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Remove support for uncompressed FASTQ files

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This commit is contained in:
James Fellows Yates 2022-06-09 08:21:48 +02:00
parent dfcaaae1fb
commit ec13b8d608
2 changed files with 3 additions and 1 deletions
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2
bin/check_samplesheet.py
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@ -48,7 +48,7 @@ def check_samplesheet(file_in, file_out):
2613,ERR5766181,ILLUMINA,ERX5474937_ERR5766181_1.fastq.gz,ERX5474937_ERR5766181_2.fastq.gz, 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_EXTENSIONS = (
".fa", ".fa",
".fa.gz", ".fa.gz",

2
docs/usage.md
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@ -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). 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. 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: This samplesheet is then specified on the command line as follows: