diff --git a/bin/check_samplesheet.py b/bin/check_samplesheet.py
index d10ee90..47c6452 100755
--- a/bin/check_samplesheet.py
+++ b/bin/check_samplesheet.py
@@ -48,7 +48,7 @@ def check_samplesheet(file_in, file_out):
     2613,ERR5766181,ILLUMINA,ERX5474937_ERR5766181_1.fastq.gz,ERX5474937_ERR5766181_2.fastq.gz,
     """
 
-    FQ_EXTENSIONS = (".fq", ".fq.gz", ".fastq", ".fastq.gz")
+    FQ_EXTENSIONS = (".fq.gz", ".fastq.gz")
     FA_EXTENSIONS = (
         ".fa",
         ".fa.gz",
diff --git a/docs/usage.md b/docs/usage.md
index 54ffce0..8b40745 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -12,6 +12,8 @@
 
 nf-core/taxprofiler can accept as input raw or preprocessed single- or paired-end short-read (e.g. Illumina) FASTQ files, long-read FASTQ files (e.g. Oxford Nanopore), or FASTA sequences (available for a subset of profilers).
 
+> ⚠️ Input FASTQ files _must_ be gzipped, while FASTA files may optionally be uncompressed (although this is not recommended)
+
 You will need to create a samplesheet with information about the samples you would like to analyse before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 6 columns, and a header row as shown in the examples below. Furthermother, nf-core/taxprofiler also requires a second comma-separated file of 3 columns with a header row as in the examples below.
 
 This samplesheet is then specified on the command line as follows: