Add ability to explore various values of AED and LD.

[mahesh-panchal]

Adds parameters to allow for a parameter sweep across values of AED and locus distance. Closes https://github.com/NBISweden/pipelines-nextflow/issues/57

Changes the params.enable_conda to conda.enabled. Closes #94

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Additionally fixes other workflows broken by module updates and other nf-core tweeks.

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Tests run:

nextflow run main.nf -profile test,docker,gitpod --subworkflow 'abinitio_training' -resume  # passes
nextflow run main.nf -profile test,docker,gitpod --subworkflow 'annotation_preprocessing' -resume # passes
nextflow run main.nf -profile test,docker,gitpod --subworkflow 'functional_annotation' -resume # fails: Interproscan is still flaky
nextflow run main.nf -profile test,docker,gitpod --subworkflow 'transcript_assembly' -resume # passes

[LucileSol]

I have not tested it yet, planning to do that next week.

[LucileSol]

The pipeline seems to be splitting the gff file into mrna.gff and trna.gff, four times (I gave it 2 sets of parameters). It would be more efficient/faster if it does it only once.

[LucileSol]

I got an error message :

Error executing process > 'ABINITIO_TRAINING:BLAST_RECURSIVE (codingGeneFeatures.filter.longest_cds.complete.good_distance_proteins)'

Caused by:
  Process `ABINITIO_TRAINING:BLAST_RECURSIVE` input file name collision -- There are multiple input files for each of the following file names: blast_db

[mahesh-panchal]

Yes, I'm debugging that now. I just updated the test profile.

[mahesh-panchal]

😮 All tests pass 🚀

[mahesh-panchal]

Going to add summary script too now. https://github.com/NBISweden/annotation-cluster/wiki/Old-Abinitio_pipeline

[mahesh-panchal]

All tests pass locally.