ieres-amgen

I encountered the exact same error; has there been any fix for this? Thanks!

FYI, the error seems sporadic--it did not occur in a re-run using the exact same data & parameters.

Hi @chris-cheshire, I am not particularly fluent with nextflow, but I did try splitting the pipe up to ascertain the cause of the break, and found that the `samtools view`...

I found that I was able to resolve by replacing the current process for collecting fragment lengths with the below implementation of Picard CollectInsertSizeMetrics. I note a custom process label...

To give some further context, when inputting very large FASTQ files, the .splitFastq implementation currently being used will in INPUT_CHECK will: 1. Read and decompress every imported FASTQ.gz 2. Parse...

@Krithika-Bhuvan, this thread is about changing the general way split_fastq is implemented, not troubleshooting its current functionality. Based on what you wrote, my guess is that you encounter issues because...

No, to my knowledge, part of the disadvantage of not having this in a dedicated process is that there is no way to check on progress.

+1!