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guigolab / grape-nf

An automated RNA-seq pipeline using Nextflow
GNU General Public License v3.0
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grape-nf does not execute some steps #57

Open asalhab opened 3 years ago

asalhab commented 3 years ago

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 commented 3 years ago

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 commented 3 years ago

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

Best, Abdul