Workflow is not operating on a collection

workflow
dataset-collection
#1

Hi,

I’m trying to use an RNAseq analysis workflow on a collection constructed by NCBI fastq dump of paired-end reads.

My workflow involves Trim Galore!, FastQC, HISAT2 and featurecounts; all I believe set to the needed settings to deal with paired-end collections. However despite the workflow claiming to be invoked nothing happens. Similar workflows just for paired-end files will work however the workflow is not operating for collections. I can use the programs individually on the collection and they work but never together as a workflow.

I have attached links to the workflow and an example collection for which it isn’t working for:

workflow: https://usegalaxy.org/u/t_little/w/rnaseqpairedendpairedcollection

history with dataset example: https://usegalaxy.org:/u/t_little/h/test

Best wishes,
Tim.

#2

Hi - Add in an “input” paired-end collection dataset to your workflow before the Trim Galore! step.

This screenshot of a sample workflow in the editor shows how to make the connection:

workflow_collection_list_paired_input
workflow_collection_list_paired_input.png2432×1024 307 KB