Skip to content

Commit

Permalink
add light/dark mode switch
Browse files Browse the repository at this point in the history
  • Loading branch information
rob-p committed Dec 1, 2023
1 parent 35521d3 commit bf7a738
Show file tree
Hide file tree
Showing 2 changed files with 54 additions and 0 deletions.
37 changes: 37 additions & 0 deletions docs/index.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,37 @@
# Documentation for `seqproc`

`seqproc` is a program for interpreting and transforming sequencing data
according to the extended fragment geometry description language (EFGDL).
In fact, currently, the `seqproc` executable is a rather thin wrapper around
the underlying `seqproc` library, whose main purpose it to accept an input
stream of reads (consisting of single-end or paired-end reads) and an EFGDL
specification, and to transform the input reads into the desired output format
according to the specification.

Thus, most of the important information regarding `seqproc` actually pertains
to the EFGDL, which has its own documentation. For detailed documentation
describing EFGDL, please visit the EFGDL specification documentation
[here](https://efgdl-spec.readthedocs.io/en/latest/).

## Using `seqproc`

The `seqproc` program is an executable that exposes a single command that takes
several command line arguments. You can pass the `-h` or `--help` flag to `seqproc`
to see the various command line arguments and their descriptions.

$ ./target/release/seqproc -h
General puprose sequence preprocessor

Usage: seqproc [OPTIONS] --geom <GEOM> --file1 <FILE1> --file2 <FILE2>

Options:
-g, --geom <GEOM> EFGDL string
-1, --file1 <FILE1> r1 fastq file
-2, --file2 <FILE2> r2 fastq file
-o, --out1 <OUT1> r1 out fastq file [default: ]
-w, --out2 <OUT2> r2 out fastq file [default: ]
-t, --threads <THREADS> number of threads to use [default: 1]
-a, --additional <ADDITIONAL>...
-h, --help Print help


17 changes: 17 additions & 0 deletions mkdocs.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,17 @@
site_name: Documentation for seqproc

theme:
name: material
palette:

# Palette toggle for light mode
- scheme: default
toggle:
icon: material/brightness-7
name: Switch to dark mode

# Palette toggle for dark mode
- scheme: slate
toggle:
icon: material/brightness-4
name: Switch to light mode

0 comments on commit bf7a738

Please sign in to comment.