fix: linting issues

nf-core · Jun 20, 2023 · 536e80d · 536e80d
1 parent 6ed6b31
commit 536e80d
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Showing 6 changed files with 6 additions and 6 deletions.
diff --git 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
@@ -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
@@ -4,7 +4,7 @@
   <meta http-equiv="X-UA-Compatible" content="IE=edge">
   <meta name="viewport" content="width=device-width, initial-scale=1">
 
-  <meta name="description" content="nf-core/marsseq: MARS-seq 1/2 preprocessing pipeline">
+  <meta name="description" content="nf-core/marsseq: MARS-seq v2 preprocessing pipeline">
   <title>nf-core/marsseq Pipeline Report</title>
 </head>
 <body>

diff --git 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
@@ -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
@@ -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": {