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nf-core / sarek

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
https://nf-co.re/sarek
MIT License
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SPRING format support #1418

Open kunstner opened 4 months ago

kunstner commented 4 months ago

Description of feature

Hi, we are storing our sequencing data in spring-format to reduce disc space. Do you plan to support spring-format besides fastq for sequencing reads in the near future? Best, Axel

FriederikeHanssen commented 4 months ago

So far we haven't had any plans for this. Can you elaborate what would be needed for this? from quick googleing: just a conversion step for spring->fastq?

kunstner commented 4 months ago

Yes, basically it should just perform the conversion to fastq (gzip-ed) and next sarek starts as usual.

Here my outline:

The basic idea would be to use spring compressed files (see below for references) in the sample sheet.

The sarek workflow would take the spring files, performs the decompression and runs the sarek pipeline as usual.

./spring -d -i file.spring -o file_1.fastq.gz file_2.fastq.gz -g

Publication https://academic.oup.com/bioinformatics/article/35/15/2674/5232998

github https://github.com/shubhamchandak94/Spring