diff --git a/assets/master_template.html b/assets/master_template.html
index 2ce5a05..5adfb04 100644
--- a/assets/master_template.html
+++ b/assets/master_template.html
@@ -53,9 +53,9 @@
Sample Report
Weighted Histogram |
Weighted Log-transformed Histogram |
Yield by Length |
- Execution Report |
- Execution Timeline |
- Pipeline DAG |
+ Execution Report |
+ Execution Timeline |
+ Pipeline DAG |
{% endfor %}
diff --git a/bin/generate_master_html.py b/bin/generate_master_html.py
index 346be3f..7714864 100755
--- a/bin/generate_master_html.py
+++ b/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)
diff --git a/nextflow.config b/nextflow.config
index f079444..e481c1f 100644
--- a/nextflow.config
+++ b/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 {
diff --git a/workflows/gmsemu.nf b/workflows/gmsemu.nf
index d5791e9..57128f7 100644
--- a/workflows/gmsemu.nf
+++ b/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, KRONA_KTIMPORTTAXONOMY.out.html, MULTIQC.out.report, NANOPLOT1.out.html)
}
/*