diff --git a/bin/conda_versions.py b/bin/conda_versions.py deleted file mode 100644 index 92be7d0..0000000 --- a/bin/conda_versions.py +++ /dev/null @@ -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 diff --git a/bin/report.py b/bin/report.py index c1ba670..42955aa 100755 --- a/bin/report.py +++ b/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(): diff --git a/main.nf b/main.nf index 579cf23..c17ce06 100644 --- a/main.nf +++ b/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 """ }