nf-core · KateSakharova · Oct 29, 2025 · Oct 28, 2025 · Oct 28, 2025 · Oct 28, 2025
diff --git a/.gitignore b/.gitignore
@@ -7,3 +7,5 @@ testing/
 testing*
 *.pyc
 null/
+.idea/
+test_data
diff --git a/.nf-core.yml b/.nf-core.yml
@@ -1,22 +1,21 @@
-repository_type: pipeline
-
-nf_core_version: 3.4.1
-
 lint:
   files_exist:
     - conf/igenomes.config
     - conf/igenomes_ignored.config
-
+  files_unchanged:
+    - .github/PULL_REQUEST_TEMPLATE.md
+nf_core_version: 3.4.1
+repository_type: pipeline
 template:
-  org: nf-core
-  name: seqsubmit
-  description: Submit sequences, assmeblies, mags, etc., to publich archives
   author: Martin Beracochea, Ekaterina Sakharova, Sofiia Ochkalova, Evangelos Karatzas
-  version: 1.0.0dev
-  force: true
+  description: Submit sequences, assemblies, MAGs, etc., to public archives
+  force: false
+  is_nfcore: true
+  name: seqsubmit
+  org: nf-core
   outdir: .
   skip_features:
     - igenomes
     - fastqc
     - gpu
-  is_nfcore: true
+  version: 1.0.0dev
diff --git a/assets/email_template.html b/assets/email_template.html
@@ -1,113 +1,53 @@
 <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/seqsubmit: Submit sequences, assmeblies, mags, etc., to publich archives"
-    />
-    <title>nf-core/seqsubmit 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" />
+  <meta name="description" content="nf-core/seqsubmit: Submit sequences, assmeblies, mags, etc., to publich archives">
+  <title>nf-core/seqsubmit Pipeline Report</title>
+</head>
+<body>
+<div style="font-family: Helvetica, Arial, sans-serif; padding: 30px; max-width: 800px; margin: 0 auto;">
 
-      <h1>nf-core/seqsubmit ${version}</h1>
-      <h2>Run Name: $runName</h2>
+<img src="cid:nfcorepipelinelogo">
 
-      <% 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/seqsubmit execution completed unsuccessfully!</h4>
+<h1>nf-core/seqsubmit ${version}</h1>
+<h2>Run Name: $runName</h2>
+
+<% if (!success){
+    out << """
+    <div style="color: #a94442; background-color: #f2dede; border-color: #ebccd1; padding: 15px; margin-bottom: 20px; border: 1px solid transparent; border-radius: 4px;">
+        <h4 style="margin-top:0; color: inherit;">nf-core/seqsubmit execution completed unsuccessfully!</h4>
         <p>The exit status of the task that caused the workflow execution to fail was: <code>$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/seqsubmit 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/seqsubmit</p>
-      <p><a href="https://github.com/nf-core/seqsubmit">https://github.com/nf-core/seqsubmit</a></p>
-    </div>
-  </body>
+<p>nf-core/seqsubmit</p>
+<p><a href="https://github.com/nf-core/seqsubmit">https://github.com/nf-core/seqsubmit</a></p>
+
+</div>
+
+</body>
 </html>
diff --git a/assets/samplesheet.csv b/assets/samplesheet.csv
@@ -1,3 +1,3 @@
 sample,fasta,accession,assembly_software,binning_software,binning_parameters,stats_generation_software,completeness,contamination,genome_coverage,metagenome,co-assembly,broad_environment,local_environment,environmental_medium,rRNA_presence,NCBI_lineage
 lachnospira_eligens,https://github.com/nf-core/test-datasets/raw/seqsubmit/test_data/bins/bin_lachnospira_eligens.fa.gz,SRR24458089,spades_v3.15.5,mags_v1,default,CheckM2_v1.0.1,61.0,0.21,32.07,sediment metagenome,False,marine,cable bacteria,marine sediment,False,d__Bacteria;p__Proteobacteria;c__Deltaproteobacteria;o__Desulfobacterales;f__Desulfobulbaceae;g__Candidatus Electrothrix;s__
-lachnospiraceae,https://github.com/nf-core/test-datasets/raw/seqsubmit/test_data/bins/bin_lachnospiraceae.fa.gz,SRR24458087,spades_v3.15.5,mags_v1,default,CheckM2_v1.0.1,92.81,1.09,66.04,sediment metagenome,False,marine,cable bacteria,marine sediment,False,d__Bacteria;p__Proteobacteria;c__Deltaproteobacteria;o__Desulfobacterales;f__Desulfobulbaceae;g__Candidatus Electrothrix;s__Candidatus Electrothrix marina
+lachnospiraceae,https://github.com/nf-core/test-datasets/raw/seqsubmit/test_data/bins/bin_lachnospiraceae.fa.gz,SRR24458087,spades_v3.15.5,mags_v1,default,CheckM2_v1.0.1,92.81,1.09,66.04,sediment metagenome,False,marine,cable bacteria,marine sediment,False,d__Bacteria;p__Proteobacteria;c__Deltaproteobacteria;o__Desulfobacterales;f__Desulfobulbaceae;g__Candidatus Electrothrix;s__Candidatus Electrothrix marina
diff --git a/docs/images/nf-core-seqsubmit_logo_light.png b/docs/images/nf-core-seqsubmit_logo_light.png
-Original file line number
+Diff line change
@@ Expand Up / @@ -7,3 +7,5 @@ testing/ @@
     testing*
     *.pyc
     null/
+    .idea/
+    test_data