Change pipeline execution output filenames

assets/master_template.html

@@ -53,9 +53,9 @@ <h2 class="card-title mb-0">Sample Report</h2>
                                 <td><a href="./nanoplot/{{ sample_id }}_T1_nanoplot_unprocessedWeightedHistogramReadlength.html">Weighted Histogram</a></td>
                                 <td><a href="./nanoplot/{{ sample_id }}_T1_nanoplot_unprocessedWeightedLogTransformed_HistogramReadlength.html">Weighted Log-transformed Histogram</a></td>
                                 <td><a href="./nanoplot/{{ sample_id }}_T1_nanoplot_unprocessedYield_By_Length.html">Yield by Length</a></td>
-                                <td><a href="./pipeline_info/execution_report_{{ date_id }}.html">Execution Report</a></td>
-                                <td><a href="./pipeline_info/execution_timeline_{{ date_id }}.html">Execution Timeline</a></td>
-                                <td><a href="./pipeline_info/pipeline_dag_{{ date_id }}.html">Pipeline DAG</a></td>
+                                <td><a href="./pipeline_info/execution_report.html">Execution Report</a></td>
+                                <td><a href="./pipeline_info/execution_timeline.html">Execution Timeline</a></td>
+                                <td><a href="./pipeline_info/pipeline_dag.html">Pipeline DAG</a></td>
                             </tr>
                             {% endfor %}
                         </tbody>

bin/generate_master_html.py

@@ -69,20 +69,6 @@
 
 args = parser.parse_args()
 
-def get_date_id(samplesheet_csv_fpath):
-    date_ids = []
-    parent_dir = os.path.dirname(samplesheet_csv_fpath)
-    pipeline_info_dir = os.path.join(parent_dir, 'pipeline_info')
-    for filename in os.listdir(pipeline_info_dir):
-        if filename.startswith("execution_report"):
-            execution_report_fpath = os.path.join(pipeline_info_dir, filename)
-            date_id = find_date_in_string(execution_report_fpath, r'(\d{4}-\d{2}-\d{2}[^.]+)')
-            date_ids.append(date_id)
-    date_list = map(find_date_in_string, date_ids, [r'\b(\d{4}-\d{2}-\d{2})']*len(date_ids))
-    date_id_zipped = list(zip(date_ids, date_list))
-    sorted_date_ids = [date_id[0] for date_id in sorted(date_id_zipped, key=lambda date: datetime.strptime(date[1], "%Y-%m-%d"), reverse=True)]    
-    return sorted_date_ids[0]
-
 def find_date_in_string(input_string, date_pattern):
     """Searches for a date within a given string."""
     date = ""
@@ -103,19 +89,18 @@ def get_sample_ids(samplesheet_csv):
     sample_ids = df['sample'].tolist()
     return sample_ids
 
-def generate_master_html(template_html_fpath, sample_ids, seqrun_date, date_id):
+def generate_master_html(template_html_fpath, sample_ids, seqrun_date):
     """Read the template from an HTML file."""
     with open(template_html_fpath, "r") as file:
         master_template = file.read()
     template = Template(master_template)
-    rendered_html = template.render(sample_ids=sample_ids, seqrun_date=seqrun_date, date_id=date_id)
+    rendered_html = template.render(sample_ids=sample_ids, seqrun_date=seqrun_date)
     return rendered_html
 
 def main():
     sample_ids = get_sample_ids(args.csv)
     seqrun_date = find_date_in_string(args.csv, r'/(\d{8})_')
-    date_id = get_date_id(args.csv)
-    rendered_html = generate_master_html(args.html, sample_ids, seqrun_date, date_id)
+    rendered_html = generate_master_html(args.html, sample_ids, seqrun_date)
     with open("master.html", "w") as fout:
         fout.write(rendered_html)
 

nextflow.config

@@ -208,22 +208,25 @@ env {
 // Capture exit codes from upstream processes when piping
 process.shell = ['/bin/bash', '-euo', 'pipefail']
 
-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"
+    overwrite = true
+    file    = "${params.tracedir}/execution_timeline.html"
 }
 report {
     enabled = true
-    file    = "${params.tracedir}/execution_report_${trace_timestamp}.html"
+    overwrite = true
+    file    = "${params.tracedir}/execution_report.html"
 }
 trace {
     enabled = true
-    file    = "${params.tracedir}/execution_trace_${trace_timestamp}.txt"
+    overwrite = true
+    file    = "${params.tracedir}/execution_trace.txt"
 }
 dag {
     enabled = true
-    file    = "${params.tracedir}/pipeline_dag_${trace_timestamp}.html"
+    overwrite = true
+    file    = "${params.tracedir}/pipeline_dag.html"
 }
 
 manifest {

workflows/gmsemu.nf

@@ -88,8 +88,6 @@ workflow GMSEMU {
         ch_input = GENERATE_INPUT.out.sample_sheet_merged
     }
 
-    GENERATE_MASTER_HTML(GENERATE_INPUT.out.sample_sheet_merged)
-
     // Validate and stage input files
     INPUT_CHECK(ch_input)
     ch_versions = ch_versions.mix(INPUT_CHECK.out.versions)
@@ -197,6 +195,7 @@ workflow GMSEMU {
     )
     multiqc_report = MULTIQC.out.report.toList()
 
+    GENERATE_MASTER_HTML(GENERATE_INPUT.out.sample_sheet_merged)
 
 }
 /*