IGV cannot open the session file

[ktrns]

Description of the bug

Hi there,

The pipeline produces an IGV session file. IGV can no longer open this file, as the "genome" folder is missing in the results folder, and the genome file cannot be found. This has been briefly discussed in the slack channel, and I wanted to copy-paste it into the issue section over here so it doesn't get lost.

The genome folder has been there before, so I suppose that this bug came with one of the recent updates.

By manually copying the genome.fa to the correct location, and generating an index, I can again open the IGV session file.

Best wishes & thanks
Katrin

Command used and terminal output

nextflow run $base/nf-core/atacseq/workflow --input $base/samples.csv \
--outdir $base/results \
--genome GRCm39 \
--read_length 100 \
-c $base/nf-core/atacseq/dcgc.config \
-c $base/nf-core/atacseq/genomes.config

Relevant files

No response

System information

No response

[JoseEspinosa]

The reason for this behavior is that the save_reference parameter needs to be set to make the fasta file available in the genome folder, see here. But it is true that this is not documented and probably, makes little sense. So I think we should revert this behavior.

[JoseEspinosa]

This should be fixed now in dev, if you find any further issue do not hesitate to reopen the issue.