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nf-core / sarek

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
https://nf-co.re/sarek
MIT License
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Unable to start #1725

Open dbarras2 opened 2 weeks ago

dbarras2 commented 2 weeks ago

Description of the bug

Dear sarek developers,

First of all, congrats and thanks for your work.

I am new to the Nextflow/nf-core field and I am trying to run the pipeline with my own MOUSE dataset but I get the following error:

[- ] process > NFCORE_SAREK:PREPARE_GENOME:BWAMEM1_INDEX - [- ] process > NFCORE_SAREK:PREPARE_GENOME:BWAMEM2_INDEX - [- ] process > NFCORE_SAREK:PREPARE_GENOME:DRAGMAP_HASHTABLE - [- ] process > NFCORE_SAREK:PREPARE_GENOME:GATK4_CREATESEQUENCEDICTIONARY - [- ] process > NFCORE_SAREK:PREPARE_GENOME:MSISENSORPRO_SCAN - [- ] process > NFCORE_SAREK:PREPARE_GENOME:SAMTOOLS_FAIDX - [- ] process > NFCORE_SAREK:PREPARE_GENOME:TABIX_BCFTOOLS_ANNOTATIONS - [- ] process > NFCORE_SAREK:PREPARE_GENOME:TABIX_DBSNP - [- ] process > NFCORE_SAREK:PREPARE_GENOME:TABIX_GERMLINE_RESOURCE - [- ] process > NFCORE_SAREK:PREPARE_GENOME:TABIX_KNOWN_SNPS - [- ] process > NFCORE_SAREK:PREPARE_GENOME:TABIX_KNOWN_INDELS - [- ] process > NFCORE_SAREK:PREPARE_GENOME:TABIX_PON - Missing process or function Channel.empty([[]])

-- Check script '/home/localadmin/.nextflow/assets/nf-core/sarek/main.nf' at line: 342 or see '.nextflow.log' file for more details

Command line: nextflow run nf-core/sarek \ -profile singularity \ --genome GRCm38 \ --input /media/localadmin/DATA/dbarras/Nextflow/WES_mouse_BRCA1/samplesheet.csv \ --outdir /media/localadmin/DATA/dbarras/Nextflow/WES_mouse_BRCA1/

The dataset comes from an AVITI paired-end machine. (Twist exome mouse library)

I was able to run the test dataset using singularity.

Thanks so much in advance for your help!

David

Command used and terminal output

Command line: nextflow run nf-core/sarek \ -profile singularity \ --genome GRCm38 \ --input /media/localadmin/DATA/dbarras/Nextflow/WES_mouse_BRCA1/samplesheet.csv \ --outdir /media/localadmin/DATA/dbarras/Nextflow/WES_mouse_BRCA1/

Relevant files

samplesheet.csv nextflow.log

System information

Hardware: Desktop Executor: local OS: Ubuntu 22.04.3 LTS Nextflow version: 24.10.0.5928 Engine: singularity nf-core version: 3.0.2

allyssonallan commented 2 weeks ago

Same error, looks like a typo in:

Channel.empty([]) at main... I am not sure. You can check it out my comment:

https://github.com/nf-core/sarek/commit/bfec02fcda0bfcdb3ce1ced5792bcc9552d8b26f#r148761964

allyssonallan commented 2 weeks ago

1622

asp8200 commented 2 weeks ago

Try reverting to Nextflow v24.04.4. It can be done like this:

NXF_VER=24.04.4 nextflow run … <your parameters here>

The problem seems to first have appeared with NF 24.07.0-edge.

allyssonallan commented 2 weeks ago

It worked smoothly here after changing Channel.empty([]) to Channel.empty() in main.nf:

Here:

https://github.com/nf-core/sarek/blob/5cc30494a6b8e7e53be64d308b582190ca7d2585/main.nf#L180C203-L180C225

allyssonallan commented 2 weeks ago

https://github.com/nf-core/sarek/pull/1624

This fix the problem