process tcoffee { tag {fasta} // publishDir "${params.outdir}/tcoffee" //not working publishDir "${baseDir}/results/tcoffee", mode: 'copy' container 'quay.io/biocontainers/t_coffee:11.0.8--py27pl5.22.0_5' input: path(fasta) output: path("${fasta}.aln") script: """ t_coffee -seq $fasta -outfile ${fasta}.aln """ }