Change sra-tools version and its implementation

[sk-sahu]

Problem

Based on error reported on slack about GTEx samples download issue. This is because lately the behaviour of accepting the key file in sra-tools changed.

Solution

• [x] Change sra-tools in container
• [x] Change download behaviour with latest version of sra-tools based on this slack thread from Anne

[sk-sahu]

With sra-tools=2.10.8

prefetch --ngc proj_id_key_file.ngc SRR1070208 -o SRR1070208
fasterq-dump --ngc key_file.ngc SRR1070208

This will generate -

• SRR1070208_1.fastq
• SRR1070208_2.fastq

Note

This download lot of files apart from *.sra (such as dependency files - GL* and NC*). We might want to increase the process get_accession instance disk size

[cgpu]

Note

This download lot of files apart from *.sra (such as dependency files - GL* and NC*). We might want to increase the process get_accession instance disk size

Thanks for looking into this @sk-sahu 👍 Let's test this tomorrow to see how much space is needed for all the files. We can delete the files in the same process as well, to decrease the size of workdirs if the jobs is resumable.

[sk-sahu]

For one example dependency files size given bellow, but with Nextflow's work directory need to check again.