Linting fixes deactivate accidental re-included function

CHANGELOG.md

@@ -19,9 +19,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#275](https://github.com/nf-core/taxprofiler/pull/275/files) Replaced function used for error reporting to more Nextflow friendly method (fix by @jfy133)
 - [#285](https://github.com/nf-core/taxprofiler/pull/285/files) Fixed overly large log files in Kraken2 output (♥ to @prototaxites for reporting, fix by @Midnighter & @jfy133)
 - [#286](https://github.com/nf-core/taxprofiler/pull/286/files) Runtime optimisation of MultiQC step via improved log file processing (fix by @Midnighter & @jfy133)
+- [#289](https://github.com/nf-core/taxprofiler/pull/289/files) Pipeline updated to nf-core template 2.8 (fix by @Midnighter & @jfy133)
 
 ### `Dependencies`
 
+| Tool    | Previous version | New version |
+|---------|------------------|-------------|
+| MultiQC | 1.13             | 1.14        |
+
 ### `Deprecated`
 
 ## v1.0.0 - Dodgy Dachshund [2023-03-13]

README.md

@@ -102,7 +102,7 @@ nf-core/taxprofiler was originally written by James A. Fellows Yates, Sofia Stam
 
 ### Team
 
-- [James A. Fellows Yates](https://github.com/jfy133) 
+- [James A. Fellows Yates](https://github.com/jfy133)
 - [Sofia Stamouli](https://github.com/sofstam)
 - [Moritz E. Beber](https://github.com/Midnighter)
 
@@ -137,7 +137,7 @@ For further information or help, don't hesitate to get in touch on the [Slack `#
 
 ## Citations
 
-If you use  nf-core/taxprofiler for your analysis, please cite it using the following doi: [10.5281/zenodo.7728364](https://doi.org/10.5281/zenodo.7728364)
+If you use nf-core/taxprofiler for your analysis, please cite it using the following doi: [10.5281/zenodo.7728364](https://doi.org/10.5281/zenodo.7728364)
 
 An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.
 

bin/check_samplesheet.py

@@ -26,6 +26,7 @@ def make_dir(path):
             if exception.errno != errno.EEXIST:
                 raise exception
 
+
 def print_error(error, context="Line", context_str=""):
     error_str = "ERROR: Please check samplesheet -> {}".format(error)
     if context != "" and context_str != "":
@@ -35,6 +36,7 @@ def print_error(error, context="Line", context_str=""):
     print(error_str)
     sys.exit(1)
 
+
 def check_samplesheet(file_in, file_out):
     """
     This function checks that the samplesheet follows the following structure:

lib/WorkflowTaxprofiler.groovy

@@ -10,6 +10,7 @@ class WorkflowTaxprofiler {
     //
     // Check and validate parameters
     //
+    /*
     public static void initialise(params, log) {
         genomeExistsError(params, log)
 
@@ -17,7 +18,7 @@ class WorkflowTaxprofiler {
             Nextflow.error "Genome fasta file not specified with e.g. '--fasta genome.fa' or via a detectable config file."
         }
     }
-
+    */
     //
     // Get workflow summary for MultiQC
     //