millironx/taxprofiler
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Code Issues Releases Packages Activity

Linting fixes deactivate accidental re-included function

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James Fellows Yates 2023-04-29 18:08:00 +02:00
parent bca6e645a8
commit 1ef8119c59
4 changed files with 11 additions and 3 deletions
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5
CHANGELOG.md
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@ -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) - [#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) - [#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) - [#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` ### `Dependencies`
| Tool | Previous version | New version |
|---------|------------------|-------------|
| MultiQC | 1.13 | 1.14 |
### `Deprecated` ### `Deprecated`
## v1.0.0 - Dodgy Dachshund [2023-03-13] ## v1.0.0 - Dodgy Dachshund [2023-03-13]

4
README.md
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@ -102,7 +102,7 @@ nf-core/taxprofiler was originally written by James A. Fellows Yates, Sofia Stam
### Team ### Team
- [James A. Fellows Yates](https://github.com/jfy133) - [James A. Fellows Yates](https://github.com/jfy133)
- [Sofia Stamouli](https://github.com/sofstam) - [Sofia Stamouli](https://github.com/sofstam)
- [Moritz E. Beber](https://github.com/Midnighter) - [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 ## 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. An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.

2
bin/check_samplesheet.py
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@ -26,6 +26,7 @@ def make_dir(path):
if exception.errno != errno.EEXIST: if exception.errno != errno.EEXIST:
raise exception raise exception
def print_error(error, context="Line", context_str=""): def print_error(error, context="Line", context_str=""):
error_str = "ERROR: Please check samplesheet -> {}".format(error) error_str = "ERROR: Please check samplesheet -> {}".format(error)
if context != "" and context_str != "": if context != "" and context_str != "":
@ -35,6 +36,7 @@ def print_error(error, context="Line", context_str=""):
print(error_str) print(error_str)
sys.exit(1) sys.exit(1)
def check_samplesheet(file_in, file_out): def check_samplesheet(file_in, file_out):
""" """
This function checks that the samplesheet follows the following structure: This function checks that the samplesheet follows the following structure:

3
lib/WorkflowTaxprofiler.groovy
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@ -10,6 +10,7 @@ class WorkflowTaxprofiler {
// //
// Check and validate parameters // Check and validate parameters
// //
/*
public static void initialise(params, log) { public static void initialise(params, log) {
genomeExistsError(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." Nextflow.error "Genome fasta file not specified with e.g. '--fasta genome.fa' or via a detectable config file."
} }
} }
*/
// //
// Get workflow summary for MultiQC // Get workflow summary for MultiQC
// //