From ec13b8d608c5a95e9a2e27ae6c2b76691d5b0448 Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Thu, 9 Jun 2022 08:21:48 +0200 Subject: [PATCH] Remove support for uncompressed FASTQ files --- bin/check_samplesheet.py | 2 +- docs/usage.md | 2 ++ 2 files changed, 3 insertions(+), 1 deletion(-) 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: