docs: Add mkdocs documentation

.github/workflows/docs.yml

@@ -0,0 +1,31 @@
+# This workflow will automatically deploy the mkdocs documentation
+# See https://parkererickson.github.io/portfolio/blog/MkDocsCD/
+
+name: docs
+
+on:
+  push:
+    branches: [main]
+  workflow_dispatch:
+
+jobs:
+  build:
+    name: Build and Deploy Documentation
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout Master
+        uses: actions/checkout@v2
+
+      - name: Set up Python 3
+        uses: actions/setup-python@v2
+        with:
+          python-version: "3.10.8"
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install mkdocs
+      - name: Deploy
+        run: |
+          git pull
+          mkdocs gh-deploy

README.md

@@ -30,30 +30,33 @@ The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool
 
 3. Download the pipeline and test it on a minimal dataset with a single command:
 
-   ```bash
-   nextflow run dalmolingroup/bulkrna -profile test,YOURPROFILE --outdir <OUTDIR>
-   ```
+```bash
+nextflow run dalmolingroup/bulkrna -profile test,YOURPROFILE --outdir <OUTDIR>
+```
 
    For example, run the test with Docker:
 
-   ```bash
-   nextflow run dalmolingroup/bulkrna -profile test,docker --outdir bulkrna_results
-   ```
+```bash
+nextflow run dalmolingroup/bulkrna -profile test,docker --outdir bulkrna_results
+```
 
-   Note that some form of configuration will be needed so that Nextflow knows how to fetch the required software. This is usually done in the form of a config profile (`YOURPROFILE` in the example command above). You can chain multiple config profiles in a comma-separated string.
+Note that some form of configuration will be needed so that Nextflow knows how to fetch the required software. This is usually done in the form of a config profile (`YOURPROFILE` in the example command above). You can chain multiple config profiles in a comma-separated string.
 
-   > - The pipeline comes with config profiles called `docker`, `singularity`, `podman`, `shifter`, `charliecloud` and `conda` which instruct the pipeline to use the named tool for software management. For example, `-profile test,docker`.
-   > - Please check [nf-core/configs](https://github.com/nf-core/configs#documentation) to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use `-profile <institute>` in your command. This will enable either `docker` or `singularity` and set the appropriate execution settings for your local compute environment.
-   > - If you are using `singularity`, please use the [`nf-core download`](https://nf-co.re/tools/#downloading-pipelines-for-offline-use) command to download images first, before running the pipeline. Setting the [`NXF_SINGULARITY_CACHEDIR` or `singularity.cacheDir`](https://www.nextflow.io/docs/latest/singularity.html?#singularity-docker-hub) Nextflow options enables you to store and re-use the images from a central location for future pipeline runs.
-   > - If you are using `conda`, it is highly recommended to use the [`NXF_CONDA_CACHEDIR` or `conda.cacheDir`](https://www.nextflow.io/docs/latest/conda.html) settings to store the environments in a central location for future pipeline runs.
+- The pipeline comes with config profiles called `docker`, `singularity`, `podman`, `shifter`, `charliecloud` and `conda` which instruct the pipeline to use the named tool for software management. For example, `-profile test,docker`.
+- Please check [nf-core/configs](https://github.com/nf-core/configs#documentation) to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use `-profile <institute>` in your command. This will enable either `docker` or `singularity` and set the appropriate execution settings for your local compute environment.
+- If you are using `singularity`, please use the [`nf-core download`](https://nf-co.re/tools/#downloading-pipelines-for-offline-use) command to download images first, before running the pipeline. Setting the [`NXF_SINGULARITY_CACHEDIR` or `singularity.cacheDir`](https://www.nextflow.io/docs/latest/singularity.html?#singularity-docker-hub) Nextflow options enables you to store and re-use the images from a central location for future pipeline runs.
+- If you are using `conda`, it is highly recommended to use the [`NXF_CONDA_CACHEDIR` or `conda.cacheDir`](https://www.nextflow.io/docs/latest/conda.html) settings to store the environments in a central location for future pipeline runs.
 
 4. Start running your own analysis!
 
-   <!-- TODO nf-core: Update the example "typical command" below used to run the pipeline -->
+```bash
+nextflow run dalmolingroup/bulkrna --input samplesheet.csv --outdir <OUTDIR> --transcriptome <PATH TO TRANSCRIPTOME FASTA> --gtf <PATH TO GTF FILE> -profile <docker/singularity/podman/shifter/charliecloud/conda/institute>
+```
 
-   ```bash
-   nextflow run dalmolingroup/bulkrna --input samplesheet.csv --outdir <OUTDIR> --transcriptome <PATH TO TRANSCRIPTOME FASTA> --gtf <PATH TO GTF FILE> -profile <docker/singularity/podman/shifter/charliecloud/conda/institute>
-   ```
+## References
+
+To acquire reference transcriptome and GTF files to use in your execution,
+we recommend using the [Ensembl](https://www.ensembl.org/index.html) database.
 
 ## Credits
 
@@ -68,8 +71,6 @@ If you would like to contribute to this pipeline, please see the [contributing g
 <!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->
 <!-- If you use  dalmolingroup/bulkrna for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->
 
-<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->
-
 An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.
 
 This pipeline uses code and infrastructure developed and maintained by the [nf-core](https://nf-co.re) community, reused here under the [MIT license](https://github.com/nf-core/tools/blob/master/LICENSE).

docs/CITATIONS.md

@@ -0,0 +1 @@
+../CITATIONS.md

docs/README.md

@@ -0,0 +1 @@
+../README.md

docs/params.md

@@ -0,0 +1,89 @@
+# dalmolingroup/bulkrna pipeline parameters
+
+Workflow for pre-processing, alignment and quantification of bulk RNA-Seq data
+
+## Input/output options
+
+Define where the pipeline should find input data and save output data.
+
+| Parameter | Description | Type | Default |
+|-----------|-----------|-----------|-----------|
+| `input` | Path to comma-separated file containing information about the samples in the experiment. <details><summary>Help</summary><small>You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row.</small></details>| `string` |  |
+| `outdir` | The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure. | `string` |  |
+| `email` | Email address for completion summary. <details><summary>Help</summary><small>Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to specify this on the command line for every run.</small></details>| `string` |  |
+| `multiqc_title` | MultiQC report title. Printed as page header, used for filename if not otherwise specified. | `string` |  |
+
+## FastP trimming options
+
+Define fastp parameters for trimming
+
+| Parameter | Description | Type | Default |
+|-----------|-----------|-----------|-----------|
+| `reads_minlength` | reads shorter than length_required will be discarded | `integer` | 15 |
+| `fastp_adapter_fasta` | specify a FASTA file to trim both read1 and read2 (if PE) by all the sequences in this FASTA file | `string` | https://gist.githubusercontent.com/jvfe/2d569adf47791b9d1e1b4ff810d410b8/raw/e970485d7fe2c9a5b501966eb26e9eb51789c86d/sample_adapters.fa |
+| `fastp_save_trimmed_fail` | save reads that cannot pass the filters | `boolean` |  |
+| `fastp_save_merged` | for paired-end input, merge each pair of reads into a single read if they are overlapped | `boolean` |  |
+| `fastp_qualified_quality` | the quality value that a base is qualified | `integer` | 15 |
+| `fastp_cut_mean_quality` | the mean quality requirement option shared by the cut_front and cut_tail sliding windows | `integer` | 15 |
+
+## Kallisto options
+
+Options for the alignment/quantification
+
+| Parameter | Description | Type | Default |
+|-----------|-----------|-----------|-----------|
+| `transcriptome` | Path to the transcriptome FASTA file to use for reference | `string` | None |
+| `index` |  | `string` | None |
+| `fragment_length` | Estimated average fragment length | `integer` | 100 |
+| `fragment_length_sd` | Estimated standard deviation of fragment length | `integer` | 1 |
+
+## TXimport options
+
+Options for importing Kallisto results into a count matrix
+
+| Parameter | Description | Type | Default |
+|-----------|-----------|-----------|-----------|
+| `gtf` |  | `string` | None |
+
+## Institutional config options
+
+Parameters used to describe centralised config profiles. These should not be edited.
+
+| Parameter | Description | Type | Default |
+|-----------|-----------|-----------|-----------|
+| `custom_config_version` | Git commit id for Institutional configs. | `string` | master |
+| `custom_config_base` | Base directory for Institutional configs. <details><summary>Help</summary><small>If you're running offline, Nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell Nextflow where to find them with this parameter.</small></details>| `string` | https://raw.githubusercontent.com/nf-core/configs/master |
+| `config_profile_name` | Institutional config name. | `string` |  |
+| `config_profile_description` | Institutional config description. | `string` |  |
+| `config_profile_contact` | Institutional config contact information. | `string` |  |
+| `config_profile_url` | Institutional config URL link. | `string` |  |
+
+## Max job request options
+
+Set the top limit for requested resources for any single job.
+
+| Parameter | Description | Type | Default |
+|-----------|-----------|-----------|-----------|
+| `max_cpus` | Maximum number of CPUs that can be requested for any single job. <details><summary>Help</summary><small>Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. `--max_cpus 1`</small></details>| `integer` | 16 |
+| `max_memory` | Maximum amount of memory that can be requested for any single job. <details><summary>Help</summary><small>Use to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. `--max_memory '8.GB'`</small></details>| `string` | 128.GB |
+| `max_time` | Maximum amount of time that can be requested for any single job. <details><summary>Help</summary><small>Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. `--max_time '2.h'`</small></details>| `string` | 240.h |
+
+## Generic options
+
+Less common options for the pipeline, typically set in a config file.
+
+| Parameter | Description | Type | Default |
+|-----------|-----------|-----------|-----------|
+| `help` | Display help text. | `boolean` |  |
+| `publish_dir_mode` | Method used to save pipeline results to output directory. <details><summary>Help</summary><small>The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.</small></details>| `string` | copy |
+| `email_on_fail` | Email address for completion summary, only when pipeline fails. <details><summary>Help</summary><small>An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.</small></details>| `string` |  |
+| `plaintext_email` | Send plain-text email instead of HTML. | `boolean` |  |
+| `max_multiqc_email_size` | File size limit when attaching MultiQC reports to summary emails. | `string` | 25.MB |
+| `monochrome_logs` | Do not use coloured log outputs. | `boolean` |  |
+| `hook_url` | Incoming hook URL for messaging service <details><summary>Help</summary><small>Incoming hook URL for messaging service. Currently, only MS Teams is supported.</small></details>| `string` |  |
+| `multiqc_config` | Custom config file to supply to MultiQC. | `string` |  |
+| `multiqc_logo` | Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file | `string` |  |
+| `multiqc_methods_description` | Custom MultiQC yaml file containing HTML including a methods description. | `string` |  |
+| `tracedir` | Directory to keep pipeline Nextflow logs and reports. | `string` | ${params.outdir}/pipeline_info |
+| `validate_params` | Boolean whether to validate parameters against the schema at runtime | `boolean` | True |
+| `show_hidden_params` | Show all params when using `--help` <details><summary>Help</summary><small>By default, parameters set as _hidden_ in the schema are not shown on the command line when a user runs with `--help`. Specifying this option will tell the pipeline to show all parameters.</small></details>| `boolean` |  |

mkdocs.yml

@@ -0,0 +1,16 @@
+site_name: BulkRNA
+site_description: Pre-processing, alignment and quantification of bulk RNA-seq data
+site_author: Dalmolin Group
+nav:
+  - Home: README.md
+  - Usage: usage.md
+  - Output: output.md
+  - Citations: CITATIONS.md
+  - Reference:
+      - Parameters: params.md
+repo_url: https://github.com/dalmolingroup/bulkrna
+theme:
+  name: "readthedocs"
+  logo: assets/BulkRNA_light.png
+plugins:
+  - search