8000 Incomplete pre-processing when running from "--step prepare_recalibration"? · Issue #1875 · nf-core/sarek · GitHub
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DHelix opened this issue Apr 28, 2025 · 0 comments
Open

Incomplete pre-processing when running from "--step prepare_recalibration"? #1875

DHelix opened this issue Apr 28, 2025 · 0 comments
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@FriederikeHanssen
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3.6

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@DHelix
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DHelix commented Apr 28, 2025

Hi,

First of all, thanks so much for developing this pipeline!
I'm very new to variant calling and nf-core/sarek, so apologies in advance for any naive questions.

I'm working on normal-tumor pairs and have aligned BAM files with duplicates already marked.

When I started the pipeline from --step markduplicates, it finished without any errors and seemed to complete all pre-processing steps from marking duplicates to recalibration.
However, when I started the pipeline from --step prepare_recalibration, it also finished without any errors but seemed to stop before recalibration.

Here are the details from when I ran with --step markduplicates

nextflow run nf-core/sarek \
-r 3.5.1 \
-profile singularity \
-c sys.config \
-params-file params_ct01chr7p_mkDup.yaml \
--step markduplicates

params_ct01chr7p_mkDup.yaml

input: '/pipeline_test/nfcore_sarek/sample_sheet/ss_ct01chr7p_mkDup.csv'
outdir: '/pipeline_test/nfcore_sarek/output/ct01chr7p_mkDup'
genome: 'GATK.GRCh38'

ss_ct01chr7p_mkDup.csv

patient,status,sample,lane,bam,bai
test,0,normal,L1,/pipeline_test/data/ct01_chr7p/normal_chr7p.bam,/pipeline_test/data/ct01_chr7p/normal_chr7p.bam.bai
test,1,tumor,L1,/pipeline_test/data/ct01_chr7p/tumor_chr7p.bam,/pipeline_test/data/ct01_chr7p/tumor_chr7p.bam.bai

Here are the details from when I ran with --step prepare_recalibration

nextflow run nf-core/sarek \
-r 3.5.1 \
-profile singularity \
-c sys.config \
-params-file params_ct01chr7p_prepReCal.yaml \
--step prepare_recalibration

params_ct01chr7p_prepReCal.yaml

input: '/pipeline_test/nfcore_sarek/sample_sheet/ss_ct01chr7p_prepReCal.csv'
outdir: '/pipeline_test/nfcore_sarek/output/ct01chr7p_prepReCal'
genome: 'GATK.GRCh38'

ss_ct01chr7p_prepReCal.csv

patient,status,sample,lane,bam,bai
test,0,normal,L1,/pipeline_test/data/ct01_chr7p/normal_chr7p.bam,/pipeline_test/data/ct01_chr7p/normal_chr7p.bam.bai
test,1,tumor,L1,/pipeline_test/data/ct01_chr7p/tumor_chr7p.bam,/pipeline_test/data/ct01_chr7p/tumor_chr7p.bam.bai

Thanks so much for your help in advance!
Best,
Dan
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