Updates README.

Author: s-t-h

README.md

@@ -4,92 +4,102 @@
 
 # MUSIAL
 
-**MUSIAL** (MUlti Sample varIant AnaLysis) is a Java command-line tool designed to analyze and summarize single nucleotide variants (SNVs) and insertions/deletions (indels) across multiple prokaryotic samples.
-The software aggregates and analyzes variant calls from multiple samples of a prokaryotic species and provides an interface to generate comprehensive statistics and alignments at the genome, gene and protein level.
-MUSIAL enables a comprehensive assessment of variability within a species at the genome, gene and protein level, providing insights into, for example, conserved and variable regions, diversity at the gene level and common proteoforms among samples.
-
-## ✨ Features
+**MUSIAL** (MUlti Sample varIant AnaLysis) is a Java command-line tool to analyze large sets of VCF files with prokaryotic single nucleotide variants (SNVs) and insertions/deletions (indels). It provides an interface for generating comprehensive statistics and alignments, as well as assessing variability at genome, gene and protein levels.
 
 - **Integrates SnpEff and other Sequence Ontology compliant annotations** to help interpret variants.
 - **Projection to genomic features (genes) facilitates allele- and proteoform-specific information** that supports the characterization of individual samples.
 - **VCF based sequence reconstruction** at nucleotide and protein sequence level and tabular reports on sample, feature and variant statistics.
 
-## 📖 Usage
+### 📖 Usage
 
 An executable `jar` file (`Java 21`) is available from the [Releases](https://github.com/Integrative-Transcriptomics/MUSIAL/releases) section.
 MUSIAL operates on a modular, task-based architecture that is primarily initiated by the `build` task, which creates a JSON file (_storage_) as its primary output; this is then used as input for all other tasks.
 
-The general CLI usage is `java -jar MUSIAL-v2.4.0.jar <task>`, whereby the following tasks are available:
+Details on the use of the software and tutorials can be found in the repository [Wiki](https://github.com/Integrative-Transcriptomics/MUSIAL/wiki). The general CLI usage is `java -jar MUSIAL-v2.4.2.jar <task>`, whereby the following tasks are available:
 
 <details>
 <summary><code>build</code> - Build a local database file (storage) in JSON format from variant calls; the mandatory input for other tasks.</summary>
 
 ```
 Command line arguments of task build
 
- -C,--configuration <arg>   Path to a JSON file specifying the build task parameter configuration for MUSIAL.
+ -C,--configuration <arg>   Path to a JSON file specifying the build task parameter configuration for MUSIAL. Visit the documentation for details.
 ```
 </details>
 
 <details>
-<summary><code>expand</code> - Expand an existing storage file from variant call format (VCF) files.</summary>
+<summary><code>expand</code> - Expand an existing storage file from variant call files and/or meta data.</summary>
 
 ```
 Command line arguments of task expand
 
+ -d,--dry-run          Only report on novel entries without writing the updated storage.
  -I,--storage <arg>    Path to a .json(.gz) file generated with the build task of MUSIAL.
  -m,--vcfMeta <arg>    Path to a .tsv or .csv file specifying sample annotations.
  -o,--output <arg>     Path to write the output file (default: overwrite input file).
- -p,--preview          Only report on novel entries without writing the updated storage.
- -V,--vcfInput <arg>   List of file or directory paths. All files must be in VCF format.
+ -V,--vcfFiles <arg>   List of file or directory paths. All files must be in VCF format.
 ```
 </details>
 
 <details>
-<summary><code>view</code> - View the content (features, samples or variants) and their attributes, of a MUSIAL storage file.</summary>
+<summary><code>view</code> - View the content (features, samples or variants; and their attributes) of a MUSIAL storage file.</summary>
 
 ```
 Command line arguments of task view
 
- -C,--content <arg>   One of sample, allele, call, variant, type, feature.
- -f,--filter <arg>    List of feature-, sample names, and/or positions for which the output is to be filtered (default: no filters). Entries may be
-                      ignored depending on the content.
+ -C,--content <arg>   The content to view. One of FEATURES, SAMPLES, VARIANTS (case-insensitive).
  -I,--storage <arg>   Path to a .json(.gz) file generated with the build task of MUSIAL.
- -o,--output <arg>    Path to directory or file to write the output to (default: stdout).
+ -o,--output <arg>    Path to write the output file. If not provided, a default file will be created based on the input file (default). If `print` or
+                      `stdout` is specified, the output will be printed to the console.
+ -q,--query <arg>     One or multiple identifiers or genomic ranges (contig:start-end) to query.
 ```
 </details>
 
 <details>
-<summary><code>sequence</code> - Export FASTA format sequences of features from a MUSIAL storage file.</summary>
+<summary><code>profile</code> - Profile samples with respect to variants, alleles, or proteoforms.</summary>
 
 ```
-Command line arguments of task sequence
+Command line arguments of task profile
 
- -c,--content <arg>    One of `nt` or `aa` (default: `nt`).
- -F,--features <arg>   List of feature names to export data for. Non-coding features are skipped if `content` is `aa`.
- -I,--input <arg>      Path to a .json(.gz) file generated with the build task of MUSIAL.
- -k,--conserved        Export conserved sites.
- -m,--merge            Export sequences per allele or proteoform instead of per sample.
- -o,--output <arg>     Path to a directory to write the output files to (default: parent of input).
- -r,--reference        Include the reference sequence within the export.
- -s,--samples <arg>    List of sample names to restrict the sequence export to.
- -x,--strip            Strip all gap characters from the exported sequences.
+ -C,--content <arg>   The content to view. One of VARIANTS, ALLELES, PROTEOFORMS (case-insensitive).
+ -I,--storage <arg>   Path to a .json(.gz) file generated with the build task of MUSIAL.
+ -o,--output <arg>    Path to write the output file. If not provided, a default file will be created based on the input file (default). If `print` or
+                      `stdout` is specified, the output will be printed to the console.
+ -q,--query <arg>     One or multiple identifiers or genomic ranges (contig:start-end) to consider.
+ -x,--reduced         Represent entries in a reduced format, i.e., sequence types as numbers with 0 as the reference or synonymous sequence and
+                      variants without detailed call information.
 ```
 </details>
 
----
+<details>
+<summary><code>sequence</code> - Generate and write sequence data.</summary>
 
-Further details on the use of the software and internal workflows can be found in the repository [Wiki](https://github.com/Integrative-Transcriptomics/MUSIAL/wiki).
+```
+Command line arguments of task sequence
+
+ -a,--align             Whether to align sequences (optional, default: false).
+ -c,--content <arg>     Whether to generate NUCLEOTIDE or AMINOACID sequences (optional, case-insensitive, default: NUCLEOTIDE).
+ -f,--split <arg>       Whether to split output files by FEATURE, SAMPLE, BOTH, or NONE (optional, case-insensitive, default: FEATURE).
+ -I,--storage <arg>     Path to a .json(.gz) file generated with the build task of MUSIAL.
+ -l,--locations <arg>   One or multiple feature identifiers or genomic ranges (contig:start-end) to generate sequence data of. If none are provided,
+                        all features or full contig ranges will be considered.
+ -m,--merge             Whether to merge identical sequences (optional, default: false).
+ -o,--output <arg>      Path to write the output. If not provided, the directory of the input storage is used. If a directory is provided, files are
+                        created there. If a file is provided, its parent directory is used.
+ -s,--samples <arg>     One or multiple sample identifiers to retrieve sequences for (optional).
+ -v,--variable          Whether to only consider variable positions (optional, default: false).
+```
+</details>
 
-## 🌐 Web Interface
+### 🌐 Web Interface
 
-To provide user-friendly access to its functionalities, MUSIAL is available via a web interface at https://musial-tuevis.cs.uni-tuebingen.de/ currently running version `v2.3.10`. The code is deposited in the `web` branch.
+MUSIAL is also available via a web interface at https://musial-tuevis.cs.uni-tuebingen.de/ currently running version `v2.3.10`.
 
-## 🔨 Build
+### Build
 
-MUSIAL `v2.4` is built with `JDK 21.0.6` and `Gradle 8.2.1`. If you want to compile the source code, run `gradle clean build` in the root directory of the project. The JavaDoc of the software is available at [https://integrative-transcriptomics.github.io/MUSIAL/javadoc/](https://integrative-transcriptomics.github.io/MUSIAL/javadoc/).
+MUSIAL `v2.4` is built with `JDK 21.0.6` and `Gradle 9.1.0`. If you want to compile the source code, run `gradle clean build` in the root directory of the project. The JavaDoc of the software is available at [https://integrative-transcriptomics.github.io/MUSIAL/javadoc/](https://integrative-transcriptomics.github.io/MUSIAL/javadoc/).
 
-## 🙋 Need Help?
+### Need Help?
 
-- 🎓 Detailed information about the software can be found in the repository's [Wiki](https://github.com/Integrative-Transcriptomics/MUSIAL/wiki). 
-- 🐛 Found an issue or have a feature request? Feel free to [Open a GitHub issue](https://github.com/Integrative-Transcriptomics/MUSIAL/issues/new).
+- Detailed information about the software can be found in the repository's [Wiki](https://github.com/Integrative-Transcriptomics/MUSIAL/wiki). 
+- Found an issue or have a feature request? Feel free to [Open a GitHub issue](https://github.com/Integrative-Transcriptomics/MUSIAL/issues/new).