mcvickerlab · Jaureguy760 · Mar 6, 2026 · Mar 6, 2026 · Mar 6, 2026 · Mar 6, 2026
diff --git a/pipelines/nf-atacseq/assets/email_template.html b/pipelines/nf-atacseq/assets/email_template.html
@@ -0,0 +1,48 @@
+<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">
+  <title>${workflow.manifest.name} Pipeline Report</title>
+</head>
+<body>
+<div style="font-family: Helvetica, Arial, sans-serif; padding: 30px; max-width: 800px; margin: 0 auto;">
+
+<img src="cid:nfcorepipelinelogo">
+
+<h1>${workflow.manifest.name} v${workflow.manifest.version}</h1>
+<h2>Run Name: $runName</h2>
+
+<% if (!success) { %>
+<div style="color: #a94442; background-color: #f2dede; border-color: #ebccd1; padding: 15px; margin-bottom: 20px; border: 1px solid transparent; border-radius: 4px;">
+<h4 style="color: inherit; margin-top: 0;">⚠️ ${workflow.manifest.name} execution completed unsuccessfully!</h4>
+<p>The exit status of the task that caused the workflow execution to fail was: <code>$exitStatus</code>.</p>
+<p>The full error message was:</p>
+<pre style="white-space: pre-wrap; overflow: visible; margin-bottom: 0;">${errorReport}</pre>
+</div>
+<% } else { %>
+<div style="color: #3c763d; background-color: #dff0d8; border-color: #d6e9c6; padding: 15px; margin-bottom: 20px; border: 1px solid transparent; border-radius: 4px;">
+${workflow.manifest.name} execution completed successfully!
+</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;">$commandLine</pre>
+
+<h3>Pipeline Configuration:</h3>
+<table cellpadding="5" style="width:100%; max-width:600px; border-collapse: collapse;">
+<tr><td>Nextflow Version</td><td>$nextflowVersion</td></tr>
+<tr><td>Run Name</td><td>$runName</td></tr>
+<tr><td>Session ID</td><td>$sessionId</td></tr>
+<% if (summary.size() > 0) { %>
+<% for (e in summary) { %><tr><td>${e.key}</td><td>${e.value}</td></tr>
+<% } %>
+<% } %>
+</table>
+
+<p>--- <em>${workflow.manifest.name}</em></p>
+
+</div>
+</body>
+</html>
diff --git a/pipelines/nf-atacseq/assets/nf-core-pipeline_logo_light.png b/pipelines/nf-atacseq/assets/nf-core-pipeline_logo_light.png
diff --git a/pipelines/nf-atacseq/environment.yml b/pipelines/nf-atacseq/environment.yml
@@ -0,0 +1,23 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+# Conda environment for nf-atacseq local Python/WASP2 modules
+# (wasp2_make_reads, wasp2_filter_remapped, wasp2_count_variants, wasp2_find_imbalance)
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - python>=3.10
+  - numpy>=1.21,<2.0
+  - pandas>=2.0
+  - polars>=0.19
+  - scipy>=1.10
+  - pysam
+  - pybedtools
+  - samtools
+  - bcftools
+  - bedtools
+  - typer
+  - rich
+  - pip
+  - pip:
+    - wasp2==1.2.1
diff --git a/pipelines/nf-atacseq/modules.json b/pipelines/nf-atacseq/modules.json
@@ -1,5 +1,5 @@
 {
   "name": "wasp2/nf-atacseq",
-  "homePage": "",
+  "homePage": "https://github.com/mcvickerlab/WASP2",
   "repos": {}
 }
diff --git a/pipelines/nf-atacseq/nextflow.config b/pipelines/nf-atacseq/nextflow.config
@@ -15,6 +15,8 @@ plugins {
 manifest {
     name            = 'wasp2/nf-atacseq'
     author          = 'WASP2 Team'
+    homePage        = 'https://github.com/mcvickerlab/WASP2'
+    doi             = 'https://doi.org/10.1038/nmeth.3582'
     description     = 'ATAC-seq Allelic Imbalance Pipeline with WASP2 mapping bias correction'
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
@@ -73,6 +75,7 @@ params {
     help                    = false
     version                 = false
     tracedir                = "${params.outdir}/pipeline_info"
+    validate_params         = true
 }
 
 // Load configuration files
@@ -97,7 +100,6 @@ profiles {
         conda.enabled           = true
         docker.enabled          = false
         singularity.enabled     = false
-        process.conda           = "${projectDir}/../../environment.yml"
     }
     docker {
         docker.enabled          = true
@@ -153,15 +155,15 @@ profiles {
 def trace_timestamp = new java.util.Date().format('yyyy-MM-dd_HH-mm-ss')
 timeline {
     enabled = true
-    file    = "${params.tracedir}/execution_timeline_${trace_timestamp}.html"
+    file    = "${params.tracedir}/timeline_${trace_timestamp}.html"
 }
 report {
     enabled = true
-    file    = "${params.tracedir}/execution_report_${trace_timestamp}.html"
+    file    = "${params.tracedir}/report_${trace_timestamp}.html"
 }
 trace {
     enabled = true
-    file    = "${params.tracedir}/execution_trace_${trace_timestamp}.txt"
+    file    = "${params.tracedir}/trace_${trace_timestamp}.txt"
 }
 dag {
     enabled = true
@@ -184,7 +186,7 @@ process {
     withName: 'WASP2_MAKE_READS|WASP2_FILTER_REMAPPED|WASP2_COUNT_VARIANTS|WASP2_FIND_IMBALANCE' {
         container = wasp2_container
     }
-    withName: 'BWA_MEM' {
+    withName: 'BWA_INDEX|BWA_MEM' {
         container = bwa_samtools_container
     }
     withName: 'SAMTOOLS_INDEX|SAMTOOLS_FAIDX|SAMTOOLS_STATS|SAMTOOLS_FLAGSTAT|SAMTOOLS_IDXSTATS|SAMTOOLS_SORT' {
@@ -201,27 +203,24 @@ def check_max(obj, type) {
         try {
             if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
                 return params.max_memory as nextflow.util.MemoryUnit
-            else
-                return obj
-        } catch (all) {
-            println "WARNING: Invalid max_memory '${params.max_memory}', using default"
+            else return obj
+        } catch (Exception e) {
+            log.warn "Invalid memory config (${obj}, max=${params.max_memory}): ${e.message}. Using ${obj}"
             return obj
         }
     } else if (type == 'time') {
         try {
             if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1)
                 return params.max_time as nextflow.util.Duration
-            else
-                return obj
-        } catch (all) {
-            println "WARNING: Invalid max_time '${params.max_time}', using default"
+            else return obj
+        } catch (Exception e) {
+            log.warn "Invalid time config (${obj}, max=${params.max_time}): ${e.message}. Using ${obj}"
             return obj
         }
     } else if (type == 'cpus') {
-        try {
-            return Math.min(obj, params.max_cpus as int)
-        } catch (all) {
-            println "WARNING: Invalid max_cpus '${params.max_cpus}', using default"
+        try { return Math.min(obj, params.max_cpus as int) }
+        catch (Exception e) {
+            log.warn "Invalid CPU config (${obj}, max=${params.max_cpus}): ${e.message}. Using ${obj}"
             return obj
         }
     }

diff --git a/pipelines/nf-atacseq/tests/data/annotation.gtf b/pipelines/nf-atacseq/tests/data/annotation.gtf