Open julicudini opened 1 month ago
Should also be a bug report in demultiplex, we might have to do a release for 1.5.1 to fix this
cc @atrigila / @nschcolnicov
@julicudini Thank you very much for the detailed description and proposed solution, I'll fix this ASAP
Have you checked the docs?
Description of the bug
I noticed when running the nfcore/demultiplex pipeline with
cellranger_mkfastq
as the demultiplexer module that the outputs do not match what I get when I runcellranger mkfastq
(same version, and same version ofbcl2fastq
) on its own, independent of nextflow. I tracked down that this is not an issue with the demultiplex pipeline but instead thecellranger_mkfastq
module. What is missing is theouts/fastq_path/Sample_Project
dir, which contains the sample fastqs, whereas theouts/fastq_path
dir only contains the Undetermined fastqs (explained here):What this means is that the line that defines the output of cellranger mkfastq in main.nf as
outs/fastq_path/*.fastq.gz
only captures the Undetermined files and misses the actual sample files. Currently the line readspath "**/outs/fastq_path/*.fastq.gz", emit: fastq
and I was able to fix this by changing the line to
path("*_outs/outs/fastq_path/{*.fastq.gz,**/*.fastq.gz}"), emit: fastq
Which instead captures any fastq file in any nested dir. I think this is better than trying to infer the flowcell id in order to search the directory that may or may not be made. I have a PR that I can submit to make this small fixCommand used and terminal output
No response
Relevant files
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System information
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