Replaced nf-core/neoprednf with Akazhiel/NeoPred-NF to account for th…

…e fact this pipeline is not part of nf-core and also specify the proper name of the pipeline. And updated version.
Akazhiel · Mar 1, 2023 · 51136dd · 51136dd
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,11 +1,11 @@
-# nf-core/neoprednf: Changelog
+# Akazhiel/NeoPred-NF: Changelog
 
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 ## v1.0dev - [date]
 
-Initial release of nf-core/neoprednf, created with the [nf-core](https://nf-co.re/) template.
+Initial release of Akazhiel/NeoPred-NF, created with the [nf-core](https://nf-co.re/) template.
 
 ### `Added`
 

diff --git a/CITATIONS.md b/CITATIONS.md
@@ -1,4 +1,4 @@
-# nf-core/neoprednf: Citations
+# Akazhiel/NeoPred-NF: Citations
 
 ## [nf-core](https://pubmed.ncbi.nlm.nih.gov/32055031/)
 

diff --git a/README.md b/README.md
@@ -48,7 +48,7 @@ We thank the following people for their extensive assistance in the development
 ## Citations
 
 <!-- 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  nf-core/neoprednf for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->
+<!-- If you use  Akazhiel/NeoPred-NF 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.

diff --git a/assets/email_template.html b/assets/email_template.html
@@ -4,21 +4,21 @@
   <meta http-equiv="X-UA-Compatible" content="IE=edge">
   <meta name="viewport" content="width=device-width, initial-scale=1">
 
-  <meta name="description" content="nf-core/neoprednf: Pipeline that performs variant calling on DNA Tumor-Normal samples and RNA Tumor to predict putative neoantigens that bind to the hla of the patient.">
-  <title>nf-core/neoprednf Pipeline Report</title>
+  <meta name="description" content="Akazhiel/NeoPred-NF: Pipeline that performs variant calling on DNA Tumor-Normal samples and RNA Tumor to predict putative neoantigens that bind to the hla of the patient.">
+  <title>Akazhiel/NeoPred-NF Pipeline Report</title>
 </head>
 <body>
 <div style="font-family: Helvetica, Arial, sans-serif; padding: 30px; max-width: 800px; margin: 0 auto;">
 
 <img src="cid:nfcorepipelinelogo">
 
-<h1>nf-core/neoprednf v${version}</h1>
+<h1>Akazhiel/NeoPred-NF v${version}</h1>
 <h2>Run Name: $runName</h2>
 
 <% if (!success){
     out << """
     <div style="color: #a94442; background-color: #f2dede; border-color: #ebccd1; padding: 15px; margin-bottom: 20px; border: 1px solid transparent; border-radius: 4px;">
-        <h4 style="margin-top:0; color: inherit;">nf-core/neoprednf execution completed unsuccessfully!</h4>
+        <h4 style="margin-top:0; color: inherit;">Akazhiel/NeoPred-NF execution completed unsuccessfully!</h4>
         <p>The exit status of the task that caused the workflow execution to fail was: <code>$exitStatus</code>.</p>
         <p>The full error message was:</p>
         <pre style="white-space: pre-wrap; overflow: visible; margin-bottom: 0;">${errorReport}</pre>
@@ -27,7 +27,7 @@ <h4 style="margin-top:0; color: inherit;">nf-core/neoprednf execution completed
 } else {
     out << """
     <div style="color: #3c763d; background-color: #dff0d8; border-color: #d6e9c6; padding: 15px; margin-bottom: 20px; border: 1px solid transparent; border-radius: 4px;">
-        nf-core/neoprednf execution completed successfully!
+        Akazhiel/NeoPred-NF execution completed successfully!
     </div>
     """
 }
@@ -44,8 +44,8 @@ <h3>Pipeline Configuration:</h3>
     </tbody>
 </table>
 
-<p>nf-core/neoprednf</p>
-<p><a href="https://github.com/nf-core/neoprednf">https://github.com/nf-core/neoprednf</a></p>
+<p>Akazhiel/NeoPred-NF</p>
+<p><a href="https://github.com/Akazhiel/NeoPred-NF">https://github.com/Akazhiel/NeoPred-NF</a></p>
 
 </div>
 

diff --git a/assets/email_template.txt b/assets/email_template.txt
@@ -4,16 +4,16 @@
   |\\ | |__  __ /  ` /  \\ |__) |__         }  {
   | \\| |       \\__, \\__/ |  \\ |___     \\`-._,-`-,
                                         `._,._,'
-  nf-core/neoprednf v${version}
+  Akazhiel/NeoPred-NF v${version}
 ----------------------------------------------------
 
 Run Name: $runName
 
 <% if (success){
-    out << "## nf-core/neoprednf execution completed successfully! ##"
+    out << "## Akazhiel/NeoPred-NF execution completed successfully! ##"
 } else {
     out << """####################################################
-## nf-core/neoprednf execution completed unsuccessfully! ##
+## Akazhiel/NeoPred-NF execution completed unsuccessfully! ##
 ####################################################
 The exit status of the task that caused the workflow execution to fail was: $exitStatus.
 The full error message was:
@@ -36,5 +36,5 @@ Pipeline Configuration:
 <% out << summary.collect{ k,v -> " - $k: $v" }.join("\n") %>
 
 --
-nf-core/neoprednf
-https://github.com/nf-core/neoprednf
+Akazhiel/NeoPred-NF
+https://github.com/Akazhiel/NeoPred-NF
diff --git a/assets/multiqc_config.yaml b/assets/multiqc_config.yaml
@@ -1,7 +1,7 @@
 report_comment: >
-    This report has been generated by the <a href="https://github.com/nf-core/neoprednf" target="_blank">nf-core/neoprednf</a>
+    This report has been generated by the <a href="https://github.com/Akazhiel/NeoPred-NF" target="_blank">Akazhiel/NeoPred-NF</a>
     analysis pipeline. For information about how to interpret these results, please see the
-    <a href="https://github.com/nf-core/neoprednf" target="_blank">documentation</a>.
+    <a href="https://github.com/Akazhiel/NeoPred-NF" target="_blank">documentation</a>.
 report_section_order:
     software_versions:
         order: -1000

diff --git a/assets/schema_input.json b/assets/schema_input.json
@@ -1,7 +1,7 @@
 {
     "$schema": "http://json-schema.org/draft-07/schema",
-    "$id": "https://raw.githubusercontent.com/nf-core/neoprednf/master/assets/schema_input.json",
-    "title": "nf-core/neoprednf pipeline - params.input schema",
+    "$id": "https://raw.githubusercontent.com/Akazhiel/NeoPred-NF/master/assets/schema_input.json",
+    "title": "Akazhiel/NeoPred-NF pipeline - params.input schema",
     "description": "Schema for the file provided with params.input",
     "type": "array",
     "items": {

diff --git a/bin/check_samplesheet.py b/bin/check_samplesheet.py
@@ -10,7 +10,7 @@
 
 
 def parse_args(args=None):
-    Description = "Reformat nf-core/neoprednf samplesheet file and check its contents."
+    Description = "Reformat Akazhiel/NeoPred-NF samplesheet file and check its contents."
     Epilog = "Example usage: python check_samplesheet.py <FILE_IN> <FILE_OUT>"
 
     parser = argparse.ArgumentParser(description=Description, epilog=Epilog)

diff --git a/bin/scrape_software_versions.py b/bin/scrape_software_versions.py
@@ -8,7 +8,7 @@
 
     software = version_file.replace(".version.txt", "")
     if software == "pipeline":
-        software = "nf-core/neoprednf"
+        software = "Akazhiel/NeoPred-NF"
 
     with open(version_file) as fin:
         version = fin.read().strip()
@@ -18,8 +18,8 @@
 print(
     """
 id: 'software_versions'
-section_name: 'nf-core/neoprednf Software Versions'
-section_href: 'https://github.com/nf-core/neoprednf'
+section_name: 'Akazhiel/NeoPred-NF Software Versions'
+section_href: 'https://github.com/Akazhiel/NeoPred-NF'
 plot_type: 'html'
 description: 'are collected at run time from the software output.'
 data: |

diff --git a/conf/base.config b/conf/base.config
@@ -1,6 +1,6 @@
 /*
 ========================================================================================
-    nf-core/neoprednf Nextflow base config file
+    Akazhiel/NeoPred-NF Nextflow base config file
 ========================================================================================
     A 'blank slate' config file, appropriate for general use on most high performance
     compute environments. Assumes that all software is installed and available on

diff --git a/conf/test.config b/conf/test.config
@@ -5,15 +5,15 @@
     Defines input files and everything required to run a fast and simple pipeline test.
 
     Use as follows:
-        nextflow run nf-core/neoprednf -profile test,<docker/singularity>
+        nextflow run Akazhiel/NeoPred-NF -profile test,<docker/singularity>
 
 ----------------------------------------------------------------------------------------
 */
 
 params {
     config_profile_name        = 'Test profile'
     config_profile_description = 'Minimal test dataset to check pipeline function'
-    
+
     // Input data
     // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
     // TODO nf-core: Give any required params for the test so that command line flags are not needed

diff --git a/conf/test_full.config b/conf/test_full.config
@@ -5,7 +5,7 @@
     Defines input files and everything required to run a full size pipeline test.
 
     Use as follows:
-        nextflow run nf-core/neoprednf -profile test_full,<docker/singularity>
+        nextflow run Akazhiel/NeoPred-NF -profile test_full,<docker/singularity>
 
 ----------------------------------------------------------------------------------------
 */

diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy
@@ -1,5 +1,5 @@
 //
-// This file holds several functions specific to the main.nf workflow in the nf-core/neoprednf pipeline
+// This file holds several functions specific to the main.nf workflow in the Akazhiel/NeoPred-NF pipeline
 //
 
 class WorkflowMain {

diff --git a/lib/WorkflowNeoprednf.groovy b/lib/WorkflowNeoprednf.groovy
@@ -1,5 +1,5 @@
 //
-// This file holds several functions specific to the workflow/neoprednf.nf in the nf-core/neoprednf pipeline
+// This file holds several functions specific to the workflow/neoprednf.nf in the Akazhiel/NeoPred-NF pipeline
 //
 
 class WorkflowNeoprednf {

diff --git a/main.nf b/main.nf
@@ -54,7 +54,7 @@ include { MERGE_RESULTS }   from './workflows/merge_results'
 include { MHC_PREDICT }     from './workflows/mhc_predict'
 
 //
-// WORKFLOW: Run main nf-core/neoprednf analysis pipeline
+// WORKFLOW: Run main Akazhiel/NeoPred-NF analysis pipeline
 //
 workflow NEOPREDNF {
 

diff --git a/modules.json b/modules.json
@@ -1,6 +1,6 @@
 {
-    "name": "nf-core/neoprednf",
-    "homePage": "https://github.com/nf-core/neoprednf",
+    "name": "Akazhiel/NeoPred-NF",
+    "homePage": "https://github.com/Akazhiel/NeoPred-NF",
     "repos": {
         "nf-core/modules": {
             "fastqc": {

diff --git a/modules/local/get_software_versions.nf b/modules/local/get_software_versions.nf
@@ -20,7 +20,7 @@ process GET_SOFTWARE_VERSIONS {
     path "software_versions.tsv"     , emit: tsv
     path 'software_versions_mqc.yaml', emit: yaml
 
-    script: // This script is bundled with the pipeline, in nf-core/neoprednf/bin/
+    script: // This script is bundled with the pipeline, in Akazhiel/NeoPred-NF/bin/
     """
     echo $workflow.manifest.version > pipeline.version.txt
     echo $workflow.nextflow.version > nextflow.version.txt

diff --git a/nextflow.config b/nextflow.config
@@ -1,6 +1,6 @@
 /*
 ========================================================================================
-    nf-core/neoprednf Nextflow config file
+    Akazhiel/NeoPred-NF Nextflow config file
 ========================================================================================
     Default config options for all compute environments
 ----------------------------------------------------------------------------------------
@@ -112,7 +112,7 @@ manifest {
     description     = 'Pipeline that performs variant calling on DNA Tumor-Normal samples and RNA Tumor to predict putative neoantigens that bind to the hla of the patient.'
     mainScript      = 'main.nf'
     nextflowVersion = '!>=21.04.0'
-    version         = '1.0dev'
+    version         = '0.8.0'
 }
 
 // Function to ensure that resource requirements don't go beyond

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -1,7 +1,7 @@
 {
     "$schema": "http://json-schema.org/draft-07/schema",
-    "$id": "https://raw.githubusercontent.com/nf-core/neoprednf/master/nextflow_schema.json",
-    "title": "nf-core/neoprednf pipeline parameters",
+    "$id": "https://raw.githubusercontent.com/Akazhiel/NeoPred-NF/master/nextflow_schema.json",
+    "title": "Akazhiel/NeoPred-NF pipeline parameters",
     "description": "Pipeline that performs variant calling on DNA Tumor-Normal samples and RNA Tumor to predict putative neoantigens that bind to the hla of the patient.",
     "type": "object",
     "definitions": {