Issue with running the CLIP-seq pipeline with manually specified genome inputs

Flow App
1

Issue with running the CLIP-seq pipeline with manually specified genome inputs

Dear Flow team,

I recently tried to run CLIP-seq analysis pipeline by manually specifying genome input files. I ran into the problem that when I try to manually specify the genome fasta file from the dropdown menu (so not specifying the prepare genome execution), no files are shown, even though I have uploaded them and the fasta file that I could use is also public.

Same goes when I try to manually select the GTF file.

I attached three screnshots that show that I have uploaded the data, and the empty menus when I try to select these genome files for running the CLIP-seq pipeline.

owned_data
owned_data2437×734 97.3 KB

select_fasta_empty_menu
select_fasta_empty_menu1962×1047 117 KB

select_gtf_empty_menu
select_gtf_empty_menu1809×984 59.8 KB

I would really appreciate the help on this.

2

Hi Klara, thanks very much for reporting this - we’re looking into this now and will get back to you with a fix ASAP - cheers

3

I have the exact same issue - I can’t manyally specify the Prepared CLIP-Seq genomes on the CLIP-seq pipeline. The issue seems to occur randomly, but since last week I consistently do not see any of the recently prepared CLIP-Seq Genomes.

4

Hi all - this should be resolved permanently now. It was an issue with some special characters in the regex for these specific fields that has now been fixed.