From 536e80d1aa566c510adf6d5c74302c5d4e9d5467 Mon Sep 17 00:00:00 2001 From: Martin Proks Date: Tue, 20 Jun 2023 11:50:40 +0200 Subject: [PATCH] fix: linting issues --- .github/workflows/ci.yml | 2 +- README.md | 2 +- assets/email_template.html | 2 +- bin/split_amp_batch.py | 2 +- bin/velocity.py | 2 +- nextflow_schema.json | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index b2ccc3d..540d7f4 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -24,7 +24,7 @@ jobs: strategy: matrix: NXF_VER: - - "22.10.1" + - "23.04.0" - "latest-everything" steps: - name: Check out pipeline code diff --git a/README.md b/README.md index 881381a..db730cf 100644 --- a/README.md +++ b/README.md @@ -2,7 +2,7 @@ [![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/marsseq/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) -[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A522.10.1-23aa62.svg)](https://www.nextflow.io/) +[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/) [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/) [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/) diff --git a/assets/email_template.html b/assets/email_template.html index b4af38a..4a0dbab 100644 --- a/assets/email_template.html +++ b/assets/email_template.html @@ -4,7 +4,7 @@ - + nf-core/marsseq Pipeline Report diff --git a/bin/split_amp_batch.py b/bin/split_amp_batch.py index ba1f943..14e6665 100755 --- a/bin/split_amp_batch.py +++ b/bin/split_amp_batch.py @@ -106,7 +106,7 @@ def load_files(input_folder: str, output_folder: str, amp_batch: str) -> Tuple[s def main() -> None: - arg_parser = argparse.ArgumentParser(description="Filter reads per amplification batch from MARS-seq 1/2.") + arg_parser = argparse.ArgumentParser(description="Filter reads per amplification batch from MARS-seq v2.") arg_parser.add_argument("input", type=str, help="Input folder with fastq files") arg_parser.add_argument("output", type=str, help="Output folder") arg_parser.add_argument("--amp_batch", type=str, help="Batch name", required=True) diff --git a/bin/velocity.py b/bin/velocity.py index 1cce047..7ffcc01 100755 --- a/bin/velocity.py +++ b/bin/velocity.py @@ -180,7 +180,7 @@ def whitelist(batch: str, amp_batches: str, well_cells: str): logging.getLogger().setLevel(logging.INFO) formatter = logging.Formatter("%(asctime)s %(message)s", "%d-%m-%Y %H:%M:%S") - arg_parser = argparse.ArgumentParser(description="Plugin for converting and running velocity on MARS-seq 1/2.") + arg_parser = argparse.ArgumentParser(description="Plugin for converting and running velocity on MARS-seq v2.") arg_parser.add_argument("--version", "-v", action="version", version=f"velocity 0.1") command_parser = arg_parser.add_subparsers(dest="command") diff --git a/nextflow_schema.json b/nextflow_schema.json index 6426aa2..03ab576 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -2,7 +2,7 @@ "$schema": "http://json-schema.org/draft-07/schema", "$id": "https://raw.githubusercontent.com/nf-core/marsseq/master/nextflow_schema.json", "title": "nf-core/marsseq pipeline parameters", - "description": "MARS-seq 1/2 preprocessing pipeline", + "description": "MARS-seq v2 preprocessing pipeline", "type": "object", "definitions": { "skip_steps": {