-r 0.1.0 fails with ERROR re. assembly_title

[Surbhigrewal]

Hi @DLBPointon

I ran the ascc version recommended on Slack with the below command and attached config yaml (renamed yaml.txt in attachment).

nextflow run sanger-tol/ascc \ -profile singularity \ --input samplesheet.csv \ --params-input input.yaml \ --outdir results \ --include ALL \ --exclude pacbio_barcodes,nr_diamond,kraken,fcs-adaptor \ --r 0.1.0

But the pipeline failed

ERROR ~ No such variable: assembly_title

-- Check script '/gpfs01/home/sbzsm11/.nextflow/assets/sanger-tol/ascc/./workflows/../subworkflows/local/yaml_input.nf' at line: 22 or see '.nextflow.log' file for more details

nextflow.log

yaml.txt

[DLBPointon]

This is quite odd as v0.1.0 no longer uses the yaml_input subworkflow, hence the use of --params-yaml.

You will need to change taxid value to 4601 in your case (without the quotes) otherwise blobtoolkit will crash, just as a warning.

Can you check and then clear your Nextflow cache please
echo $NXF_HOME/assets/sanger-tol/ascc <-- should show us whether you have a downloaded copy of the pipeline.

rm -rf $NXF_HOME/assets/sanger-tol/ascc to remove it.

On the next run of the pipeline it should then download a fresh copy of the branch, it should have done this time and i'm not sure why not.

Hopefully that will get us further.

[Surbhigrewal]

@DLBPointon That was my first time running ascc. Anyways, I followed your instructions and ran it again and got the same error.

[DLBPointon]

Just spoken on Slack, sent a command:

nextflow run sanger-tol/ascc -profile singularity --input samplesheet.csv -params-file test.yaml --outdir results --exclude pacbio_barcodes,nr_diamond,kraken,fcs-adaptor -r 0.1.0