pinellolab · cmatKhan · Apr 29, 2026 · Apr 29, 2026 · Apr 29, 2026 · Apr 29, 2026
diff --git a/.gitignore b/.gitignore
@@ -1,23 +1,11 @@
-/.nextflow
-/work
-.nextflow.log*
-*.img
-inference_mudata.h5mu
-per_element_output.tsv
-per_guide_output.tsv
-nf-*-reports.tsv
-/pipeline_outputs
-/pipeline_dashboard
-/results
-pipeline-service-key.json
-debug_dashboard.ipynb
-.vscode/
-GCP_user_notebook.ipynb
-.params_2026-01-29_13-02-48.json
-.params_2026-02-03_23-14-20.json
-.params_2026-02-03_23-14-49.json
-GCP_user_notebook.ipynb
-*.pyc
-__pycache__/
+.nextflow*
+work/
+data/
+results/
 .DS_Store
-sample_metadata
+testing/
+testing*
+*.pyc
+null/
+.lineage/
+nf-core-perturbseq.code-workspace
diff --git a/.vscode/settings.json b/.vscode/settings.json
@@ -0,0 +1,3 @@
+{
+    "nextflow.telemetry.enabled": true
+}
diff --git a/assets/email_template.html b/assets/email_template.html
@@ -1,53 +1,113 @@
 <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/perturbseq: A nf-core template based adaptation of https://github.com/pinellolab/CRISPR_Pipeline">
-  <title>nf-core/perturbseq 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/perturbseq: A nf-core template based adaptation of https://github.com/pinellolab/CRISPR_Pipeline"
+    />
+    <title>nf-core/perturbseq 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/perturbseq ${version}</h1>
+      <h2>Run Name: $runName</h2>
 
-<h1>nf-core/perturbseq ${version}</h1>
-<h2>Run Name: $runName</h2>
-
-<% if (!success){
-    out << """
-    <div style="color: #a94442; background-color: #f2dede; border-color: #ebccd1; padding: 15px; margin-bottom: 20px; border: 1px solid transparent; border-radius: 4px;">
-        <h4 style="margin-top:0; color: inherit;">nf-core/perturbseq execution completed unsuccessfully!</h4>
+      <% if (!success){ out << """
+      <div
+        style="
+          color: #a94442;
+          background-color: #f2dede;
+          border-color: #ebccd1;
+          padding: 15px;
+          margin-bottom: 20px;
+          border: 1px solid transparent;
+          border-radius: 4px;
+        "
+      >
+        <h4 style="margin-top: 0; color: inherit">nf-core/perturbseq execution completed unsuccessfully!</h4>
         <p>The exit status of the task that caused the workflow execution to fail was: <code>$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/perturbseq 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/perturbseq</p>
-<p><a href="https://github.com/nf-core/perturbseq">https://github.com/nf-core/perturbseq</a></p>
-
-</div>
-
-</body>
+      <p>nf-core/perturbseq</p>
+      <p><a href="https://github.com/nf-core/perturbseq">https://github.com/nf-core/perturbseq</a></p>
+    </div>
+  </body>
 </html>
diff --git a/assets/samplesheet.csv b/assets/samplesheet.csv
diff --git a/assets/schema_input.json b/assets/schema_input.json
@@ -43,11 +43,11 @@
                 "meta": ["measurement_sets"]
             },
             "sequencing_run": {
-                "type": "string",
+                "type": ["string", "integer"],
                 "meta": ["sequencing_run"]
             },
             "lane": {
-                "type": "string",
+                "type": ["string", "integer"],
                 "meta": ["lane"]
             },
             "flowcell_id": {

diff --git a/main.nf b/main.nf
@@ -19,17 +19,16 @@ include { PERTURBSEQ  } from './workflows/perturbseq'
 include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_perturbseq_pipeline'
 include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_perturbseq_pipeline'
 include { getGenomeAttribute      } from './subworkflows/local/utils_nfcore_perturbseq_pipeline'
+include { PREPAREREFERENCERESOURCES } from './subworkflows/local/preparereferenceresources'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     GENOME PARAMETER VALUES
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-// TODO nf-core: Remove this line if you don't need a FASTA file
-//   This is an example of how to use getGenomeAttribute() to fetch parameters
-//   from igenomes.config using `--genome`
-params.fasta = getGenomeAttribute('fasta')
+params.reference_fasta = params.reference_fasta ?: getGenomeAttribute('fasta')
+params.reference_gtf   = params.reference_gtf   ?: getGenomeAttribute('gtf')
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -44,6 +43,10 @@ workflow NFCORE_PERTURBSEQ {
 
     take:
     samplesheet // channel: samplesheet read in from --input
+    transcriptome_index
+    transcriptome_t2g
+    reference_gtf
+    reference_versions
 
     main:
 
@@ -52,6 +55,10 @@ workflow NFCORE_PERTURBSEQ {
     //
     PERTURBSEQ (
         samplesheet,
+        transcriptome_index,
+        transcriptome_t2g,
+        reference_gtf,
+        reference_versions,
         params.multiqc_config,
         params.multiqc_logo,
         params.multiqc_methods_description,
@@ -78,29 +85,67 @@ workflow {
         params.monochrome_logs,
         args,
         params.outdir,
-        params.input,
         params.help,
         params.help_full,
         params.show_hidden
     )
 
+    def ch_input = file(params.input, checkIfExists: true)
+    def ch_samplesheet = channel
+        .fromPath(ch_input)
+        .splitCsv(header: true)
+        .map { row ->
+            def meta = [
+                id: "sample_${row.file_modality}_${row.measurement_sets}",
+                measurement_sets: row.measurement_sets,
+                modality: (row.file_modality ?: '').toLowerCase(),
+                seqspec: row.seqspec,
+                barcode_onlist: row.barcode_onlist,
+                guide_design: row.guide_design,
+                barcode_hashtag_map: row.barcode_hashtag_map,
+            ]
+            def reads = [file(row.R1_path, checkIfExists: true)]
+            if (row.R2_path) {
+                reads += file(row.R2_path, checkIfExists: true)
+            }
+            [meta, reads]
+        }
+
+    def ch_rna_workflow = channel.value('standard')
+    def ch_reference_fasta = params.reference_fasta
+        ? channel.value(file(params.reference_fasta, checkIfExists: true))
+        : channel.empty()
+    def ch_reference_gtf = params.reference_gtf
+        ? channel.value(file(params.reference_gtf, checkIfExists: true))
+        : channel.empty()
+
+    def ReferenceResources = PREPAREREFERENCERESOURCES(
+        ch_reference_fasta,
+        ch_reference_gtf,
+        ch_rna_workflow
+    )
+
     //
     // WORKFLOW: Run main workflow
     //
     NFCORE_PERTURBSEQ (
-        PIPELINE_INITIALISATION.out.samplesheet
-    )
-    //
-    // SUBWORKFLOW: Run completion tasks
-    //
-    PIPELINE_COMPLETION (
-        params.email,
-        params.email_on_fail,
-        params.plaintext_email,
-        params.outdir,
-        params.monochrome_logs,
-        NFCORE_PERTURBSEQ.out.multiqc_report
+        ch_samplesheet,
+        ReferenceResources.out.transcriptome_index,
+        ReferenceResources.out.transcriptome_t2g,
+        ReferenceResources.out.reference_gtf,
+        ReferenceResources.out.versions
     )
+    // //
+    // // SUBWORKFLOW: Run completion tasks
+    // //
+    // PIPELINE_COMPLETION (
+    //     params.email,
+    //     params.email_on_fail,
+    //     params.plaintext_email,
+    //     params.outdir,
+    //     params.monochrome_logs,
+    //     NFCORE_PERTURBSEQ.out.multiqc_report
+    // )
 }
 
 /*