fasta_explore_search_plot_tidk

Uses Telomere Identification toolKit (TIDK) to identify the frequency of telomeric repeats along a sliding window for each sequence in the input fasta file. Results are presented in TSV and SVG formats. The user can specify an a priori sequence for identification. Possible a posteriori sequences are also explored and the most frequent sequence is used for identification similar to the a priori sequence. seqkit/seq and seqkit/sort modules are also included to filter out small sequences and sort sequences by length.

genomicstelomererepeatsearchplot

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

Description

Input

name:type

description

pattern

`ch_fasta :file`

Input assembly
Structure: [ val(meta), path(fasta) ]

*.{fsa/fa/fasta}

`ch_apriori_sequence :string`

A priori sequence
Structure: [ val(meta), val(sequence) ]

Output

name:type

description

pattern

`apriori_tsv :file`

Frequency table for the identification of the a priori sequence
Structure: [ val(meta), path(tsv) ]

*.tsv

`apriori_svg :file`

Frequency graph for the identification of the a priori sequence
Structure: [ val(meta), path(svg) ]

*.svg

`aposteriori_sequence :file`

The most frequent a posteriori sequence
Structure: [ val(meta), path(txt) ]

*.txt

`aposteriori_tsv :file`

Frequency table for the identification of the a aposteriori sequence
Structure: [ val(meta), path(tsv) ]

*.tsv

`aposteriori_svg :file`

Frequency graph for the identification of the a aposteriori sequence
Structure: [ val(meta), path(svg) ]

*.svg

`versions :file`

File containing software versions
Structure: [ path(versions.yml) ]

versions.yml