José Luis Villanueva-Cañas

Did you manage to reproduce the issue?

That's great! I just send you an email with the relevant files.

-resume [name_run] also doesn't seem to work, as it does not recover the bwa-mem2 or fastqc processes, that were finished.

yes, they are exomes (it's been modified in the nextflow.config, analysis_type = 'wes'). I managed to have -resume working but it gets the same error: `path value cannot be null...

Any idea where the error might be?

Yes, in theory they are not related. Should I process every "case" separately in a difference nextflow run - samplesheet instance?

I will try to do it separately, but I need to process ~120 exomes with certain urgency. This is one of the samplesheets ``` cat samplesheet_R1080.csv sample,lane,fastq_1,fastq_2,sex,phenotype,paternal_id,maternal_id,case_id 200851803,1,/playground/fastq/R1080/200851803_S1_R1_001.fastq.gz,/playground/fastq/R1080/200851803_S1_R2_001.fastq.gz,other,2,0,0,200851803 192631319,1,/playground/fastq/R1080/192631319_S2_R1_001.fastq.gz,/playground/fastq/R1080/192631319_S2_R2_001.fastq.gz,2,2,0,0,192631319 192629071,1,/playground/fastq/R1080/192629071_S3_R1_001.fastq.gz,/playground/fastq/R1080/192629071_S3_R2_001.fastq.gz,1,2,0,0,192629071...

Hi, I get a different error when processing samples one by one (error at the end). The command is this one ``` nextflow run /playground/nf-core-raredisease_1.1.1/1_1_1/ -profile singularity \ --input /playground/dataset_cnvs/samplesheets_raredisease/samplesheet_$sample.csv...

Hi, The coordinates where the pipeline complains are right in the middle of chromosome 4. This is the bed file: [...] chr4 112654064 112654163 chr4 112657238 112657337 chr4 112904434 112904592

Here [Illumina-truseq-rapid-exome_v1.2_hg38_target_orig.zip](https://github.com/nf-core/raredisease/files/14373353/Illumina-truseq-rapid-exome_v1.2_hg38_target_orig.zip)