I want to run 3 samples of WGS.
I prepared uBAM files from fastq.
However, I can't go further due to absence of flowcell_unmapped_bams_list file.
How can I make this from uBAM or fastq?
I've answered this a bit in your other thread, but I do need additional information from you there in order to figure out what the flowcell_unmapped_bams_list refers to. Once we figure that out, I can answer your question here.
I'm trying to run the Method "gatk/pre-processing-hg38-gatk4" and I have the same question about what is supposed to go into the flowcell_unmapped_bams_list file. I'm getting the error message "PairedEndSingleSampleWorkflow.flowcell_unmapped_bams_list -
Expected single value for workflow input, but evaluated result set was empty" but I couldn't figure out how to fix the error from the other thread referred to above. Any suggestions?? Thanks!
@buchnerd Looking into this right now and will get back to you soon!
@buchnerd The flowcell_unmapped_bams_list is just a list of input ubam files from a single sample. “One or more read groups, one per uBAM file, all belonging to a single sample (SM)” as listed in the WDL requirements! The format of what this should look like can be found in this link of the json file. This list is essentially used to scatter and align the input bam files in parallel. Let us know if this helps!