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See error:
"Execution aborted due to an unexpected error
-- Check script '.nextflow/assets/nf-core/nanoseq/./workflows/../subworkflows/local/../../modules/local/graphmap2_align.nf' at line: 8 or see '.nextflow.log' file for more details
"
Expected behaviour
Graphmap2 pipeline stage to complete and for pipeline to continue.
Log files
Have you provided the following extra information/files:
The command used to run the pipeline (see point 1 above)
The .nextflow.log file
System
Hardware: internal server Kernel Linux 5.4.0-105-generic x86_64
Check Documentation
I have checked the following places for your error:
Description of the bug
Piepline crashes at the Grapmap2_Align stage
Steps to reproduce
Steps to reproduce the behaviour:
nextflow run nf-core/nanoseq --monochrome_logs --input /mnt/blah-blah-blah/samplesheet.csv --outdir /home/mike.harbourblah-blah-blah --protocol directRNA --skip_basecalling --skip_demultiplexing --aligner graphmap2 --quantification_method bambu -profile singularity --skip_bigbed --skip_bigwig --skip_pycoqc --skip_nanoplot --skip_fastqc --skip_multiqc --skip_qc
"Execution aborted due to an unexpected error
-- Check script '.nextflow/assets/nf-core/nanoseq/./workflows/../subworkflows/local/../../modules/local/graphmap2_align.nf' at line: 8 or see '.nextflow.log' file for more details
"
Expected behaviour
Graphmap2 pipeline stage to complete and for pipeline to continue.
Log files
Have you provided the following extra information/files:
.nextflow.log
fileSystem
Nextflow Installation
Container engine
Additional context
nextflow.log
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