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Ticlla Ccenhua Monica Roxana authored
add module PhlAnProf, and update existing rules, READMEs accordingly. Also add rules to pull singularity containers and to download reference data
Ticlla Ccenhua Monica Roxana authoredadd module PhlAnProf, and update existing rules, READMEs accordingly. Also add rules to pull singularity containers and to download reference data
README_phlanprof.md 1.53 KiB
MetaSnk: PhlAnProf
Description
PhlAnProf performs taxonmic and strain-level profiling using MetaPhlAn2 and StrainPhlAn. If pre-processing was not performed PhlAnProf will trigger execution of preQC.
Usage
Case 1:
From within the MetaSnk directory (i.e where it was installed, where the Snakefile is located):
snakemake --profile ./profiles/local --directory='path/to/workdir' -n PhlAnProf--directory : specifies the working directory and it is where snakemake will store its files for tracking the status of the workflow before/during/after execution. You should change the working directory depending on your current working project.
After preQC is completed we can generate a html report:
snakemake --directory='path/to/workdir' -n PhlAnProf_make_reportThe report will be created in the path specified for OUT_DIR in the configuration file.
Case2:
Execute preQC from a working directory outside the MetaSnk directory:
snakemake --profile $metasnk/profiles/local -s $metasnk/Snakefile -n PhlAnProf