From 1ef8119c59ee26849c77ef3203d16189295206e1 Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Sat, 29 Apr 2023 18:08:00 +0200 Subject: [PATCH] Linting fixes deactivate accidental re-included function --- CHANGELOG.md | 5 +++++ README.md | 4 ++-- bin/check_samplesheet.py | 2 ++ lib/WorkflowTaxprofiler.groovy | 3 ++- 4 files changed, 11 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index b0187f1..a02681e 100644 --- a/CHANGELOG.md +++ b/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] diff --git a/README.md b/README.md index 4900f29..09a1e3a 100644 --- a/README.md +++ b/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. diff --git a/bin/check_samplesheet.py b/bin/check_samplesheet.py index 9ae509f..9f0f7a6 100755 --- a/bin/check_samplesheet.py +++ b/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: diff --git a/lib/WorkflowTaxprofiler.groovy b/lib/WorkflowTaxprofiler.groovy index 4b5a8f8..7e016da 100755 --- a/lib/WorkflowTaxprofiler.groovy +++ b/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 //