Description

Run telomere/findtelomere on an assembly and motif string; optionally bgzip/tabix strand BED (*.fwd.telomere.bed, *.rev.telomere.bed) and windows files (*.windows or *.fwd.windows / *.rev.windows).

Input

Name
Description
Pattern

ch_reference (file)

Channel shape [ val(meta), path(reference) ].

ch_telomereseq (string)

Channel shape [ val(meta), val(telomere_motif) ] — DNA motif sequence string (same meta.id as ch_reference entries).

val_split_telomere (boolean)

When true, run FindTelomereWindows in --split mode (*.fwd.windows, *.rev.windows). When false, emit a single *.windows file.

val_zip_bed (boolean)

When true, run htslib/bgziptabix on strand telomere BED outputs and all windows files from this sample (one HTSLIB task per file). When false, gz_index is an empty channel.

Output

Name
Description
Pattern

telomere (file)

[ val(meta), path(*.telomere) ] — merged motif-hit table from find_telomere.

telomere_bed_fwd (file)

[ val(meta), path(*.fwd.telomere.bed) ] (optional if tool emits).

telomere_bed_rev (file)

[ val(meta), path(*.rev.telomere.bed) ] (optional if tool emits).

windows_all (file)

[ val(meta), path(*.all.windows) ] when val_split_telomere is false; otherwise empty.

windows_fwd (file)

[ val(meta), path(*.fwd.windows) ] when split is true; otherwise empty.

windows_rev (file)

[ val(meta), path(*.rev.windows) ] when split is true; otherwise empty.

gz_index (file)

[ val(meta), path(*.gz), path(*.{tbi,csi}) ] per bgzip/tabixed file when val_zip_bed is true (from HTSLIB_BGZIPTABIX output/index join); empty when val_zip_bed is false.

Components

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