.

Author: DaanJansen94

CITATION.cff

@@ -25,7 +25,7 @@ abstract: >-
   FASTQ, then proceed with read quality control, alignment, host depletion, and taxonomic profiling, followed by
   consensus genome building—polishing, refinement, and consensus calling. One container image per process keeps
   runs portable and reproducible under Docker, Singularity/Apptainer, and typical HPC setups.
-version: 0.1.0
+version: 0.1.1
 date-released: 2026-03-31
 url: https://github.com/Clinical-Virology-Unit/Metatropics
 license: MIT

README.md

@@ -6,7 +6,7 @@
 
 # Metatropics: A Viral Metagenomics ONT Pipeline
 
-**Metatropics (v0.1.0)** is a Nextflow-driven bioinformatics pipeline for metagenomic Oxford Nanopore sequencing data. It is built to detect viral pathogens in complex samples (e.g. blood and swabs from a range of body sites) and, where coverage allows, to generate high-quality viral consensus genomes and to perform variant analysis.
+**Metatropics (v0.1.1)** is a Nextflow-driven bioinformatics pipeline for metagenomic Oxford Nanopore sequencing data. It is built to detect viral pathogens in complex samples (e.g. blood and swabs from a range of body sites) and, where coverage allows, to generate high-quality viral consensus genomes and to perform variant analysis.
 
 **Metatropics** is an abbreviation of **Metagenomics for Tropical Fevers**, and reflects how the project began, with an emphasis on finding human viral pathogens in patients presenting with tropical fevers. The same pipeline has since been validated and applied outside that first setting, including for other febrile syndromes, for genomic surveillance, and for research and diagnostic questions around viral pathogens relevant to human health.
 
@@ -150,7 +150,7 @@ You can run Metatropics on a high-performance cluster instead of a local worksta
 If you use Metatropics in your research, please cite:
 
 ```
-Jansen, D., De Souza Novaes, A., de Block, T., Rezende, A. M., & Vercauteren, K. (2026). Metatropics: Human viral pathogen identification and consensus genome calling from nanopore metagenomic sequencing data. (v0.1.0). Zenodo. https://doi.org/10.5281/zenodo.20430617
+Jansen, D., De Souza Novaes, A., de Block, T., Rezende, A. M., & Vercauteren, K. (2026). Metatropics: Human viral pathogen identification and consensus genome calling from nanopore metagenomic sequencing data. (v0.1.1). Zenodo. https://doi.org/10.5281/zenodo.20430617
 ```
 
 Also cite the nf-core framework, and other tools you rely on; see [`nf-metatropics/assets/citing/CITATIONS.md`](nf-metatropics/assets/citing/CITATIONS.md).

nf-metatropics/assets/submission/metatropics_samplesheet/__init__.py

@@ -1 +1,3 @@
 """Samplesheet helpers for the Metatropics Nextflow pipeline (``metatropics-samplesheet``)."""
+
+__version__ = "0.1.1"

nf-metatropics/assets/submission/metatropics_samplesheet/samplesheet.py

@@ -19,6 +19,7 @@
 import sys
 from pathlib import Path
 
+from . import __version__
 from .twist import TWIST_KITS, mock_twist_run_rows, twist_run_to_pod5_rows
 
 # Longest suffix first so e.g. .fastq.gz is not parsed as .fastq
@@ -33,6 +34,14 @@
 HELP_FLAGS = frozenset({"-h", "--help", "-help", "-?"})
 
 
+def add_version_arg(parser: argparse.ArgumentParser) -> None:
+    parser.add_argument(
+        "--version",
+        action="version",
+        version=f"%(prog)s {__version__}",
+    )
+
+
 def wants_top_level_help(argv: list[str]) -> bool:
     """True for bare help flags; subcommand help (e.g. pod5 -h) stays mode-specific."""
     if not argv:
@@ -257,6 +266,7 @@ def build_fastq_parser(subparsers: argparse._SubParsersAction) -> argparse.Argum
         default_help="Directory of demultiplexed FASTQ files (default: current directory).",
         output_help="Output CSV (default: DIR/samplesheet.csv).",
     )
+    add_version_arg(parser)
     return parser
 
 
@@ -290,6 +300,7 @@ def build_twist_pod5_parser() -> argparse.ArgumentParser:
         metavar="FILE",
         help="Output file (default: run.txt or POD5.csv).",
     )
+    add_version_arg(parser)
     return parser
 
 
@@ -310,6 +321,7 @@ def build_pod5_parser(subparsers: argparse._SubParsersAction) -> argparse.Argume
         default_help="POD5 or fastq_pass directory (default: current directory).",
         output_help="Output CSV (default: DIR/POD5.csv).",
     )
+    add_version_arg(parser)
     return parser
 
 
@@ -325,6 +337,7 @@ def build_parser() -> argparse.ArgumentParser:
     subparsers = parser.add_subparsers(dest="command", help=argparse.SUPPRESS)
     build_fastq_parser(subparsers)
     build_pod5_parser(subparsers)
+    add_version_arg(parser)
     return parser
 
 
@@ -340,6 +353,11 @@ def dispatch(mode: str, args: argparse.Namespace) -> None:
 
 def main(argv: list[str] | None = None) -> None:
     argv = list(sys.argv[1:] if argv is None else argv)
+
+    if argv == ["--version"]:
+        print(f"metatropics-samplesheet {__version__}")
+        return
+
     parser = build_parser()
 
     # Top-level help lists both modes and examples (-help is treated like --help).

nf-metatropics/nextflow.config

@@ -251,7 +251,7 @@ manifest {
     description     = """Analyze Nanopore metagenomic data (fast5/fastq) to identify virus pathogen."""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=22.10.1'
-    version         = '0.0.9'
+    version         = '0.1.1'
     doi             = ''
 }
 

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "metatropics-samplesheet"
-version = "0.0.9"
+version = "0.1.1"
 description = "Metatropics samplesheet helper (FASTQ and POD5/fastq_pass CSV)"
 readme = "README.md"
 license = { text = "GPL-3.0-or-later" }

setup.py

@@ -7,7 +7,7 @@
 
 setup(
     name="metatropics-samplesheet",
-    version="0.0.9",
+    version="0.1.1",
     author="Metatropics Team",
     description="Metatropics samplesheet helper (FASTQ and POD5/fastq_pass CSV)",
     long_description=long_description,