Closed splaisan closed 1 year ago
HI again Sam, Apparently the samplesheet I used wongtains more barcodes than there are barcodes in the fastq which lead to crash I re-ran with ./test_data/sample_sheet.csv and it now finished
I was misled by the example command included in the --help output
|||||||||| _____ ____ ___ ____ __ __ _____ _ _
|||||||||| | ____| _ \_ _|___ \| \/ | ____| | | __ _| |__ ___
||||| | _| | |_) | | __) | |\/| | _| _____| |/ _` | '_ \/ __|
||||| | |___| __/| | / __/| | | | |__|_____| | (_| | |_) \__ \
|||||||||| |_____|_| |___|_____|_| |_|_____| |_|\__,_|_.__/|___/
|||||||||| wf-bacterial-genomes v0.4.0-g70714be
--------------------------------------------------------------------------------
Typical pipeline command:
nextflow run epi2me-labs/wf-bacterial-genomes \
--fastq 'wf-bacterial-genomes-demo/isolates_fastq' \
--isolates \
--reference_based_assembly \
--reference 'wf-bacterial-genomes-demo/ref/ref.fasta.gz' \
--sample_sheet 'wf-bacterial-genomes-demo/isolates_sample_sheet.csv'
maybe just edit this in the next version to use the right sample_sheet.csv
cheers,
@splaisan Thanks for pointing that out, I'll raise a ticket!
nice report, looking forward to see my own data there!
Operating System
Ubuntu 22.04
Other Linux
No response
Workflow Version
v0.4.0-g70714be
Workflow Execution
Command line
EPI2ME Version
No response
CLI command run
nextflow run epi2me-labs/wf-bacterial-genomes --fastq ./test_data/fastq --isolates --reference_based_assembly --reference ./test_data/ref/reference.subseq.fa.gz --sample_sheet ./test_data/isolates_sample_sheet.csv --out_dir test_run
Workflow Execution - CLI Execution Profile
None
What happened?
Relevant log output
Application activity log entry
No response