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minor fixes
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parent
7709245874
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11db981a88
3 changed files with 5 additions and 12 deletions
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@ -50,13 +50,9 @@ def check_samplesheet(file_in, file_out):
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FQ_EXTENSIONS = (".fq.gz", ".fastq.gz")
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FA_EXTENSIONS = (
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".fa",
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".fa.gz",
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".fasta",
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".fasta.gz",
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".fna",
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".fna.gz",
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".fas",
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".fas.gz",
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)
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INSTRUMENT_PLATFORMS = [
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@ -12,7 +12,7 @@
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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).
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> ⚠️ Input FASTQ files _must_ be gzipped, while FASTA files may optionally be uncompressed (although this is not recommended)
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> ⚠️ Input FASTQ and FASTA files _must_ be gzipped
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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.
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@ -18,23 +18,20 @@ workflow INPUT_CHECK {
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fastq: true
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}
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parsed_samplesheet.fastq
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fastq = parsed_samplesheet.fastq
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.map { create_fastq_channel(it) }
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.set { fastq }
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parsed_samplesheet.nanopore
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nanopore = parsed_samplesheet.nanopore
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.map { create_fastq_channel(it) }
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.set { nanopore }
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parsed_samplesheet.fasta
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fasta = parsed_samplesheet.fasta
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.map { create_fasta_channel(it) }
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.set { fasta }
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emit:
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fastq = fastq ?: [] // channel: [ val(meta), [ reads ] ]
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nanopore = nanopore ?: [] // channel: [ val(meta), [ reads ] ]
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fasta = fasta ?: [] // channel: [ val(meta), fasta ]
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versions = SAMPLESHEET_CHECK.out.versions.first() // channel: [ versions.yml ]
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versions = SAMPLESHEET_CHECK.out.versions.first() // channel: [ versions.yml ]
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}
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// Function to get list of [ meta, [ fastq_1, fastq_2 ] ]
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