_view
- circulocov
- core_genome_evaluation
- datasets_download
- datasets_summary
- drprg
- elgato
- emmtyper
- fastani
- fastp
- fastqc
- flag
- heatcluster
- iqtree2
- json_convert
- kleborate
- kraken2
- mash_dist
- mash_err
- mash_sketch_fasta
- mash_sketch_fastq
- mashtree
- mlst
- mqc_prep
- multiqc
- mykrobe
- names
- panaroo
- pbptyper
- phytreeviz
- plasmidfinder
- prokka
- quast
- references
- seqsero2
- serotypefinder
- shigatyper
- snp_dists
- spades
- species
- summary
- versions
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- amrfinderplus
- bbduk
- blastn
- blobtools_*
- core_genome_evaluation
- circulocov
- datasets_*
- drprg
- elgato
- emmtyper
- fastani
- fastp
- fastqc
- heatcluster
- iqtree2
- kaptive
- kleborate
- kraken2
- mash_*
- mashtree
- mlst
- multiqc
- mykrobe
- panaroo
- pbptyper
- phytreeviz
- plasmidfinder
- prokka
- quast
- seqsero2
- serotypefinder
- shigatyper
- snp_dists
- spades