abinitio pipeline not copying proper folder into /projects/references/augustus/config/species/

[LucileSol]

I am running the abinitio pipeline with :

params.yml :

subworkflow: 'abinitio_training'
genome: 'genome.fa'
maker_evidence_gff: 'maker_evidence.gff'
species_label: 'Lin_leo'
codon_table: 1
aed_value:
  - 0.05
locus_distance:
  - 1500
outdir: 'results_leo'
maker_species_publishdir : '/projects/references/augustus/config/species/'

and the following command line :

nextflow run ~/git/NBIS/pipelines-nextflow -profile singularity,nbis -params-file params.yml

Instead of creating me a folder called Lin_leo in /projects/references/augustus/config/species/ It is creating me a folder called LD-1500_AED-0.05 in /projects/references/augustus/config/species/ with inside the folder Lin_leo.

My problem then is when I run maker, maker does not find the folder Lin_leo and then fail.

[mahesh-panchal]

The issue here is that you want to copy a selected folder after the pipeline has finished. Until we have automated selection of a best run, there's no way to know during the run which folder you want to copy. If we remove the AED or LD information, then files will collide I think. The only way to solve this in the current state is manual copying so you select the correct run. Edit: You only have one pairing in your example above, but then the workflow would need to calculate the number of pairings and only remove the aed and ld folder when the number of pairings is one.

[LucileSol]

I see so what I did was rerun the pipeline with my chosen parameter to have them directly copied in the augustus folder, but I see that just copying the folder would work (if given the proper species name).

[mahesh-panchal]

It would be nice to have a method to auto select, but we can also perhaps just have a make file/shell script with targets or something that one can just run to copy the folder and rename it. We can try that when I'm back