Closed alexmascension closed 10 months ago
The reason why your attempts to override --minAssignedFrags 1
via extra_salmon_quant_args
fail is, that the pipeline stops much earlier, namely during the infer strandedness step
.
To skip that step, you just have to provide the strandedness of your samples upfront in the samplesheet (forward
or reverse
instead of auto
).
If the strandedness is unknown to you and you must run it, then provide a custom config with a process selector
withName: '.*:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_QUANT' {
ext.args = '--skipQuant --minAssignedFrags 1'
}
Apart from this problem specifically, I wonder if the dualrnaseq pipeline wouldn't be more applicable to the research question you are seemingly working on?
Hi @MatthiasZepper , so far adding strandness seems to be doing the trick. I will keep you informed if anything happens. Regarding the dualrnaseq, seems like a good option, although I need to do a more specific analysis and does not quite fit.
Thanks!
Description of the bug
I am running the nfcore/rnaseq pipeline with human samples to do a next step in the recognition of bacterial reads. In this analysis I include several human samples, and two control samples with only bacterial reads. The aim of this step is (in part) to use the unmapped reads for further processing. The problem comes with the controls with bacterial reads that, unexpectedly, have only a few human reads, and I think this step conflicts with quantification by salmon. The error I receive is the following:
Additionally, it states
I don't really know what can I do, aside from removing the bacterial controls. I tried --aligner star_rsem, --skip_qualimap and --skip_pseudo_aligment and the error is the same. Can I run the pipeline without running salmon, or something like that?
Command used and terminal output
Relevant files
nextflow.log
System information
Nextflow version: 23.04.1.5866 Hardware: Desktop Executor: local Container engine: Docker OS: Ubuntu 22.04 Version of nf-core/rnaseq: v3.12.0