[BUG] * --vep_cache_version: expected type: String, found: Integer (99)

[leipzig]

Check Documentation

I have checked the following places for your error:

• [X] nf-core website: troubleshooting
• [X] nf-core/sarek pipeline documentation

Description of the bug

* --vep_cache_version: expected type: String, found: Integer (99)

Steps to reproduce

Steps to reproduce the behaviour:

./nextflow run sarek-2.7.1  \
--input tiny-manta-https.gcs.tsv     \
--step 'mapping'     \
--outdir './results'             \
--nucleotides_per_second 1000.0                                              \
--aligner 'bwa-mem'  \
--markdup_java_options '-Xms4000m -Xmx7g'                        \
--cf_coeff 0.05          \
--cf_ploidy 2.0                                                                              \
--genome 'smallGRCh37'                                                                   \
--snpeff_db 'WBcel235.86'    \
--species 'caenorhabditis_elegans'   \
--igenomes_base 's3://ngi-igenomes/igenomes'     \
--genomes_base 'raw.githubusercontent.com/nf-core/test-datasets/sarek/reference'     \
--igenomes_ignore        \
--publish_dir_mode 'copy'        \
--validate_params            \
--max_multiqc_email_size '25.MB'             \
--tracedir './results/pipeline_info'             \
--cpus 8     \
--single_cpu_mem '7 GB'  \
--max_cpus 16    \
--max_memory '128.GB'    \
--max_time '240.h'   \
--custom_config_version 'master'     \
--vep_cache_version '99'         \
--custom_config_base 'https://raw.githubusercontent.com/nf-core/configs/master'  \
-w gs://somebucket

Expected behaviour

not treat vep_cache_version as numeric when it is quoted

Log files

• [X] The command used to run the pipeline

System

• Hardware: GCP
• Executor:
• OS:
• Version

Nextflow Installation

• Version: nextflow version 21.10.6.5660

Container engine

• Engine: Docker in GCP LS
• Image tag: sarek 2.7.1

Additional context

there is no type of quote that will solve this to my knowledge

[tdanhorn]

Don't know what OS/shell you are using, but Unix shells strip the quotes, so nextflow (or the pipeline) never gets to see them, i.e it makes no difference (in this case) if you put them there. If you really want quotes to be seen by the pipeline, \'99\' or "'99'" should do the trick. On the other hand, if something should be read as a string and the code autodetects a number and complains, because it thinks it is smarter than you, I'd call that a bug.

[maxulysse]

@leipzig sorry for late reply. As @tdanhorn said, it is indeed a bug which is fixed on the current dev.

[maxulysse]

@leipzig can you try that: --vep_cache_version \"99\"

[FriederikeHanssen]

Hm I think there is still something :fish: going on with the vep_cache_version number:

ERROR: Validation of pipeline parameters failed!
* --vep_cache_version: expected type: Number, found: String (104)

when running:

nextflow run nf-core/sarek -r dev -profile cfc \
--input samplesheet.csv \
--outdir ./results \
--genome GATK.GRCh38 \
--aligner bwa-mem2 \
--bwa false \
--save_reference \
-resume

Dev version: 5d0a0b9755

Edit: tried also --vep_cache_version \"104\", same thing Edit2: --vep_cache_version 104 works with no quotes. So something in the igenomes.config not quite right yet

[maxulysse]

So the issue with igenomes has been fixed. Afraid there's nothing we can do at the moment params from the command line, except using --schema_ignore_params and said params to avoid validation from the schema.

Closing the issue for now.