Unable to start

[dbarras2]

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]

Same error, looks like a typo in:

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

bfec02f#r148761964

[allyssonallan]

#1622

[asp8200]

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]

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]

#1624

This fix the problem