Original VGP workflows may be helpful

[fubar2]

There is an interesting resource available in 3 year old VGP processing code that may provide the logic for some of the required work.

For example this might be the basis for Nadolina's decontaminated curation request.

That material, updated to suit future VGP requirements, could be easier to translate into tools and workflows than NF DDL :)
Certainly easier than starting with a blank slate.

Below is an edited essence of the decontamination pipeline.
Uses Kraken, a mitochondrial blast search, and dustmasking - those are already available as tools I'd guess so relatively easy to get a workflow prototyped using the logic and data flows in this code.

tr a-z A-Z < $scaffs | \
    dustmasker -level 40 -out $newdir/masked_$scaffs -outfmt 'fasta'  
tr [:lower:] 'N' < $newdir/masked_$scaffs > $newdir/N_sub_masked_$scaffs
tr [:lower:] 'N' < $newdir/masked_$scaffs > $newdir/N_sub_masked_$scaffs
name=kraken.$genome_id
script=$decontam/RELEASE_THE_KRAKEN3.sh
sbatch -p vgl -c $cores --error=$logs --output=$logs $script $newdir $scaffs $scaffList | awk '{print $4}' > kraken_jid

name=mitoBlast.$genome_id 
script=$decontam/submit_blast_mito_2.sh
sbatch -p vgl -c $cores --error=$logs --output=$logs \
    $script $newdir/N_sub_masked_$scaffs $newdir/mito_blast_$scaffs $scaffList | awk '{print $4}' > mito_jid

jid1=`cat kraken_jid` ## Creating dependencies to delay removal of scaffolds until kraken and mito-blast are both complete. 
jid2=`cat mito_jid`
script=$decontam/clean_fasta.sh
sbatch -p vgl --error=$logs --output=$logs --dependency=afterok:$jid1,$jid2 \
    $script $scaffs $newdir/trimmed_$scaffs $scaffList $newdir/mito_scaff_names.txt $newdir

Anyone find any decontamination steps in TreeVal? Perhaps it needs some?