Predict the likely coding regions from the ORFs identified by Transdecoder.LongOrfs. Optionally include results from homology searches (blast/hmmer results) as ORF retention criteria.
This meta-wrapper can be used in the following way:
rule transdecoder_predict: input: fasta="test.fa.gz", # required input; optionally gzipped pfam_hits="pfam_hits.txt", # optionally retain ORFs with hits by inputting pfam results here (run separately) blastp_hits="blastp_hits.txt", # optionally retain ORFs with hits by inputting blastp results here (run separately) # you may also want to add your transdecoder longorfs result here - predict will fail if you haven't first run longorfs #longorfs="test.fa.transdecoder_dir/longest_orfs.pep" output: "test.fa.transdecoder.bed", "test.fa.transdecoder.cds", "test.fa.transdecoder.pep", "test.fa.transdecoder.gff3" log: "logs/transdecoder/test-predict.log" params: extra="" wrapper: "0.66.0/bio/transdecoder/predict"
Note that input, output and log file paths can be chosen freely. When running with
the software dependencies will be automatically deployed into an isolated environment before execution.