millironx/taxprofiler
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minor fixes

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This commit is contained in:
James Fellows Yates 2022-12-20 13:55:15 +01:00
parent 7709245874
commit 11db981a88
3 changed files with 5 additions and 12 deletions
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4
bin/check_samplesheet.py
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@ -50,13 +50,9 @@ def check_samplesheet(file_in, file_out):
FQ_EXTENSIONS = (".fq.gz", ".fastq.gz") FQ_EXTENSIONS = (".fq.gz", ".fastq.gz")
FA_EXTENSIONS = ( FA_EXTENSIONS = (
".fa",
".fa.gz", ".fa.gz",
".fasta",
".fasta.gz", ".fasta.gz",
".fna",
".fna.gz", ".fna.gz",
".fas",
".fas.gz", ".fas.gz",
) )
INSTRUMENT_PLATFORMS = [ INSTRUMENT_PLATFORMS = [

2
docs/usage.md
View file

@ -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). 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. 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.

11
subworkflows/local/input_check.nf
View file

@ -18,23 +18,20 @@ workflow INPUT_CHECK {
fastq: true fastq: true
} }
parsed_samplesheet.fastq fastq = parsed_samplesheet.fastq
.map { create_fastq_channel(it) } .map { create_fastq_channel(it) }
.set { fastq }
parsed_samplesheet.nanopore nanopore = parsed_samplesheet.nanopore
.map { create_fastq_channel(it) } .map { create_fastq_channel(it) }
.set { nanopore }
parsed_samplesheet.fasta fasta = parsed_samplesheet.fasta
.map { create_fasta_channel(it) } .map { create_fasta_channel(it) }
.set { fasta }
emit: emit:
fastq = fastq ?: [] // channel: [ val(meta), [ reads ] ] fastq = fastq ?: [] // channel: [ val(meta), [ reads ] ]
nanopore = nanopore ?: [] // channel: [ val(meta), [ reads ] ] nanopore = nanopore ?: [] // channel: [ val(meta), [ reads ] ]
fasta = fasta ?: [] // channel: [ val(meta), fasta ] 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 ] ] // Function to get list of [ meta, [ fastq_1, fastq_2 ] ]