millironx/taxprofiler
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Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
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James A. Fellows Yates 2023-03-07 11:27:19 +01:00 committed by GitHub
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docs/usage.md
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@ -17,7 +17,7 @@ Both contain metadata and paths to the data of your input samples and databases.
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. 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.
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. 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.
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. 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.

5
lib/WorkflowTaxprofiler.groovy
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@ -12,11 +12,6 @@ class WorkflowTaxprofiler {
public static void initialise(params, log) { public static void initialise(params, log) {
genomeExistsError(params, log) genomeExistsError(params, log)
// TODO update as necessary
//if (!params.fasta) {
// log.error "Genome fasta file not specified with e.g. '--fasta genome.fa' or via a detectable config file."
// System.exit(1)
//}
} }
// //