Merge branch 'versions' into 'dev'

Add version report

See merge request epi2melabs/workflow-containers/wf-template!12

bin/conda_versions.py

@@ -0,0 +1,37 @@
+"""Scrape versions of conda packages."""
+
+from collections import namedtuple
+import subprocess
+
+
+try:
+    import pandas as pd
+except ImportError:
+    pass
+
+
+PackageInfo = namedtuple(
+    'PackageInfo', ('Name', 'Version', 'Build', 'Channel'))
+
+
+def scrape_data(as_dataframe=False, include=None):
+    """Return versions of conda packages in base environment."""
+    cmd = """
+. ~/conda/etc/profile.d/mamba.sh;
+micromamba activate;
+micromamba list;
+    """
+    proc = subprocess.run(cmd, shell=True, check=True, capture_output=True)
+    versions = dict()
+    for line in proc.stdout.splitlines()[3:]:
+        items = line.decode().strip().split()
+        if len(items) == 3:
+            # sometimes channel isn't listed :/
+            items.append("")
+        if include is None or items[0] in include:
+            versions[items[0]] = PackageInfo(*items)
+    if as_dataframe:
+        versions = pd.DataFrame.from_records(
+            list(versions.values()),
+            columns=PackageInfo._fields)
+    return versions

bin/report.py

@@ -4,7 +4,8 @@
 import argparse
 
 from aplanat.components import fastcat
-from aplanat.report import HTMLReport
+from aplanat.report import WFReport
+import conda_versions
 
 
 def main():
@@ -12,29 +13,31 @@ def main():
     parser = argparse.ArgumentParser()
     parser.add_argument("report", help="Report output file")
     parser.add_argument("summaries", nargs='+', help="Read summary file.")
+    parser.add_argument(
+        "--revision", default='unknown',
+        help="git branch/tag of the executed workflow")
+    parser.add_argument(
+        "--commit", default='unknown',
+        help="git commit of the executed workflow")
     args = parser.parse_args()
 
-    report = HTMLReport(
+    report = WFReport(
-        "Workflow Template Sequencing report",
+        "Workflow Template Sequencing report", "wf-template",
-        ("Results generated through the wf-template nextflow "
+        revision=args.revision, commit=args.commit)
-            "workflow by Oxford Nanopore Technologies"))
 
     report.add_section(
         section=fastcat.full_report(args.summaries))
 
-    report.markdown('''
+    section = report.add_section()
-### About
+    section.markdown('''
-
+### Software versions
-**Oxford Nanopore Technologies products are not intended for use for health
+The table below highlights versions of key software used within the analysis.
-assessment or to diagnose, treat, mitigate, cure or prevent any disease or
-condition.**
-
-This report was produced using the
-[epi2me-labs/wf-template](https://github.com/epi2me-labs/wf-template).  The
-workflow can be run using `nextflow epi2me-labs/wf-template --help`
-
----
 ''')
+    req = [
+        'python', 'aplanat', 'pysam', 'fastcat']
+    versions = conda_versions.scrape_data(
+        as_dataframe=True, include=req)
+    section.table(versions[['Name', 'Version', 'Build']], index=False)
 
     # write report
     report.write(args.report)

environment.yaml

@@ -5,7 +5,7 @@ channels:
     - conda-forge
     - defaults
 dependencies:
-    - python==3.6.*
+    - python==3.8.*
     - aplanat >=0.3.5
     - pysam
     - fastcat