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Apply suggestions from code review
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
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@ -17,7 +17,7 @@ Both contain metadata and paths to the data of your input samples and databases.
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When running nf-core/taxprofiler, every step and tool is 'opt in'. To run a given classifier or profiler you must make sure to supply both a database in your `<database>.csv` and supply `--run_<profiler>` flag to your command. Omitting either will result in the profiling tool not executing.
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nf-core/profiler also includes optional pre-processing (adapter clipping, merge running etc.) or post-processing (visualisation) steps. These are also opt in with a `--perform_<step>` flag. In some cases, the pre- and post-processing steps may also require additional files. Please check the parameters tab of this documentation for more information.
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nf-core/taxprofiler also includes optional pre-processing (adapter clipping, merge running etc.) or post-processing (visualisation) steps. These are also opt in with a `--perform_<step>` flag. In some cases, the pre- and post-processing steps may also require additional files. Please check the parameters tab of this documentation for more information.
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Please see the rest of this page for information about how to prepare input samplesheets and databases and how to run Nextflow pipelines. See the [parameters](https://nf-co.re/taxprofiler/parameters) documentation for more information about specific options the pipeline also offers.
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@ -12,11 +12,6 @@ class WorkflowTaxprofiler {
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public static void initialise(params, log) {
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genomeExistsError(params, log)
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// TODO update as necessary
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//if (!params.fasta) {
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// log.error "Genome fasta file not specified with e.g. '--fasta genome.fa' or via a detectable config file."
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// System.exit(1)
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//}
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}
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//
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