Fix typos

bin/conda_versions.py

@@ -1,37 +0,0 @@
-"""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

@@ -6,7 +6,6 @@ import argparse
 from aplanat.components import fastcat
 from aplanat.components import simple as scomponents
 from aplanat.report import WFReport
-import conda_versions
 
 
 def main():

main.nf

@@ -53,7 +53,7 @@ process getVersions {
         path "versions.txt"
     script:
     """
-    python -c "import pysam; print(f'pysam,{pysam.__version})" >> versions.txt
+    python -c "import pysam; print(f'pysam,{pysam.__version__}')" >> versions.txt
     fastcat --version | sed 's/^/fastcat,/' >> versions.txt
     """
 }