{"description": "Transcriptome index for salmon, produced with salmon index using selective alignment method. Improves quantification accuracy compared to the regular index.", "required_files": [], "required_assets": [{"key": "fasta", "default": "fasta", "description": "fasta asset for genome"}, {"key": "fasta_txome", "default": "fasta_txome", "description": "fasta asset for transcriptome"}], "required_parameters": [{"key": "threads", "default": "8", "description": "Number of threads to use for parallel computing"}, {"key": "kmer", "default": "31", "description": "The length of kmer to use to create the indices"}], "container": "combinelab/salmon", "assets": {"salmon_sa_index": "."}, "command_list": ["grep '^>' {fasta} | cut -d ' ' -f 1 > {asset_outfolder}/decoys.txt", "sed -i.bak -e 's/>//g' {asset_outfolder}/decoys.txt", "rm {asset_outfolder}/decoys.txt.bak", "cat {fasta_txome} {fasta} > {asset_outfolder}/gentrome.fa", "salmon index -t {asset_outfolder}/gentrome.fa -d {asset_outfolder}/decoys.txt -i {asset_outfolder} -k {kmer} -p {threads}", "rm {asset_outfolder}/gentrome.fa {asset_outfolder}/decoys.txt"]}