profiles { docker { docker.temp = 'auto' docker.enabled = true process { $index_fasta { container = "bowtie:1.2.2" } $mapping_fastq { container = "bowtie:1.2.2" } } } sge { process{ $index_fasta { beforeScript = "module purge; module load Bowtie/1.2.2" } $mapping_fastq { beforeScript = "module purge; module load SAMtools/1.7; module load Bowtie/1.2.2" } } } }