Split fastq files per RG

[bintriz]

I just reviewed all of the steps. One thing I'm not sure is whether each fastq files is split by RG again. This step is critical because not all of the data keep the separate fastq files per lane. Some data include reads which came from multiple lanes in one set of R1 and R2 fastq files. The purpose of reprocessing is to standardize RG separation using FLOW_CELL and LANE information.

[kdaily]

Can you highlight the parts of the existing pipeline that do this, please?

[bintriz]

https://github.com/bsmn/bsmn-pipeline/blob/master/genome_mapping/job_scripts/pre_2.split_fastq_by_RG.sh <https://github.com/bsmn/bsmn-pipeline/blob/master/genome_mapping/job_scripts/pre_2.split_fastq_by_RG.sh> is the part of splitting fasts by read group.

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On May 28, 2019, at 3:02 PM, Kenneth Daily ***@***.***> wrote: Can you highlight the parts of the existing pipeline that do this, please? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#5?email_source=notifications&email_token=AABYM65U77ARM5YC4F2K6N3PXWFTZA5CNFSM4HJQ4DPKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODWNIUTI#issuecomment-496667213>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AABYM67YOV5NPBNIICQKQULPXWFTZANCNFSM4HJQ4DPA>.

[kdaily]

I used this as a guide to build a standalone tool:

https://github.com/bsmn/fastq-split-readgroup-tool

It needs to be wrapped in CWL for it to work!

Another option that I tested is to use this package: https://github.com/kmhernan/gdc-fastq-splitter (I forked it here too: https://github.com/bsmn/gdc-fastq-splitter). It is not as fast as the shell script. I made the output of my version match this though.

[kdaily]

Built a Dockerfile to containerize this step: https://hub.docker.com/r/bsmnetwork/fastq-split-readgroup-tool