nf-core · maxulysse · Feb 16, 2024 · Feb 16, 2024 · Feb 16, 2024 · Feb 16, 2024
diff --git a/LICENSE b/LICENSE
@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) Kübra Narcı
+Copyright (c) kuebra.narci@dkfz.de
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/README.md b/README.md
@@ -1,9 +1,5 @@
-<h1>
-  <picture>
-    <source media="(prefers-color-scheme: dark)" srcset="docs/images/nf-core-variantbenchmarking_logo_dark.png">
-    <img alt="nf-core/variantbenchmarking" src="docs/images/nf-core-variantbenchmarking_logo_light.png">
-  </picture>
-</h1>
+# ![nf-core/variantbenchmarking](docs/images/nf-core-variantbenchmarking_logo_light.png#gh-light-mode-only)
+
 [![GitHub Actions CI Status](https://github.com/nf-core/variantbenchmarking/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/variantbenchmarking/actions?query=workflow%3A%22nf-core+CI%22)
 [![GitHub Actions Linting Status](https://github.com/nf-core/variantbenchmarking/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/variantbenchmarking/actions?query=workflow%3A%22nf-core+linting%22)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/variantbenchmarking/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
 
@@ -13,7 +9,7 @@
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
 [![Launch on Nextflow Tower](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Nextflow%20Tower-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/nf-core/variantbenchmarking)
 
-[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23variantbenchmarking-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/variantbenchmarking)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)
+[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23benchmark-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/variantbenchmarking)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)
 
 ## Introduction
 
@@ -29,13 +25,24 @@
      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 -->
 
-1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
-2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))
+1. Standardization of SVs in test VCF files
+2. Normalization of SVs in test VCF files
+3. Normalization of SVs in truth VCF files
+4. SV stats and histograms
+5. Germline benchmarking of SVs
+6. Somatic benchmarking of SVs
+7. Final report and comparisons
 
 ## 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.
+:::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.
+:::
+
+Supported SV callers: Manta, SVaba, Dragen, Delly, Lumpy ..
+Available Truth samples: HG002, SEQC2
 
 <!-- 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):
@@ -45,12 +52,11 @@ First, prepare a samplesheet with your input data that looks as follows:
 `samplesheet.csv`:
 
 ```csv
-sample,fastq_1,fastq_2
-CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz
+caller,test_vcf
+caller1,test1.vcf.gz
+caller2,test2.vcf
 ```
 
-Each row represents a fastq file (single-end) or a pair of fastq files (paired end).
-
 -->
 
 Now, you can run the pipeline using:
@@ -64,9 +70,11 @@ nextflow run nf-core/variantbenchmarking \
    --outdir <OUTDIR>
 ```
 
-> [!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/usage/configuration#custom-configuration-files).
+:::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/usage/configuration#custom-configuration-files).
+:::
 
 For more details and further functionality, please refer to the [usage documentation](https://nf-co.re/variantbenchmarking/usage) and the [parameter documentation](https://nf-co.re/variantbenchmarking/parameters).
 
@@ -78,7 +86,7 @@ For more details about the output files and reports, please refer to the
 
 ## Credits
 
-nf-core/variantbenchmarking was originally written by Kübra Narcı.
+nf-core/variantbenchmarking was originally written by kuebra.narci@dkfz.de.
 
 We thank the following people for their extensive assistance in the development of this pipeline:
 

diff --git a/assets/email_template.html b/assets/email_template.html
@@ -1,53 +1,134 @@
 <html>
-<head>
-  <meta charset="utf-8">
-  <meta http-equiv="X-UA-Compatible" content="IE=edge">
-  <meta name="viewport" content="width=device-width, initial-scale=1">
+  <head>
+    <meta charset="utf-8" />
+    <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/variantbenchmarking: Nextflow variant benchmarking pipeline">
-  <title>nf-core/variantbenchmarking Pipeline Report</title>
-</head>
-<body>
-<div style="font-family: Helvetica, Arial, sans-serif; padding: 30px; max-width: 800px; margin: 0 auto;">
+    <meta
+      name="description"
+      content="nf-core/variantbenchmarking: Master benchmarking pipeline for variant callers "
+    />
+    <title>nf-core/variantbenchmarking 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" />
 
-<img src="cid:nfcorepipelinelogo">
+      <h1>nf-core/variantbenchmarking v${version}</h1>
+      <h2>Run Name: $runName</h2>
 
-<h1>nf-core/variantbenchmarking ${version}</h1>
-<h2>Run Name: $runName</h2>
-
-<% if (!success){
-    out << """
-    <div style="color: #a94442; background-color: #f2dede; border-color: #ebccd1; padding: 15px; margin-bottom: 20px; border: 1px solid transparent; border-radius: 4px;">
-        <h4 style="margin-top:0; color: inherit;">nf-core/variantbenchmarking execution completed unsuccessfully!</h4>
-        <p>The exit status of the task that caused the workflow execution to fail was: <code>$exitStatus</code>.</p>
+      <% 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/variantbenchmarking 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>
-    </div>
-    """
-} else {
-    out << """
-    <div style="color: #3c763d; background-color: #dff0d8; border-color: #d6e9c6; padding: 15px; margin-bottom: 20px; border: 1px solid transparent; border-radius: 4px;">
+        <pre style="white-space: pre-wrap; overflow: visible; margin-bottom: 0">
+${errorReport}</pre
+        >
+      </div>
+      """ } 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/variantbenchmarking execution completed successfully!
-    </div>
-    """
-}
-%>
+      </div>
+      """ } %>
 
-<p>The workflow was completed at <strong>$dateComplete</strong> (duration: <strong>$duration</strong>)</p>
-<p>The command used to launch the workflow was as follows:</p>
-<pre style="white-space: pre-wrap; overflow: visible; background-color: #ededed; padding: 15px; border-radius: 4px; margin-bottom:30px;">$commandLine</pre>
+      <p>
+        The workflow was completed at <strong>$dateComplete</strong> (duration:
+        <strong>$duration</strong>)
+      </p>
+      <p>The command used to launch the workflow was as follows:</p>
+      <pre
+        style="
+          white-space: pre-wrap;
+          overflow: visible;
+          background-color: #ededed;
+          padding: 15px;
+          border-radius: 4px;
+          margin-bottom: 30px;
+        "
+      >
+$commandLine</pre
+      >
 
-<h3>Pipeline Configuration:</h3>
-<table style="width:100%; max-width:100%; border-spacing: 0; border-collapse: collapse; border:0; margin-bottom: 30px;">
-    <tbody style="border-bottom: 1px solid #ddd;">
-        <% out << summary.collect{ k,v -> "<tr><th style='text-align:left; padding: 8px 0; line-height: 1.42857143; vertical-align: top; border-top: 1px solid #ddd;'>$k</th><td style='text-align:left; padding: 8px; line-height: 1.42857143; vertical-align: top; border-top: 1px solid #ddd;'><pre style='white-space: pre-wrap; overflow: visible;'>$v</pre></td></tr>" }.join("\n") %>
-    </tbody>
-</table>
+      <h3>Pipeline Configuration:</h3>
+      <table
+        style="
+          width: 100%;
+          max-width: 100%;
+          border-spacing: 0;
+          border-collapse: collapse;
+          border: 0;
+          margin-bottom: 30px;
+        "
+      >
+        <tbody style="border-bottom: 1px solid #ddd">
+          <% out << summary.collect{ k,v -> "
+          <tr>
+            <th
+              style="
+                text-align: left;
+                padding: 8px 0;
+                line-height: 1.42857143;
+                vertical-align: top;
+                border-top: 1px solid #ddd;
+              "
+            >
+              $k
+            </th>
+            <td
+              style="
+                text-align: left;
+                padding: 8px;
+                line-height: 1.42857143;
+                vertical-align: top;
+                border-top: 1px solid #ddd;
+              "
+            >
+              <pre style="white-space: pre-wrap; overflow: visible">$v</pre>
+            </td>
+          </tr>
+          " }.join("\n") %>
+        </tbody>
+      </table>
 
-<p>nf-core/variantbenchmarking</p>
-<p><a href="https://github.com/nf-core/variantbenchmarking">https://github.com/nf-core/variantbenchmarking</a></p>
-
-</div>
-
-</body>
+      <p>nf-core/variantbenchmarking</p>
+      <p>
+        <a href="https://github.com/nf-core/variantbenchmarking"
+          >https://github.com/nf-core/variantbenchmarking</a
+        >
+      </p>
+    </div>
+  </body>
 </html>
diff --git a/assets/email_template.txt b/assets/email_template.txt
@@ -4,7 +4,7 @@
   |\\ | |__  __ /  ` /  \\ |__) |__         }  {
   | \\| |       \\__, \\__/ |  \\ |___     \\`-._,-`-,
                                         `._,._,'
-  nf-core/variantbenchmarking ${version}
+  nf-core/variantbenchmarking v${version}
 ----------------------------------------------------
 Run Name: $runName
 

diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
@@ -1,5 +1,5 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/variantbenchmarking/tree/dev" target="_blank">nf-core/variantbenchmarking</a>
+  This report has been generated by the <a href="https://github.com/nf-core/variantbenchmarking/releases/tag/dev" target="_blank">nf-core/variantbenchmarking</a>
   analysis pipeline. For information about how to interpret these results, please see the
   <a href="https://nf-co.re/variantbenchmarking/dev/docs/output" target="_blank">documentation</a>.
 report_section_order:

diff --git a/assets/samplesheet.csv b/assets/samplesheet.csv
@@ -1,3 +1,3 @@
-sample,fastq_1,fastq_2
-SAMPLE_PAIRED_END,/path/to/fastq/files/AEG588A1_S1_L002_R1_001.fastq.gz,/path/to/fastq/files/AEG588A1_S1_L002_R2_001.fastq.gz
-SAMPLE_SINGLE_END,/path/to/fastq/files/AEG588A4_S4_L003_R1_001.fastq.gz,
+sample,test_vcf,truth_vcf,caller,type
+HG002,"/Users/w620-admin/Desktop/nf-core/dataset/hg37/Broad_svaba_05052017/HG002.svaba.germline.sv.convBNDtoDEL.vcf","/Users/w620-admin/Desktop/nf-core/dataset/hg37/GIAB_Assemblytics_structural_variants_only_160618/hg002.Assemblytics_structural_variants.sorted.vcf.gz",svaba,sv
+HG003,"/Users/w620-admin/Desktop/nf-core/dataset/hg37/Broad_svaba_05052017/HG003.svaba.germline.sv.convBNDtoDEL.vcf","/Users/w620-admin/Desktop/nf-core/dataset/hg37/GIAB_Assemblytics_structural_variants_only_160618/hg003.Assemblytics_structural_variants.sorted.vcf.gz",svaba,sv
diff --git a/assets/samplesheet_HG002.csv b/assets/samplesheet_HG002.csv
@@ -0,0 +1,4 @@
+test_vcf,caller
+"/Users/w620-admin/Desktop/nf-core/dataset/hg37/dragen_paper/HG002_delly_SV_hg19.vcf.gz",delly
+"/Users/w620-admin/Desktop/nf-core/dataset/hg37/dragen_paper/HG002_lumpy_SV_hg19.vcf.gz",lumpy
+"/Users/w620-admin/Desktop/nf-core/dataset/hg37/dragen_paper/HG002_manta_SV_hg19_genotype.vcf",manta
diff --git a/assets/samplesheet_HG002_hg19.csv b/assets/samplesheet_HG002_hg19.csv
@@ -0,0 +1,5 @@
+test_vcf,caller
+"/Users/w620-admin/Desktop/nf-core/dataset/hg37/dragen_paper/HG002_DRAGEN_SV_hg19.vcf.gz",dragen
+"/Users/w620-admin/Desktop/nf-core/dataset/hg37/dragen_paper/HG002_delly_SV_hg19.vcf.gz",delly
+"/Users/w620-admin/Desktop/nf-core/dataset/hg37/dragen_paper/HG002_lumpy_SV_hg19.vcf.gz",lumpy
+"/Users/w620-admin/Desktop/nf-core/dataset/hg37/dragen_paper/HG002_manta_SV_hg19_genotype.vcf",manta
diff --git a/assets/samplesheet_HG002_hg38.csv b/assets/samplesheet_HG002_hg38.csv
@@ -0,0 +1,5 @@
+test_vcf,caller
+"/Users/w620-admin/Desktop/nf-core/dataset/hg38/GIAB_GRCh38_SVs_06252018/ajtrio.lumpy.svtyper.HG002.md.sorted.recal.vcf.gz",lumpy
+"/Users/w620-admin/Desktop/nf-core/dataset/hg38/GIAB_GRCh38_SVs_06252018/manta.HG002.vcf.gz",manta
+"/Users/w620-admin/Desktop/nf-core/dataset/hg37/Ashkenazim_unnanotated/Ashkenazim_HG002.filtered.sv.vcf.gz",merged
+
diff --git a/assets/samplesheet_SEQC2.csv b/assets/samplesheet_SEQC2.csv
@@ -0,0 +1,3 @@
+test_vcf,caller
+"/Users/w620-admin/Desktop/nf-core/dataset/hg38/SEQC_somatic_mutation_truth/test/WGS.bwa.dedup-IL_T_1_vs_IL_N_1-Strelka.indel.vcf.gz",strelka
+"/Users/w620-admin/Desktop/nf-core/dataset/hg38/SEQC_somatic_mutation_truth/test/WGS.bwa.dedup-IL_T_1_vs_IL_N_1-MuTect2.vcf.gz",mutect2
diff --git a/assets/schema_input.json b/assets/schema_input.json
@@ -1,36 +1,23 @@
 {
-    "$schema": "http://json-schema.org/draft-07/schema",
-    "$id": "https://raw.githubusercontent.com/nf-core/variantbenchmarking/master/assets/schema_input.json",
-    "title": "nf-core/variantbenchmarking pipeline - params.input schema",
-    "description": "Schema for the file provided with params.input",
-    "type": "array",
-    "items": {
-        "type": "object",
-        "properties": {
-            "sample": {
-                "type": "string",
-                "pattern": "^\\S+$",
-                "errorMessage": "Sample name must be provided and cannot contain spaces"
-            },
-            "fastq_1": {
-                "type": "string",
-                "pattern": "^\\S+\\.f(ast)?q\\.gz$",
-                "errorMessage": "FastQ file for reads 1 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
-            },
-            "fastq_2": {
-                "errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'",
-                "anyOf": [
-                    {
-                        "type": "string",
-                        "pattern": "^\\S+\\.f(ast)?q\\.gz$"
-                    },
-                    {
-                        "type": "string",
-                        "maxLength": 0
-                    }
-                ]
-            }
-        },
-        "required": ["sample", "fastq_1"]
-    }
+  "$schema": "http://json-schema.org/draft-07/schema",
+  "$id": "https://raw.githubusercontent.com/nf-core/variantbenchmarking/master/assets/schema_input.json",
+  "title": "nf-core/variantbenchmarking pipeline - params.input schema",
+  "description": "Schema for the file provided with params.input",
+  "type": "array",
+  "items": {
+    "type": "object",
+    "properties": {
+      "test_vcf": {
+        "type": "string",
+        "pattern": "",
+        "errorMessage": "Test VCF must be provided, cannot contain spaces and must have extension '.vcf.gz'"
+      },
+      "caller": {
+        "type": "string",
+        "pattern": "^\\S+$",
+        "errorMessage": "Name of the variant caller used to generate test file"
+      }
+    },
+    "required": ["test_vcf","caller"]
+  }
 }
diff --git a/assets/svync/default.yaml b/assets/svync/default.yaml