minor fixes

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 = [

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.
 

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 ] ]