fastq_subsample_fq_salmon

Subsample fastq

fastqsubsamplestrandedness

https://github.com/nf-core/modules/[...]/subworkflows/nf-core/fastq_subsample_fq_salmon

Description

Subsample fastq

Input

name

description

pattern

`ch_reads`

List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively.

Structure: [ val(meta), [ path(reads) ] ]

*.{fq,fastq}{,.gz}

`ch_genome_fasta`

Genome sequence in fasta format.

Structure: [ path(fasta) ]

`ch_transcript_fasta`

Transcript sequence in fasta format.

Structure: [ path(fasta) ]

`ch_gtf`

Genome features in GTF format.

Structure: [ path(gtf) ]

`ch_index`

Directory containing the Salmon index.

Structure: [ path(index) ]

`make_index`

Whether to create salmon index before running salmon quant

Output

name

description

pattern

`index`

Directory containing the Salmon index, either the one supplied as input or
the one built by this subworkflow.

Structure: [ path(index) ]

`reads`

Subsampled FastQ reads.

Structure: [ val(meta), [ path(fastq) ] ]

*.{fq,fastq}{,.gz}

`results`

Folder containing the quantification results for a specific sample.

Structure: [ val(meta), path(results) ]

`json_info`

File containing meta information from Salmon quant,
which could be used to infer strandedness among other things.

Structure: [ val(meta), path(json) ]

*info.json

`lib_format_counts`

File containing the library format counts.