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I would look at how the nf-core pipelines do it. For example it looks like nf-core/rnaseq defines separate inputs for the MULTIQC process: https://github.com/nf-core/rnaseq/blob/master/modules/local/multiqc/main.nf |
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Hi,
I'm new to NextFlow so forgive me if I've missed something very basic here. I'm trying to build a pipeline with the following steps:
I've tried to run the pipeline. All steps work except the final MultiQC process where I get an error:
However, checking the output folders - there are no duplicate file names. Furthermore, I've tried to avoid any collision by naming prefixing the 1M subsampled FASTQ files with "1M-" - so they do have distinct names from the post-trimming FASTQ files.
Any help would be much appreciated!
My pipeline:
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