search

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
403 stars 405 forks source link

Restart from step variantcalling fails on NGScheckmate #1615

Open FriederikeHanssen opened 2 months ago

FriederikeHanssen commented 2 months ago

Description of the bug

ERROR nextflow.processor.TaskProcessor - Error executing process > 'NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:BAM_NGSCHECKMATE:BCFTOOLS_MPILEUP (1)'

Caused by:
  Not a valid path value: '../data/references/Homo_sapiens/GATK/GRCh38/Annotation/NGSCheckMate/SNP_GRCh38_hg38_wChr.bed'

NGSCHeckmate should not even be running

ae/f697b0] process > NFCORE_SAREK:SAREK:BAM_TO_CRAM (sample_01X)                                                                                      [100%] 1 of 1, cached: 1 ✔
[-        ] process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS                                                                    [  0%] 0 of 1
[-        ] process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH                                                                          [  0%] 0 of 1
[-        ] process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:BAM_NGSCHECKMATE:BCFTOOLS_MPILEUP                                                               -
[-        ] process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:BAM_NGSCHECKMATE:NGSCHECKMATE_NCM                                                               -

Command used and terminal output

nextflow run nf-core/sarek -r 3.4.2 -latest -profile docker --input data/markduplicates_no_table_local.csv --outdir ./test_single_sample --igenomes_base ../data/references --step variant_calling --tools cnvkit,
 strelka,deepvariant,haplotypecaller -with-tower --save_output_as_bam  --max_memory 4.GB --max_cpus 2 -resume

Relevant files

No response

System information

sarek: 3.4.2

michael-ford commented 1 month ago

I get this same error even when not using -resume and is preventing me from running Sarek.

Not a valid path value: './igenomes/Homo_sapiens/GATK/GRCh38/Annotation/NGSCheckMate/SNP_GRCh38_hg38_wChr.bed'

I have confirmed that the file does in fact exist in the specified location.