Liftoff allows single base introns

[GallVp]

Description of the bug

Single base introns do not make sense and also breaks the GXF_FASTA_AGAT_SPADDINTRONS_SPEXTRACTSEQUENCES subworkflow at

genepal/subworkflows/gallvp/gxf_fasta_agat_spaddintrons_spextractsequences/main.nf

Line 64 in 24a8f50

.collect { el -> [ el.id, "${el.seqString[0..1]}${el.seqString[-2..-1]}" ].join('\t') }

Command used and terminal output

No response

Relevant files

No response

System information

plant-food-research-open/genepal 0.4.0

[GallVp]

Use agat/sp_sp_flag_short_introns.pl to mark any intron shorter than 10 and filter the corresponding genes. Relevant issues and PRs,

• Added agat/spflagshortintrons and updated modules GallVp/nxf-components#42
• new module: AGAT/SPFLAGSHORTINTRONS nf-core/modules#6963

[GallVp]

There are cases where agat/sp_sp_flag_short_introns.pl version quay.io/biocontainers/agat:1.4.1--pl5321hdfd78af_0 does not flag 1 bp introns. See NBISweden/AGAT#516

This results in a pipeline crash by gxf_fasta_agat_spaddintrons_spextractsequences splice motif extraction logic. The crash can be averted by assigning '' as a motif for less than 4 bp introns.

[GallVp]

Fix PR for gxf_fasta_agat_spaddintrons_spextractsequences GallVp/nxf-components#51

[GallVp]

Fix PR for short intron crash #131