View

This convenience command lets you view relevant details within a Harpy workflow directory without having to fish around for the right files. Since version 4.0, a harpy installation also aliases harpy view as hv for convenience.

usage
harpy view MODE DIRECTORY
# or #
hv MODE DIRECTORY

example | view the workflow configuration of an existing harpy-generated folder
harpy view config Align/bwa

The `.harpyerror` file

A feature introduced in v4 is the automatic creation of a .harpyerror file in the work directory. This file contains a string path to the last output directory that caused an error. When any of the view commands are run without the DIRECTORY argument (except envs), harpy will look for the .harpyerror

arguments

argument	description
`DIRECTORY`	Output directory of an existing harpy workflow. Defaults to path in `.harpyerror` if present and omitted

modes

MODE	description
`config`	View a workflow's config file
`error`	View the exact failture of a snakemake run
`envs`*	View the conda environments and their software in `.environments`
`log`	View a workflow's last log file
`snakefile`	View a workflow's snakefile
`profile`	View a workflow's snakemake parameter file

environments

view envs is an exception in that it does not require a DIRECTORY argument. To use environments, you can run it without arguments or give it a SOFTWARE argument to only print environments where SOFTWARE is found (it also works with partial matches).

viewing all environments
harpy view environments

.environments/f5cb053d77e72fca1c7b6463448fd855_
  - falco=1.2.4
  - fastp
  - multiqc=1.28
  - pysam=0.22
  - quickdeconvolution

.environments/9f9995de2cc77c81654693b8fb002922_
  - quarto
  - r-dt
  - r-dplyr
  - r-highcharter
  - r-magrittr
  - r-plotly
  - r-scales
  - r-tidyr
  - r-viridislite
  - r-xml2
  - r-biocircos

searching for a program
harpy view environments fast

.environments/f5cb053d77e72fca1c7b6463448fd855_
  - falco=1.2.4
  → fastp
  - multiqc=1.28
  - pysam=0.22
  - quickdeconvolution

View

The .harpyerror file

arguments

modes

environments

The `.harpyerror` file