params.file = "example/proteins.fas" Channel.fromPath(params.file).into{for_blast; for_signalp} process blast_swissprot { input: file fasta from for_blast output: file "${fasta}.blast_swissprot.tsv" into blast_results script: """ module_blast_swissprot.py --fasta $fasta > ${fasta}.blast_swissprot.tsv """ } process convert_blast_swissprot { input: file result from blast_results output: file "${result}.json" into converted_blast_results script: """ convert_blast_swissprot.py ${result} > ${result}.json """ } process signalp { input: file fasta from for_signalp output: file "${fasta}.signalp.tsv" into signalp_results script: """ module_signalp.py --fasta $fasta > ${fasta}.signalp.tsv """ } process convert_signalp { input: file result from signalp_results output: file "${result}.json" into converted_signalp_results script: """ convert_signalp.py ${result} > ${result}.json """ }