WIP: Updated readme

.vscode/settings.json

@@ -1,3 +1,6 @@
 {
-    "markdown.styles": ["public/vscode_markdown.css"]
+    "markdown.styles": [
+        "public/vscode_markdown.css"
+    ],
+    "nextflow.telemetry.enabled": true
 }

README.md

@@ -19,22 +19,31 @@
 
 ## Introduction
 
-**nf-core/gwas** is a bioinformatics pipeline that ...
-
 <!-- TODO nf-core:
    Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the
    major pipeline sections and the types of output it produces. You're giving an overview to someone new
    to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction
 -->
+**nf-core/gwas** is a bioinformatics pipeline that aims to develop a scalable and automated pipeline for Genome-Wide Association Studies (GWAS). The pipeline is designed for reproducibility, efficiency, and compatibility with large-scale genomic datasets, supporting tools such as PLINK, and GEMMA. The pipeline facilitates streamlined analysis from VCF data to interpretable GWAS results.
 
 <!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core
      workflows use the "tube map" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples.   -->
-<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))
+<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->
+- Takes VCF files
+- Filters VCF files
+- Build kinshio matrix
+- Apply model
+- Do exploratory Analysis
 
-## Usage
+![Diagram](nf-core-gwas-diagram.png)
 
 > [!NOTE]
-> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.
+> This is an intendded diagram of what the pipeline will do. Please feel free to contribute and add more tools are considered that will enhance or add new helpful features to it. Modify the following diagram as the pipeline evolves [Excalidraw diagram](https://excalidraw.com/#room=29c5ae0d0b30de77800b,idXDcLVCH_n0pzU5bXfxtA)
+
+## Usage
+
+<!-- > [!NOTE]
+> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data. -->
 
 <!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
      Explain what rows and columns represent. For instance (please edit as appropriate):
@@ -57,36 +66,37 @@ Now, you can run the pipeline using:
 <!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->
 
 ```bash
-nextflow run nf-core/gwas \
+nextflow run nf-core/gwas --input samplesheet.csv
+```
+<!-- nextflow run nf-core/gwas \
    -profile <docker/singularity/.../institute> \
    --input samplesheet.csv \
-   --outdir <OUTDIR>
-```
+   --outdir <OUTDIR> -->
 
-> [!WARNING]
+<!-- > [!WARNING]
 > Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).
 
-For more details and further functionality, please refer to the [usage documentation](https://nf-co.re/gwas/usage) and the [parameter documentation](https://nf-co.re/gwas/parameters).
+For more details and further functionality, please refer to the [usage documentation](https://nf-co.re/gwas/usage) and the [parameter documentation](https://nf-co.re/gwas/parameters). -->
 
 ## Pipeline output
 
-To see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/gwas/results) tab on the nf-core website pipeline page.
+<!-- To see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/gwas/results) tab on the nf-core website pipeline page.
 For more details about the output files and reports, please refer to the
-[output documentation](https://nf-co.re/gwas/output).
+[output documentation](https://nf-co.re/gwas/output). -->
 
 ## Credits
 
-nf-core/gwas was originally written by Chris Wyatt.
+<!-- nf-core/gwas was originally written by Chris Wyatt.
 
-We thank the following people for their extensive assistance in the development of this pipeline:
+We thank the following people for their extensive assistance in the development of this pipeline: -->
 
 <!-- TODO nf-core: If applicable, make list of people who have also contributed -->
 
 ## Contributions and Support
 
-If you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).
+<!-- If you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).
 
-For further information or help, don't hesitate to get in touch on the [Slack `#gwas` channel](https://nfcore.slack.com/channels/gwas) (you can join with [this invite](https://nf-co.re/join/slack)).
+For further information or help, don't hesitate to get in touch on the [Slack `#gwas` channel](https://nfcore.slack.com/channels/gwas) (you can join with [this invite](https://nf-co.re/join/slack)). -->
 
 ## Citations
 
@@ -95,12 +105,12 @@ For further information or help, don't hesitate to get in touch on the [Slack `#
 
 <!-- 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.
+<!-- An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.
 
 You can cite the `nf-core` publication as follows:
 
 > **The nf-core framework for community-curated bioinformatics pipelines.**
 >
 > Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.
 >
-> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).
+> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x). -->

main.nf

@@ -25,8 +25,22 @@ include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_gwas
 */
 
 //
-// WORKFLOW: Run main analysis pipeline depending on type of input
+workflow {
+    download_samplesheet()
+    process_samplesheet()
+}
 //
+params.samplesheet_url = "https://raw.githubusercontent.com/KarchinLab/TCRtoolkit-Bulk/main/test_data/minimal-example/samplesheet.csv"
+process download_samplesheet {
+    output:
+    path "samplesheet.csv"
+
+    script:
+    """
+    curl -sSL ${params.samplesheet_url} -o samplesheet.csv
+    """
+}
+
 workflow NFCORE_GWAS {
 
     take:

modules.json

@@ -8,7 +8,16 @@
                     "multiqc": {
                         "branch": "master",
                         "git_sha": "f0719ae309075ae4a291533883847c3f7c441dad",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
+                    },
+                    "plink/vcf": {
+                        "branch": "master",
+                        "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
+                        "installed_by": [
+                            "modules"
+                        ]
                     }
                 }
             },
@@ -17,20 +26,26 @@
                     "utils_nextflow_pipeline": {
                         "branch": "master",
                         "git_sha": "c2b22d85f30a706a3073387f30380704fcae013b",
-                        "installed_by": ["subworkflows"]
+                        "installed_by": [
+                            "subworkflows"
+                        ]
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
                         "git_sha": "51ae5406a030d4da1e49e4dab49756844fdd6c7a",
-                        "installed_by": ["subworkflows"]
+                        "installed_by": [
+                            "subworkflows"
+                        ]
                     },
                     "utils_nfschema_plugin": {
                         "branch": "master",
                         "git_sha": "2fd2cd6d0e7b273747f32e465fdc6bcc3ae0814e",
-                        "installed_by": ["subworkflows"]
+                        "installed_by": [
+                            "subworkflows"
+                        ]
                     }
                 }
             }
         }
     }
-}
+}