Closed
Description
openedon Sep 6, 2023
Description of the bug
The default location for SnpEff cache on AWS S3 is empty:
s3://annotation-cache/snpeff_cache/
Hence, the pipeline results in error:
Execution cancelled -- Finishing pending tasks before exit
-[nf-core/sarek] Pipeline completed with errors-
WARN: Input tuple does not match input set cardinality declared by process `NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_SNPEFF:SNPEFF_SNPEFF` -- offending value: [/annotation-cache/snpeff_cache]
WARN: Killing running tasks (87)
ERROR ~ Error executing process > 'NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_SNPEFF:SNPEFF_SNPEFF (1)'
Caused by:
Not a valid path value type: org.codehaus.groovy.runtime.NullObject (null)
Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line
-- Check '.nextflow.log' file for details
Join mismatch for the following entries: key=[id:LC_AC35_vs_LC_AC00, normal_id:LC_AC00, patient:LC_AC, sex:XX, tumor_id:LC_AC35] values=
Staging foreign file: s3://annotation-cache/vep_cache
ERROR ~ Stream Closed
-- Check '.nextflow.log' file for details
Command used and terminal output
nextflow run nf-core/sarek \
-latest \
-profile docker \
--step mapping \
--tools freebayes,mpileup,mutect2,strelka,manta,tiddit,ascat,cnvkit,controlfreec,msisensorpro,snpeff,vep,merge \
--input 'samplesheet_sarek.csv' \
--outdir '/data/nextflow/sarek/results/' \
-work-dir '/data/nextflow/sarek/work/' \
-c 'custom.config' \
-r dev \
-resumeRelevant files
No response
System information
N E X T F L O W ~ version 23.08.1-edge
local
Docker
Linux
nf-core/sarek dev
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