From eb8fe3ebab6cd9b4d3ca8b96b27a9efe16924856 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Thu, 12 Sep 2024 08:19:08 +0000 Subject: [PATCH] [automated] Fix code linting --- README.md | 1 - docs/output.md | 2 +- docs/usage.md | 31 +++++++++++++++---------------- 3 files changed, 16 insertions(+), 18 deletions(-) diff --git a/README.md b/README.md index 666d27ac..a3edf867 100644 --- a/README.md +++ b/README.md @@ -23,7 +23,6 @@ **nf-core/taxprofiler** is a bioinformatics best-practice analysis pipeline for taxonomic classification and profiling of shotgun short- and long-read metagenomic data. It allows for in-parallel taxonomic identification of reads or taxonomic abundance estimation with multiple classification and profiling tools against multiple databases, and produces standardised output tables for facilitating results comparison between different tools and databases. - ## Pipeline summary ![](docs/images/taxprofiler_tube.png) diff --git a/docs/output.md b/docs/output.md index 80b02ecb..8bd58f86 100644 --- a/docs/output.md +++ b/docs/output.md @@ -157,7 +157,7 @@ The resulting `.fastq` files may _not_ always be the 'final' reads that go into In most cases you will just want to look at the PNG files which contain the extrapolation information for estimating how much of the metagenome 'coverage' you will recover if you sequence more (i.e., to help indicate at what point you will just keep sequencing redundant reads that provide no more new taxonomic information). - The `.npo` files can be used for re-generating and customising the plots using the companion `Nonpareil` R package. +The `.npo` files can be used for re-generating and customising the plots using the companion `Nonpareil` R package. ### Porechop diff --git a/docs/usage.md b/docs/usage.md index bb7ff63e..ad735151 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -275,22 +275,21 @@ Before using this tool please note the following caveats: :::warning - It is not recommended to keep unmerged (`--shortread_qc_includeunmerged`) reads when using the calculation. -- Your shortest reads _after_ processing should not go below 24bp - - If the 'kmer' value is not correct, make sure your shortest reads _after_ processing is not less than 24bp. - - If this is the case you will need to specify in a custom config - - ```nextflow - process { - withName: NONPAREIL_NONPAREIL { - ext.args = { "-k " } - } - } - ``` - - Where `` should be at least the shortest read in your library -::: +- Your shortest reads _after_ processing should not go below 24bp + If the 'kmer' value is not correct, make sure your shortest reads _after_ processing is not less than 24bp. + + If this is the case you will need to specify in a custom config + + ```nextflow + process { + withName: NONPAREIL_NONPAREIL { + ext.args = { "-k " } + } + } + ``` + + Where `` should be at least the shortest read in your library + ::: #### Complexity Filtering