sync with main

docs/index.md

@@ -20,20 +20,20 @@ demultiplexing:
 1. Fastq files (single/paired-end).
 2. Sample sheet which contains sample indexes and their templates (will be explained in detail).
 
-Simply, the tool reads the barcodes at the end of R2 (reveres) reads for paired-end reads input or the end of
+Simply, the tool reads the barcodes at the end of R2 (reverse) reads for paired-end reads input, or the end of
 R1 (forward) reads for single read input. Based on the barcode, it assigns the read to the relevant
-sample allowing for mismatches less than a specific threshold. The tool outputs fastq files for each sample
+sample, allowing for mismatches less than a specific threshold. The tool outputs fastq files for each sample
 as well as some summary reports that can be visualised through the MultiQC tool and mgikit plugin.
 
-mgikit reports can be parsed by [mgikit-multiqc plugin](https://github.com/sagc-bioinformatics/mgikit-multiqc) to generate an html report using [multiqc](https://multiqc.info/) tool summarising the results of the demultiplexing and the quality of the output data as described [here](/mgikit/mgikit-multiqc).
+mgikit reports can be parsed by [mgikit-multiqc plugin](https://github.com/sagc-bioinformatics/mgikit-multiqc) to generate an HTML report using [multiqc](https://multiqc.info/) tool summarising the results of the demultiplexing and the quality of the output data as described [here](/mgikit/mgikit-multiqc).
 
 <hr/>
 
 ### template
 
-This command is used to detect the location and form of the indexes within the read barcode. It simply goes through a small number of the reads and investigates the number of matches with the indexes in the sample sheet within each possible location in the read barcode and considers the indexes as is and their reverse complementary.
+This command is used to detect the location and form of the indexes within the read barcode. It simply goes through a small number of the reads and investigates the number of matches with the indexes in the sample sheet within each possible location in the read barcode, and considers the indexes as is and their reverse complement.
 
-It reports matches for all possible combinations and uses the read template that has the maximum number of matches. This process happens for each sample individually and therefore, the best matching template for each sample will be reported.
+It reports matches for all possible combinations and uses the read template that has the maximum number of matches. This process happens for each sample individually, and therefore, the best-matching template for each sample will be reported.
 
 Using this comprehensive scan, the tool can detect the templates for mixed libraries.
 
@@ -53,36 +53,51 @@ This command is to reformat fastq files generated by `splitBarcode` into Illumin
 
 ## Important notes
 
-- The tools only accepts unix line breakers `\n'. If your data has other than unix line breakers, consder reformating it (using dos2unix or other tools).
+- The tools only accept Unix line breakers `\n'. If your data has other than Unix line breakers, consider reformating it (using dos2unix or other tools).
 
-- The `--flexible` parameters can handle input reads with variable length as long as there is no read longer than double the length of the shortest read. (We don't expect the user to have such case, but just in case the user is expermenting with somthing.)
+- The `--flexible` parameters can handle input reads with variable length as long as there is no read longer than double the length of the shortest read. (We don't expect the user to have such a case, but just in case the user is experimenting with something.)
 
-- The `template` functionality checks the top reads in the file, if the input data is sorted, the functionality might not find all samples. Make sure your data is not sorted or wait for our future improvements.
+- The `template` functionality checks the top reads in the file; if the input data is sorted, the functionality might not find all samples. Make sure your data is not sorted, or wait for our future improvements.
 
 <hr/>
 
 ## Installation
 
-You can use the static binary under bins directly, however, if you like to build it from the source code:
+You can use the static binary under bins directly; however, if you would like to build it from the source code:
 
-You need to have `Rust` and `Cargo` installed first, check rust [documenation](https://doc.rust-lang.org/cargo/getting-started/installation.html)
+You need to have `Rust` and `Cargo` installed first, check Rust [documentation](https://doc.rust-lang.org/cargo/getting-started/installation.html)
 
 ```bash
 git clone https://github.com/sagc-bioinformatics/mgikit.git
 cd mgikit
 cargo build --release
 ```
 
-## User Guide Table of Content
+You can also install mgikit through conda, as it is available on Bioconda.
+
+```bash
+conda install bioconda::mgikit
+```
+
+Or create a conda environment with mgikit
+
+```bash
+conda create -n mgikit_env bioconda::mgikit
+conda activate mgikit_env
+```
+
+Additionally, Biocontainers has [docker image](https://quay.io/repository/biocontainers/mgikit) and [singularity image](https://depot.galaxyproject.org/singularity/) for mgikit.
+
+## User Guide Table of Contents
 
 {% include section-navigation-tiles.html type="guides" %}
 
-## Commerical Use
+## Commercial Use
 
 Please contact us if you want to use the software for commercial purposes.
 
 ## Citation
 
-If you use mgikit in your resear ch, please cite the following publication:
+If you use mgikit in your research, please cite the following publication:
 
 > Al Bkhetan, Ziad, and Sen Wang. ["mgikit: demultiplexing toolkit for MGI fastq files."](https://academic.oup.com/bioinformatics/article/40/9/btae554/7755041) Bioinformatics 40.9 (2024): btae554.

docs/pages/contact_us.md

@@ -3,4 +3,4 @@ title: Support and Contact us
 toc: false
 ---
 
-For any help or inquiries, please contact: ziad.albkhetan@gmail.com or sagc@sahmri.com
+For any help or inquiries, please contact: <ziad.albkhetan@gmail.com> or <sagc@sahmri.com>

docs/pages/demultiplex.md

@@ -152,7 +152,7 @@ The input fastq files can be provided to the tool in two ways:
 
 2. Using `-i` or `--input` parameter which refers to the path to the lane subdirectory in the sequencing output directory (or the directory that contains the fastq files if the data is obtained from somewhere else). In this case, the tool will search for the file that ends with `_read_1.fq.gz` and `_read_2.fq.gz` as forward and reverse reads respectively and if no reverse read file is found, the tool considers the run as a single end run. These suffixes can be also customised using the parameters (`--r1-file-suf` and `--r2-file-suf`).
 
-### Sample sheet format and preparation.
+### Sample sheet format and preparation
 
 For the tool to perform demultiplexing, it needs to know the indexes of each sample to match them with the barcodes at the end of the read sequence as well as where to look for each index in the barcode. We refer to the location of the indexes within the barcode by the barcode template. For example
 This information can be provided to the tool in two different ways:
@@ -400,7 +400,7 @@ If either `--writer-threads` or `--reader-threads` is `0` (or not set), The `--t
 
 #### Default Thread Allocation
 
-mgikit will only use the minimim number of requested threads and available CPU core. The default behavoir is: 
+mgikit will only use the minimim number of requested threads and available CPU core. The default behavoir is:
 
 1. If you only have 1 CPU core, all work happens in a single processing thread.
 
@@ -420,13 +420,12 @@ mgikit will only use the minimim number of requested threads and available CPU c
 
 This default configuration showed the best performance in testing datasets.
 
-#### Example:
+#### Example
 
 threads = 8 → 2 reader threads, 6 processing threads.
 
 `reader-threads` = 4 and `writer-threads` = 2 → Uses exactly 4 readers and 2 writer threads; threads is ignored.
 
-
 ### Performance evaluation
 
 Performance time (in minutes) evaluation and comparison on different datasets.

src/hardware_resources.rs

@@ -1,5 +1,5 @@
-use sysinfo::{ SystemExt, System };
-use log::{ warn, info };
+use log::{info, warn};
+use sysinfo::{System, SystemExt};
 
 pub fn get_available_memory(memory: f64) -> f64 {
     let mut system = System::new_all();
@@ -10,16 +10,15 @@ pub fn get_available_memory(memory: f64) -> f64 {
         panic!("Available memory should be greater than 0.5 GB!");
     }
 
-    let available_memory =
-        (if memory == 0.0 {
-            sys_memory
-        } else {
-            info!("Requested memory by the user is {} GigaByte", memory);
-            if sys_memory < memory * 1000_000_000.0 {
-                panic!("Requested memory is greater than the available memory!");
-            }
-            memory * 1000_000_000.0
-        }) - 500_000_000.0;
+    let available_memory = (if memory == 0.0 {
+        sys_memory
+    } else {
+        info!("Requested memory by the user is {} GigaByte", memory);
+        if sys_memory < memory * 1000_000_000.0 {
+            panic!("Requested memory is greater than the available memory!");
+        }
+        memory * 1000_000_000.0
+    }) - 500_000_000.0;
     available_memory
 }
 
@@ -32,24 +31,21 @@ pub fn get_cpus(requested_threads: usize, paired_read_input: bool) -> (usize, us
     };
     info!(
         "Available CPUs: {}. Requested CPUs {}. Used CPUs: {}.",
-        available_cpus,
-        requested_threads,
-        used_cpus
+        available_cpus, requested_threads, used_cpus
     );
     if requested_threads > available_cpus {
         warn!(
             "Used CPUs are redueced to the available CPUs as the requested number is not available."
         );
     }
-
-    let reader_threads = if used_cpus == 1 
-    {
+
+    let reader_threads = if used_cpus == 1 {
         0
-    }else{
+    } else {
         if paired_read_input {
             if used_cpus < 5 {
                 1
-            }else if used_cpus < 9 {
+            } else if used_cpus < 9 {
                 2
             } else {
                 4
@@ -63,14 +59,11 @@ pub fn get_cpus(requested_threads: usize, paired_read_input: bool) -> (usize, us
         }
     };
 
-
-
     let processing_threads = used_cpus - reader_threads;
     if used_cpus > 1 {
         info!(
             "Multi-threading mode is enabled. Readers: {}, Processors {}.",
-            reader_threads,
-            processing_threads
+            reader_threads, processing_threads
         );
     }
     if (reader_threads == 2 && !paired_read_input) || reader_threads > 2 {