Solution
/*
* Process 1B: Create a FASTA genome sequence dictionary with Picard for GATK
*/
process '1B_prepare_genome_picard' {
input:
file genome from genome_file (1)
output:
file "${genome.baseName}.dict" into genome_dict_ch (2)
script:
"""
PICARD=`which picard.jar`
java -jar \$PICARD CreateSequenceDictionary R= $genome O= ${genome.baseName}.dict
"""
}
| 1 | Take as input the genome file from genome_file |
| 2 | Give as output the file ${genome.baseName}.dict and adds it to the channel genome_dict_ch |