search

hartwigmedical / platinum

Run multiple Pipeline5 instances at once
GNU General Public License v3.0
10 stars 1 forks source link

Support for starting from Aligned BAM files #65

Open p-smirnov opened 6 months ago

p-smirnov commented 6 months ago

Hi Platinum Devs,

I am interested in running the HMFtools pipeline on GCP, but I already have my files aligned with bwa-mem. Is there support for starting with aligned BAMs using Platinum/could you point me to where I could try to hack it together?

Thank you!

p-smirnov commented 6 months ago

I also see that there is an option in pipeline5 to pass in ALIGNMENT_COMPLETE as the starting point. What I am not sure about is how to organize the files/pass in the URIs if the alignment was done outside the pipeline, could you give some guidance on this?

DFKoetsier commented 6 months ago

Hi, I have added a small section to the Readme on this here. Please note that starting from aligned BAMs could cause issues if the reference genome against which it is aligned is different from the one we use. If you do encounter such issues, the easiest solution is probably to convert the BAMs back to FASTQ and start Platinum from FASTQ.

DFKoetsier commented 6 months ago

Also, the support we offer on this repository is quite limited. The NextFlow implementation of our pipeline is better supported. You might want to consider using that instead.