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Hello,

I'm new in Nextflow use and I try to make a pipeline for RNA_Seq analysis in Nextflow.
It looks like it works for different sample of fastq files until the Alignment steps.
From the Alignment steps it doesn't work anymore for different sample: it's just run the script for one sample and finish.
I use STAR for building the index and for the alignment step, in a pretty similar way than you in your script: https://github.com/nextflow-io/hack17-varcall/blob/master/solutions/fat_floor.adoc .
When I need to build the index (with STAR), I put the directory of the index in a channel. In the next process (Alignment with STAR), I take back the directory of the index from this channel and use it in the STAR command.
When I have different fastq files like, for example: "12CP.fastq", "6HP.fastq", "8HPT.fastq" of the Potatoes species, all process before Alignment run with all the samples and produce all the files. But from the BuildIndex and Alignment, it's running just for one sample and finish the pipeline without returning an error, like if all it's ok. Maybe it's because we can't use the same directory index for multiple STAR Alignment command ?
So I would know if your Nextflow script run for different sample? Or do you have the same problem?

Thank you for your attention
Best regards

Carole