Problem 4

Solution

/*
 * Process 1C: Create the genome index file for STAR
 */

process '1C_prepare_star_genome_index' {

  input:
      file(genome) from genome_file (1)

  output:
      file(genome_dir) into genome_dir_ch (2)

  script:
  """
  mkdir genome_dir (3)

  STAR --runMode genomeGenerate \
       --genomeDir genome_dir \
       --genomeFastaFiles ${genome} \
       --runThreadN ${task.cpus}
  """
}

1	Take as input the `genome` file from `genome_file`.
2	The `output` is a `file`* called `genome_dir` and is added `into` a channel called `genome_dir_ch`. You can call the channel whatever you wish.
3	Creates the output directory that will contain the resulting STAR genome index.

* The file in this case is a directory however it makes no difference.