diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 5d8e4954..619d853b 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -3,9 +3,9 @@ custom_logo_url: https://github.com/nf-core/mhcquant custom_logo_title: "nf-core/mhcquant" report_comment: > - This report has been generated by the nf-core/mhcquant + This report has been generated by the nf-core/mhcquant analysis pipeline. For information about how to interpret these results, please see the - documentation. + documentation. report_section_order: "nf-core-mhcquant-methods-description": order: -1000 diff --git a/docs/output.md b/docs/output.md index f39d180f..58d69c37 100644 --- a/docs/output.md +++ b/docs/output.md @@ -26,7 +26,7 @@ By default (only identification) the `best_search_engine_score[1]` holds the per The TSV output file is an alternative output of [OpenMS](https://www.openms.de/) comprising similar information to the mzTab output. The TSV output of identification runs is a simple tab-delimited file holding information about FDR-filtered peptides and currently all values produced by `MSĀ²Rescore`. The TSV file in quantification mode (by using `--quantify`) is more complex and described in more detail below
-TSV QuantTSV Quant MAP contains information about the different mzML files that were provided initially diff --git a/docs/usage.md b/docs/usage.md index 89181c81..a9a839f3 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -77,9 +77,9 @@ nextflow run nf-core/mhcquant \ --input 'samplesheet.tsv' \ --outdir \ --fasta 'SWISSPROT_2020.fasta' \ - \ + \ --peptide_min_length 8 \ ---peptide_max_length 14 \ + --peptide_max_length 14 \ --ms2pip_model 'Immuno-HCD' \ -profile docker ```