README update

umccr · Dec 12, 2024 · e2ef2db · e2ef2db
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diff --git a/README.Rmd b/README.Rmd
@@ -70,37 +70,22 @@ sigrap_cli=$(Rscript -e 'x = system.file("cli", package = "sigrap"); cat(x, "\n"
 export PATH="${sigrap_cli}:${PATH}"
 ```
 
-```{bash echo=FALSE}
+```{bash prompt=TRUE, echo=FALSE}
 sigrap_cli=$(Rscript -e 'x = system.file("cli", package = "sigrap"); cat(x, "\n")' | xargs)
 export PATH="${sigrap_cli}:${PATH}"
 
-echo "$ sigrap.R --version"
-echo "sigrap.R 0.1.1"
-echo ""
-echo "$ sigrap.R --help"
-sigrap.R --help
-echo ""
+echo "sigrap.R --version" & sigrap.R --version
 echo ""
+echo "#-----------------------------------#"
+echo "sigrap.R --help" & sigrap.R --help
 echo ""
 echo "#------- HRDetect -------#"
-echo ""
-echo ""
-echo "$ sigrap.R hrdetect --help"
-sigrap.R hrdetect --help
-echo ""
-echo ""
+echo "sigrap.R hrdetect --help" & sigrap.R hrdetect --help
 echo ""
 echo "#------- CHORD -------#"
-echo ""
-echo ""
-echo "$ sigrap.R chord --help"
-sigrap.R chord --help
-echo ""
-echo ""
+echo "sigrap.R chord --help" & sigrap.R chord --help
 echo ""
 echo "#------- MutationalPatterns -------#"
 echo ""
-echo ""
-echo "$ sigrap.R mutpat --help"
-sigrap.R mutpat --help
+echo "sigrap.R mutpat --help" & sigrap.R mutpat --help
 ```
diff --git a/README.md b/README.md
@@ -1,12 +1,11 @@
 
--   <a href="#id_-sigrap" id="toc-id_-sigrap">🎶 sigrap</a>
-    -   <a href="#installation" id="toc-installation">Installation</a>
-    -   <a href="#main-modules" id="toc-main-modules">Main Modules</a>
-        -   <a href="#id_-hrdetect" id="toc-id_-hrdetect">🔍 HRDetect</a>
-        -   <a href="#id_-chord" id="toc-id_-chord">🎸 CHORD</a>
-        -   <a href="#id_-mutationalpatterns" id="toc-id_-mutationalpatterns">🐾
-            MutationalPatterns</a>
-    -   <a href="#id_-cli" id="toc-id_-cli">💻 CLI</a>
+- [🎶 sigrap](#id_-sigrap)
+  - [Installation](#installation)
+  - [Main Modules](#main-modules)
+    - [🔍 HRDetect](#id_-hrdetect)
+    - [🎸 CHORD](#id_-chord)
+    - [🐾 MutationalPatterns](#id_-mutationalpatterns)
+  - [💻 CLI](#id_-cli)
 
 <!-- README.md is generated from README.Rmd. Please edit that file -->
 
@@ -15,7 +14,7 @@
 Wrappers for somatic mutation signature analysis tools (HRDetect, CHORD,
 MutationalPatterns).
 
--   Docs: <https://umccr.github.io/sigrap/>
+- Docs: <https://umccr.github.io/sigrap/>
 
 <!-- badges: start -->
 
@@ -29,7 +28,7 @@ install](https://anaconda.org/umccr/r-sigrap/badges/installer/conda.svg)](https:
 remotes::install_github("umccr/sigrap")
 ```
 
--   Or if used inside a conda environment:
+- Or if used inside a conda environment:
 
 ``` bash
 conda install r-sigrap -c umccr -c conda-forge -c bioconda
@@ -61,21 +60,22 @@ see vignette at
 
 A `sigrap` command line interface is available for convenience.
 
--   If you’re using the conda package, the `sigrap.R` command will
-    already be set up inside an activated conda environment.
--   If you’re *not* using the conda package, you need to export the
-    `sigrap/inst/cli/` directory to your `PATH` in order to use
-    `sigrap.R`.
+- If you’re using the conda package, the `sigrap.R` command will already
+  be set up inside an activated conda environment.
+- If you’re *not* using the conda package, you need to export the
+  `sigrap/inst/cli/` directory to your `PATH` in order to use
+  `sigrap.R`.
 
 ``` bash
 sigrap_cli=$(Rscript -e 'x = system.file("cli", package = "sigrap"); cat(x, "\n")' | xargs)
 export PATH="${sigrap_cli}:${PATH}"
 ```
 
-    $ sigrap.R --version
-    sigrap.R 0.1.1
+    sigrap.R --version
+    sigrap 0.1.1
 
-    $ sigrap.R --help
+    #-----------------------------------#
+    sigrap.R --help
     usage: sigrap [-h] [-v] {hrdetect,chord,mutpat} ...
 
     Somatic signature wrappers
@@ -87,51 +87,40 @@ export PATH="${sigrap_cli}:${PATH}"
         chord               CHORD help
         mutpat              MutationalPatterns help
 
-    optional arguments:
+    options:
       -h, --help            show this help message and exit
       -v, --version         show program's version number and exit
 
-
-
     #------- HRDetect -------#
-
-
-    $ sigrap.R hrdetect --help
+    sigrap.R hrdetect --help
     usage: sigrap hrdetect [-h] --sample SAMPLE --snv SNV --sv SV --cnv CNV
                            [--out OUT]
 
-    optional arguments:
+    options:
       -h, --help       show this help message and exit
       --sample SAMPLE  Sample name.
       --snv SNV        Input SNV (VCF format).
       --sv SV          Input SV (VCF format).
       --cnv CNV        Input CNV (TSV format).
       --out OUT        Output file ['hrdetect.json.gz'].
 
-
-
     #------- CHORD -------#
-
-
-    $ sigrap.R chord --help
+    sigrap.R chord --help
     usage: sigrap chord [-h] --sample SAMPLE --snv SNV --sv SV [--out OUT]
 
-    optional arguments:
+    options:
       -h, --help       show this help message and exit
       --sample SAMPLE  Sample name.
       --snv SNV        Input SNV (VCF format).
       --sv SV          Input SV (VCF format).
       --out OUT        Output file ['./chord.json.gz']
 
-
-
     #------- MutationalPatterns -------#
 
-
-    $ sigrap.R mutpat --help
+    sigrap.R mutpat --help
     usage: sigrap mutpat [-h] --sample SAMPLE --snv SNV --outdir OUTDIR
 
-    optional arguments:
+    options:
       -h, --help       show this help message and exit
       --sample SAMPLE  Sample name.
       --snv SNV        Input SNV file (VCF format).