Conversation
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@Magdoll do you have any small example data you can point me to that would help me here? Specifically I am looking for a subreads BAM as input to |
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@nh13 - do you really need subreads.bam. I know I wrote the ccs step in there, but at this point SQ2e generates ccs.bam directly off instrument and service providers will run ccs.bam and send that to customers. I'm waiting for the ccs.bam that is used for creating this protocol to become public in SRA. Hopefully soon. |
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Nope, so don’t need the CCS reads then, just didn’t want to overlook that step if needed. Also want to try it out on my end, but no big deal. |
nextflow/workflow/main.nf
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| ch_bams_by_sample = ch_in_lima_outputs | ||
| .join(ch_lima_bams) // join by barcode name key | ||
| .map { (key, sample, bam) -> (sample, bam) } // discard the key | ||
| .groupTuple() // collect all BAMs by sample name |
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@pditommaso I am requiring a CSV that gives the sample (patient) along with the forward and reverse barcodes used. Since the sample can have multiple F/R barcode pairs, I need to merge the BAMs after demultiplexing. I am trying to figure out a concise way of joining the output of lima (demultiplexing) with the metadata from the CSV, so I can group the BAMs to merge. Is this type of channel joining the idiomatic way, or would you recommend something different?
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it looks you have already improved it bd3d982. Can't think of anything better 👍
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@nh13 I have been busy updating our SARS-CoV-2 pipeline to DSL2 of late and just finished adding Nanopore support on Friday 😅 Be happy to consider adding |
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How about I get a working implementation here first as adding another/third code path in that repo seems too much for my limited free time at the moment. |
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Understandable. Happy to help where I can. |
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This is a work-in-progress PR to automate the steps described in https://github.com/Magdoll/CoSA/wiki/SARS-CoV-2-variant-calling-using-PacBio-HiFi-data#ccs. My motivation is to understand the process, including the inputs and outputs for all steps along the way.