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nf-core / rnavar

gatk4 RNA variant calling pipeline
https://nf-co.re/rnavar
MIT License
37 stars 32 forks source link

UNZIPPED files are not being properly staged when running on aws #135

Closed nschcolnicov closed 7 months ago

nschcolnicov commented 8 months ago

Description of the bug

When running a working command in AWS, the pipeline fails because it is not able to stage the unzipped file, it seems that the URL being used to stage the file is correct but has an additional "/" at the start [null] NOTE: Can't stage file file:///{my-s3-bucket-path}/Homo_sapiens.GRCh38.86.gtf/Homo_sapiens.GRCh38.86.gtf -- file does not exist -- Execution is retried (1) ERROR ~ Unable to re-submit taskNFCORE_RNAVAR:RNAVAR:PREPARE_GENOME:GTF2BED (1)``

Command used and terminal output

nextflow run nf-core/rnavar -profile bi,aws\
-r dev -latest \
--input $INPUT \
--outdir $OUTDIR \
-c $CONFIG \
--annotate_tools vep \
-resume

Relevant files

The config file contains custom ref files, and the input file is the test samplesheet provided with the pipeline files

System information

dev

nschcolnicov commented 7 months ago

I got confirmation that the problem was fixed with the PR, closing this issue