Update version reporting

bin/report.py

@@ -4,6 +4,7 @@
 import argparse
 
 from aplanat.components import fastcat
+from aplanat.components import simple as scomponents
 from aplanat.report import WFReport
 import conda_versions
 
@@ -13,6 +14,9 @@ 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(
+        "--versions", required=True,
+        help="directory containing CSVs containing name,version.")
     parser.add_argument(
         "--revision", default='unknown',
         help="git branch/tag of the executed workflow")
@@ -27,17 +31,8 @@ def main():
 
     report.add_section(
         section=fastcat.full_report(args.summaries))
-
+    report.add_section(
-    section = report.add_section()
+        section=scomponents.version_table(args.versions))
-    section.markdown('''
-### Software versions
-The table below highlights versions of key software used within the analysis.
-''')
-    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

@@ -6,6 +6,6 @@ channels:
     - defaults
 dependencies:
     - python==3.8.*
-    - aplanat >=0.3.5
+    - aplanat >=0.5.0
     - pysam
     - fastcat

main.nf

@@ -46,14 +46,27 @@ process summariseReads {
 }
 
 
+process getVersions {
+    label "pysam"
+    cpus 1
+    output:
+        path "versions.txt"
+    script:
+    """
+    python -c "import pysam; print(f'pysam,{pysam.__version})" >> versions.txt
+    fastcat --version | sed 's/^/fastcat,/' >> versions.txt
+    """
+}
+
 process makeReport {
     label "pysam"
     input:
         path "seqs.txt"
+        path "versions/*"
     output:
         path "wf-template-report.html"
     """
-    report.py wf-template-report.html seqs.txt
+    report.py wf-template-report.html --versions versions.txt seqs.txt
     """
 }
 
@@ -81,7 +94,8 @@ workflow pipeline {
         reads
     main:
         summary = summariseReads(reads)
-        report = makeReport(summary)
+        software_versions = getVersions()
+        report = makeReport(summary, software_versions.collect())
     emit:
         summary.concat(report)
 }

nextflow.config

@@ -55,7 +55,7 @@ profiles {
         }
         process {
             withLabel:pysam {
-                conda = "environment.yaml"
+                conda = "${projectDir}/environment.yaml"
             }
             shell = ['/bin/bash', '-euo', 'pipefail']
         }