The sample-sheet only contains normal-samples error

[ashpsnair]

Description of the bug

I have been processing tumor normal samples using sarek and I have results for 6/14 samples
The pipeline stopped and I tried re-running it but no luck. What I am trying now is to run just one sample and I am getting this error:

The sample-sheet only contains normal-samples, but the following tools, which were requested with "--tools", expect at least one tumor-sample : mutect2
Missing process or function Channel.empty([[]])

Please note that this sample was already processed using sarek and I have annotated vcf (in another directory), I was doing this exercise as a part of debugging.

There was a previous issue reported: #1260 (I tried the solutions there but it isnt working for me)

Command used and terminal output

My NF code:

nextflow run nf-core/sarek \
   -profile singularity \
   --use_annotation_cache_keys \
   --input path/to/my/pwd/samplesheet.csv \
   --outdir path/to/my/pwd/folder/YS-8-14/ \
   --tools mutect2,vep

This is my samplesheet:

patient,sex,status,sample,lane,fastq_1,fastq_2
patient01,XY,0,N01,lane_1,/home/project/11003581/Data/YS-analysis/raw_data/N01_1.fq.gz,/home/project/11003581/Data/YS-analysis/raw_data/N01_2.fq.gz
patient01,XY,1,T01,lane_1,/home/project/11003581/Data/YS-analysis/raw_data/T01_1.fq.gz,/home/project/11003581/Data/YS-analysis/raw_data/T01_2.fq.gz

Relevant files

This is my .nextflow.log
nextflow.log

System information

Nextflow version: 24.10.1 build 5930
I am running it in HPC- Linux
Version of nf-core/sarek: 3.4.4
container: singularity

[FriederikeHanssen]

Hey! Yes ths is a known issue with the latest nextflow release. We have fixed this on dev. In the meantime, using the previous stable release of nextflow should circumvent this: #1622

[ashpsnair]

Hi!
Thanks for helping me! The issue seems to be resolved as I am now able to run the pipelines.

I have reverted back to an earlier version of nextflow and I m re-running the variant calling steps using -resume arg.

My log says that the pipeline completed successfully with this message

"""
Plus 21 more processes waiting for tasks?~@?
-[nf-core/sarek] Pipeline completed successfully-
"""

However, my variant_calling/mutect/tumor_vs_normal/ folder contains only .mutect2.contamination.table and .mutect2.segmentation.table files and no vcf files.

Could this be related to the issue i posted earlier? or is it entirely different issue?