Clean up some old code

CHANGELOG.md

@@ -28,6 +28,7 @@ that users understand how the changes affect the new version.
 - Use multiple threads for Cutadapt, and reduce the compression of output files
 
 ### Changes
+- Remove run name from the report
 - Deprecate option `fusion-partners`, in favour of `report_genes`, which points
   to a list of fusion genes to report
 - Show allele frequency as a percentage in the pfd report

Snakefile

@@ -5,7 +5,6 @@ localrules:
     align_exon_cov_ref,
     align_genome_txt,
     align_json_output,
-    align_table_vars_all,
     align_table_vars_hi,
     create_summary,
     fusion_arriba_to_json,
@@ -15,7 +14,6 @@ localrules:
     itd_json_output,
     itd_plot_itd_flt3,
     itd_plot_itd_kmt2a,
-    package_results,
 
 
 rule all:
@@ -137,7 +135,6 @@ rule create_summary:
         scr=srcdir("scripts/create_summary.py"),
     params:
         pipeline_ver=PIPELINE_VERSION,
-        run_name=RUN_NAME,
     output:
         js="{sample}/{sample}.summary.json",
     log:
@@ -149,7 +146,6 @@ rule create_summary:
         python {input.scr} \
             {input.idm} \
             --pipeline-version {params.pipeline_ver} \
-            --run-name {params.run_name} \
             --sample-name {wildcards.sample} \
             --module {input.fusion_json} \
             --module {input.snv_indels_json} \

common.smk

@@ -1,5 +1,3 @@
-from functools import partial
-from os.path import dirname
 from uuid import uuid4
 
 
@@ -10,21 +8,7 @@ samples = pep.sample_table["sample_name"]
 
 containers = {
     "hamlet-scripts": "docker://quay.io/redmar_van_den_berg/hamlet-scripts:0.3",
-    "zip": "docker://quay.io/redmar_van_den_berg/zip:3.0",
 }
 
 # The version of HAMLET
 PIPELINE_VERSION = "v1.0.2-dev-1"
-RUN_NAME = config.get("run_name") or f"hamlet-{uuid4().hex[:8]}"
-
-
-def make_pattern(extension, dirname):
-    """Helper function to create a wildcard-containing path for output files."""
-    return f"{{sample}}/{dirname}/{{sample}}{extension}"
-
-
-seqqc_output = partial(make_pattern, dirname="qc-seq")
-var_output = partial(make_pattern, dirname="snv-indels")
-fusion_output = partial(make_pattern, dirname="fusion")
-expr_output = partial(make_pattern, dirname="expression")
-itd_output = partial(make_pattern, dirname="itd")

report/templates/contents_basic.html.j2

@@ -15,10 +15,6 @@
       <td>Read group count</td>
       <td>{{ modules.qc_seq.per_read_group|length }}</td>
     </tr>
-    <tr>
-      <td>Run name</td>
-      <td>{{ metadata.run_name }}</td>
-    </tr>
     <tr>
       <td>Pipeline version</td>
       <td>{{ metadata.pipeline_version }}</td>

report/templates/cover.html.j2

@@ -10,11 +10,11 @@
       <h1>HAMLET</h1>
       <p class="pipeline-subtitle">Acute Myeloid Leukemia mRNA-seq Analysis Pipeline</p>
       <h2>Analysis Report</h2>
-      <p class="report-subtitle">Sample '{{ sample_name }}' - Run '{{ run_name }}'</p>
+      <p class="report-subtitle">Sample '{{ sample_name }}'</p>
       <div class="logo">
         <img src="{{ imgs_dir }}/hamlet-logo.jpg" height="250">
       </div>
-      <p>Version {{ pipeline_version|default('unknown') }}<br />Generated on {{ timestamp.strftime('%A, %d %B %Y at %H:%M') }}</p>
+      <p>Version {{ pipeline_version }}<br />Generated on {{ timestamp.strftime('%A, %d %B %Y at %H:%M') }}</p>
       <div class="logo lumc">
         <img src="{{ imgs_dir }}/lumc-logo.jpg" height="40">
       </div>

scripts/create_summary.py

@@ -23,7 +23,6 @@ def main(args):
     combined = {
         "metadata": {
             "pipeline_version": args.pipeline_version,
-            "run_name": args.run_name,
             "sample_name": args.sample_name,
             "genes_of_interest": idm,
         },
@@ -44,7 +43,6 @@ def main(args):
     parser = argparse.ArgumentParser()
 
     parser.add_argument("id_mappings_path")
-    parser.add_argument("--run-name", help="Name of the run in which the stats were generated.")
     parser.add_argument("--sample-name", help="Name of the sample from which the stats were generated.")
     parser.add_argument("--pipeline-version", help="Version string of the pipeline.")
     parser.add_argument("--module", action="append", help="JSON outputs from various modules")

scripts/generate_report.py

@@ -29,7 +29,6 @@ def __init__(self, summaryd: dict,
         sdm = summaryd["metadata"]
         self.summary = summaryd
         self.sample_name = sdm["sample_name"]
-        self.run_name = sdm["run_name"]
         self.pipeline_version = sdm["pipeline_version"]
         self.cover_tpl_fname = cover_tpl_fname
         self.contents_tpl_fname = contents_tpl_fname
@@ -41,7 +40,6 @@ def __init__(self, summaryd: dict,
 
         hf_ctx = {
             "sample_name": self.sample_name,
-            "run_name": self.run_name,
             "timestamp": self.timestamp,
         }
         pdfkit_opts = pdfkit_opts or {
@@ -168,7 +166,6 @@ def write(self, html, pdf) -> None:
         tmp_prefix = str(Path.cwd()) + "/"
         cover_ctx = {
             "sample_name": self.sample_name,
-            "run_name": self.run_name,
             "pipeline_version": self.pipeline_version,
             "timestamp": self.timestamp,
             "css_fname": self.css_fname,
@@ -205,10 +202,8 @@ def main(input_summary_path, css_path, templates_dir,
 
     sdm = sd["metadata"]
     sample_name = sdm["sample_name"]
-    run_name = sdm["run_name"]
     pipeline_version = sdm["pipeline_version"]
-    header_caption = ("Hamlet Report -"
-                      f" Sample {sample_name!r} of Run {run_name!r}")
+    header_caption = f"Hamlet Report - Sample {sample_name!r}"
     footer_lcaption = "Generated on {timestamp:%A, %d %B %Y at %H:%M}"
     footer_rcaption = "[page]/[toPage]"
 

test/data/output/v2/SRR8615409.vardict.summary.json

@@ -17,7 +17,6 @@
       }
     ],
     "pipeline_version": "v1.0.2-dev-1",
-    "run_name": "hamlet-3080e5df",
     "sample_name": "SRR8615409"
   },
   "modules": {

test/data/output/v2/full-report.summary.json

@@ -17,7 +17,6 @@
       }
     ],
     "pipeline_version": "v1.0.2-dev-1",
-    "run_name": "hamlet-072d3448",
     "sample_name": "SRR8615409"
   },
   "modules": {

utilities/output-schema.json

@@ -5,14 +5,13 @@
     "metadata": {
       "type": "object",
       "additionalProperties": false,
-      "minProperties": 4,
+      "minProperties": 3,
       "properties": {
         "genes_of_interest": {
           "type": "array",
           "items": { "$ref": "#/definitions/metadata/gene_of_interest" }
         },
         "pipeline_version": { "type": "string" },
-        "run_name": { "type": "string" },
         "sample_name": { "type": "string" }
       },
       "gene_of_interest": {