From 6459d8920fd53a8c03680f7b4b32bf9943f00123 Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Thu, 3 Nov 2022 14:05:43 +0100
Subject: [PATCH] Linting!

---
 docs/usage.md        | 12 ++----------
 nextflow_schema.json |  6 +++---
 2 files changed, 5 insertions(+), 13 deletions(-)

diff --git a/docs/usage.md b/docs/usage.md
index 11e077f..a87102c 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -131,14 +131,6 @@ Expected (uncompressed) database files for each tool are as follows:
   - `hash.k2d`
   - `taxo.k2d`
   - `database.idx`
-  - `database.kdb.counts`
-  - `database50mers.kmer_distrib`
-  - `database75mers.kmer_distrib`
-  - `database100mers.kmer_distrib`
-  - `database150mers.kmer_distrib`
-  - `database200mers.kmer_distrib`
-  - `database300mers.kmer_distrib`
-  - `seqid2taxid.map`
   - `taxDB`
 - **Centrifuge** output of `centrifuge-build`. A directory containing:
   - `<database_name>.<number>.cf`
@@ -192,7 +184,7 @@ work                # Directory containing the nextflow working files
 
 ### Sequencing quality control
 
-nf-core taxprofiler offers [`falco`](https://github.com/smithlabcode/falco] as an alternative option to [`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
+nf-core taxprofiler offers [`falco`][https://github.com/smithlabcode/falco] as an alternative option to [`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
 
 ### Preprocessing Steps
 
@@ -457,7 +449,7 @@ NXF_OPTS='-Xms1g -Xmx4g'
 
 ## Troubleshooting and FAQs
 
-### I get a warning during centrifuge_kreport process with exit status 255.
+### I get a warning during centrifuge_kreport process with exit status 255
 
 When a sample has insufficient hits for abundance estimation, the resulting `report.txt` file will be empty.
 
diff --git a/nextflow_schema.json b/nextflow_schema.json
index c7f4825..7f52764 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -418,18 +418,18 @@
                     "help_text": "Turn on saving minimizer information in the kraken2 report thus increasing to an eight column layout.\n\nAdds `--report-minimizer-data` to the kraken2 command."
                 },
                 "run_krakenuniq": {
-                    "type": "string",
+                    "type": "boolean",
                     "fa_icon": "fas fa-toggle-on",
                     "description": "Turn on profiling with KrakenUniq. Requires database to be present CSV file passed to --databases"
                 },
                 "krakenuniq_save_reads": {
-                    "type": "string",
+                    "type": "boolean",
                     "fa_icon": "fas fa-save",
                     "description": "Turn on saving of KrakenUniq-aligned reads",
                     "help_text": "Save reads that do and do not have a taxonomic classification in your output results directory in FASTQ format.\n\n> Modifies tool parameter(s):\n> - krakenuniq: `--classified-out` and `--unclassified-out`"
                 },
                 "krakenuniq_save_readclassifications": {
-                    "type": "string",
+                    "type": "boolean",
                     "fa_icon": "fas fa-save",
                     "description": "Turn on saving of KrakenUniq per-read taxonomic assignment file",
                     "help_text": "Save a text file that contains a list of each read that had a taxonomic assignment, with information on specific taxonomic taxonomic assignment that that read recieved.\n\n> Modifies tool parameter(s):\n> - krakenuniq: `--output`"