Hi there. When I run sarek to get CNVKit results, CNVKit produces results for each lane within the sample folder. For example here is the directory structure sample1/ --sample1_lane1.cns --sample1_lane2.cns sample2/ --sample2_lane1.cns --sample2_lane2.cns Is this the intended behaviour?

Can you send us the command you used to run the pipeline, the samplesheet and the version? :)

nextflow run nf-core/sarek -r 3.8.1 --aligner parabricks -profile singularity,gpu --input samplesheet.csv --outdir sarek_results --ref genome/GRCh38.primary_assembly.genome.fa.gz --wes --intervals Twist_Oncology_DNA_CGP_hg38.bed -resume -c custom-parabricks.config --tools cnvkit --save_output_as_bam patient,sample,lane,fastq_1,fastq_2 EF3_Moderate_5ng,EF3_Moderate_5ng,C01_S3,ext_data/Twist_CGP_TrinityFreestyle_20260209/EF3_Moderate_5ng_C01_S3_R1_001.fastq.gz,ext_data/Twist_CGP_TrinityFreestyle_20260209/EF3_Moderate_5ng_C01_S3_R2_001.fastq.gz EF3_NA12878_50ng,EF3_NA12878_50ng,A05_S9,ext_data/Twist_CGP_TrinityFreestyle_20260209/EF3_NA12878_50ng_A05_S9_R1_001.fastq.gz,ext_data/Twist_CGP_TrinityFreestyle_20260209/EF3_NA12878_50ng_A05_S9_R2_001.fastq.gz EF3_NA12878_5ng,EF3_NA12878_5ng,B06_S12,ext_data/Twist_CGP_TrinityFreestyle_20260209/EF3_NA12878_5ng_B06_S12_R1_001.fastq.gz,ext_data/Twist_CGP_TrinityFreestyle_20260209/EF3_NA12878_5ng_B06_S12_R2_001.fastq.gz EF3_Mild_5ng,EF3_Mild_5ng,A01_S1,ext_data/Twist_CGP_TrinityFreestyle_20260209/EF3_Mild_5ng_A01_S1_R1_001.fastq.gz,ext_data/Twist_CGP_TrinityFreestyle_20260209/EF3_Mild_5ng_A01_S1_R2_001.fastq.gz EF3_Moderate_5ng,EF3_Moderate_5ng,D01_S4,ext_data/Twist_CGP_TrinityFreestyle_20260209/EF3_Moderate_5ng_D01_S4_R1_001.fastq.gz,ext_data/Twist_CGP_TrinityFreestyle_20260209/EF3_Moderate_5ng_D01_S4_R2_001.fastq.gz EF3_Moderate_50ng,EF3_Moderate_50ng,D02_S16,ext_data/Twist_CGP_TrinityFreestyle_20260209/EF3_Moderate_50ng_D02_S16_R1_001.fastq.gz,ext_data/Twist_CGP_TrinityFreestyle_20260209/EF3_Moderate_50ng_D02_S16_R2_001.fastq.gz EF3_Severe_50ng,EF3_Severe_50ng,G02_S7,ext_data/Twist_CGP_TrinityFreestyle_20260209/EF3_Severe_50ng_G02_S7_R1_001.fastq.gz,ext_data/Twist_CGP_TrinityFreestyle_20260209/EF3_Severe_50ng_G02_S7_R2_001.fastq.gz EF3_Moderate_50ng,EF3_Moderate_50ng,C02_S15,ext_data/Twist_CGP_TrinityFreestyle_20260209/EF3_Moderate_50ng_C02_S15_R1_001.fastq.gz,ext_data/Twist_CGP_TrinityFreestyle_20260209/EF3_Moderate_50ng_C02_S15_R2_001.fastq.gz EF3_Mild_50ng,EF3_Mild_50ng,B02_S14,ext_data/Twist_CGP_TrinityFreestyle_20260209/EF3_Mild_50ng_B02_S14_R1_001.fastq.gz,ext_data/Twist_CGP_TrinityFreestyle_20260209/EF3_Mild_50ng_B02_S14_R2_001.fastq.gz EF3_Mild_50ng,EF3_Mild_50ng,A02_S13,ext_data/Twist_CGP_TrinityFreestyle_20260209/EF3_Mild_50ng_A02_S13_R1_001.fastq.gz,ext_data/Twist_CGP_TrinityFreestyle_20260209/EF3_Mild_50ng_A02_S13_R2_001.fastq.gz EF3_Severe_5ng,EF3_Severe_5ng,G01_S18,ext_data/Twist_CGP_TrinityFreestyle_20260209/EF3_Severe_5ng_G01_S18_R1_001.fastq.gz,ext_data/Twist_CGP_TrinityFreestyle_20260209/EF3_Severe_5ng_G01_S18_R2_001.fastq.gz EF3_Severe_50ng,EF3_Severe_50ng,F02_S6,ext_data/Twist_CGP_TrinityFreestyle_20260209/EF3_Severe_50ng_F02_S6_R1_001.fastq.gz,ext_data/Twist_CGP_TrinityFreestyle_20260209/EF3_Severe_50ng_F02_S6_R2_001.fastq.gz EF3_Severe_5ng,EF3_Severe_5ng,F01_S17,ext_data/Twist_CGP_TrinityFreestyle_20260209/EF3_Severe_5ng_F01_S17_R1_001.fastq.gz,ext_data/Twist_CGP_TrinityFreestyle_20260209/EF3_Severe_5ng_F01_S17_R2_001.fastq.gz EF3_Mild_5ng,EF3_Mild_5ng,B01_S2,ext_data/Twist_CGP_TrinityFreestyle_20260209/EF3_Mild_5ng_B01_S2_R1_001.fastq.gz,ext_data/Twist_CGP_TrinityFreestyle_20260209/EF3_Mild_5ng_B01_S2_R2_001.fastq.gz EF3_NA12878_5ng,EF3_NA12878_5ng,A06_S11,ext_data/Twist_CGP_TrinityFreestyle_20260209/EF3_NA12878_5ng_A06_S11_R1_001.fastq.gz,ext_data/Twist_CGP_TrinityFreestyle_20260209/EF3_NA12878_5ng_A06_S11_R2_001.fastq.gz EF3_NA12878_50ng,EF3_NA12878_50ng,B05_S10,ext_data/Twist_CGP_TrinityFreestyle_20260209/EF3_NA12878_50ng_B05_S10_R1_001.fastq.gz,ext_data/Twist_CGP_TrinityFreestyle_20260209/EF3_NA12878_50ng_B05_S10_R2_001.fastq.gz nextflow version 25.10.4.11173 sarek_3.8.1

Ah yes, this is due to a bug in the parabricks implementation where we did not handle the lanes properly. It has been fixed and will be part of the next release. Until then you can either switch to dev or use another aligner.

AH thank you! Is there a roadmap for the next release?

Certainly somewhen after the hackathon (which is next week). But if you really need this fix fast in a release we can try and cut the release as soon as possible after that.

Do you know if this is fixed now?

It is fixed but not yet released. You can use

-r dev

if you want to test it out

Great, thanks!!