In my pipeline nextflow, I create a channel with channel.fromSRA and the channel contains lots of heavy files.fastq.gz. Then I have a first process to unzip files and transform them in files.fasta and a second process to count kmers. Is it possible to remove files.gz after first process and remove files.fasta after the second process. Can someone explain me how to do? They are too heavy to keep them in the work directory. Thanks.
In my pipeline I use kmer-ssr to count kmers present on my genome sample.
First I create a reads_ch = Channel.fromSRA
In this channel there are 12 files (. fastq.gz) of 20 Gb each one.
Then the first process unzips them and transforms them in files.fasta.
Now in my work directory there are 12 more files of 80 Gb each one. So the work directory is now 1200 Gb.
The second process counts kmer present in reads and creates 12 files of 100 Gb each one. The work directory will be 2200 Gb.
The work directory is too heavy. I want to know how I can suppress the current file. fastq.gz after first process