From 11db981a887b27a271bede8cda0406a47a84743e Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Tue, 20 Dec 2022 13:55:15 +0100 Subject: [PATCH] minor fixes --- bin/check_samplesheet.py | 4 ---- docs/usage.md | 2 +- subworkflows/local/input_check.nf | 11 ++++------- 3 files changed, 5 insertions(+), 12 deletions(-) diff --git a/bin/check_samplesheet.py b/bin/check_samplesheet.py index ca54ed9..a45cb93 100755 --- a/bin/check_samplesheet.py +++ b/bin/check_samplesheet.py @@ -50,13 +50,9 @@ def check_samplesheet(file_in, file_out): FQ_EXTENSIONS = (".fq.gz", ".fastq.gz") FA_EXTENSIONS = ( - ".fa", ".fa.gz", - ".fasta", ".fasta.gz", - ".fna", ".fna.gz", - ".fas", ".fas.gz", ) INSTRUMENT_PLATFORMS = [ diff --git a/docs/usage.md b/docs/usage.md index 685c3e3..4f3e038 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -12,7 +12,7 @@ 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) +> ⚠️ Input FASTQ and FASTA files _must_ be gzipped 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. diff --git a/subworkflows/local/input_check.nf b/subworkflows/local/input_check.nf index 7fd0072..672c0e8 100644 --- a/subworkflows/local/input_check.nf +++ b/subworkflows/local/input_check.nf @@ -18,23 +18,20 @@ workflow INPUT_CHECK { fastq: true } - parsed_samplesheet.fastq + fastq = parsed_samplesheet.fastq .map { create_fastq_channel(it) } - .set { fastq } - parsed_samplesheet.nanopore + nanopore = parsed_samplesheet.nanopore .map { create_fastq_channel(it) } - .set { nanopore } - parsed_samplesheet.fasta + fasta = parsed_samplesheet.fasta .map { create_fasta_channel(it) } - .set { fasta } emit: fastq = fastq ?: [] // channel: [ val(meta), [ reads ] ] nanopore = nanopore ?: [] // channel: [ val(meta), [ reads ] ] fasta = fasta ?: [] // channel: [ val(meta), fasta ] - versions = SAMPLESHEET_CHECK.out.versions.first() // channel: [ versions.yml ] + versions = SAMPLESHEET_CHECK.out.versions.first() // channel: [ versions.yml ] } // Function to get list of [ meta, [ fastq_1, fastq_2 ] ]