grape-nf does not execute some steps

[asalhab]

Hi @emi80

I ran grape-nf with the following command inside a conda environment (However not all the tools were installed through conda):
nextflow -c /home/abdosa/.nextflow/assets/guigolab/grape-nf/resource.config run -qs 1 -without-docker -w work grape-nf --index readIndex.tsv --genome $genomeFasta --annotation $transcriptAnnotation --steps mapping,bigwig,quantification --genomeIndex $genomeIndex

with genomeFasta=GCA_000001405.15_GRCh38_no_alt_analysis_set.fna (I'm not sure if .fna of .fa matters)

It finished successfully without any error but without performing bigwig and quantification steps.
I attached the log file and the detailed nextflow.log

grape-nf.log
nextflow.log

Best,
Abdul

[emi80]

Hi @asalhab

apologies for the late reply. First of all, you don't need to specify the resource configuration file (and by the way the file has been moved in the config folder and renamed in the last release). About the main issue, the .fna extension is the problem here. Could you please change the extension to .fa and run the pipeline again? Let me know if that solves the issue (in principle it should).

Best,
Emilio

[asalhab]

Hi @emi80 Thanks for your reply. It worked when I use .fa instead of .fna

Best,
Abdul