Our pipeline normally operates on paired FASTQ files with read lengths of 42bp and 26bp in R1 and R2 respectively. Recently, we’ve used an alternative sequencing provider and now our R1 and R2 are 150bp in length. This greatly increases the size of our FASTQ files and downstream files like BAM file…

You don’t actually need to mv or rename the file here. It’s not adding anything to the process. Instead, just capture the original file, then rename it when you need to use it. process initial_feature_count{ tag "$sample_id" input: tuple val(sample_id), path(sorted_bam) path(gtf) output…

Hi, I have the same issue using the pipeline nf-core/cellranger v 2.7 while making a custom reference with cellranger aligner. I seems that the star index is moved at the end by the cellranger executable and I have this same error in an AWSBATCH environment using fusion/wave. Thx,

Renaming large files causing possible Fusion error

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didillysquat (Benjamin C C Hume) July 3, 2024, 10:23pm 2

This seems to be the same issue: Using mv command in AWS environment with fusion

And I can confirm that replacing offending mv commands with cp, although not ideal, resolves the issue.

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Renaming large files causing possible Fusion error

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