achakroun

Hello, I have the same issue with a couple of missing cnvkit output files knowing that the pipeline has completed successfully. Currently, I am processing the cnvkit manually to end...

[Uploading .nextflow.log…]() Sure: Please find attachent .nextflow.log knowing that no custom config files were used. The command was as follow: `nextflow run nf-core/sarek -profile singularity -resume --max_cpus 10 --max_memory 40.GB...

[.nextflow.log](https://github.com/nf-core/sarek/files/13294516/default.nextflow.log) I am not sure that the log was correctly uploaded so here it is again

Hello everyone, @mhjiang97 I added gene symbols to my interval list bed file and it didn't work. The pipeline completed successfully but expected cnvkit output files still missing. Attached the...

Hello, I am thinking to use my own targets and reference files specifically with cnvkit (maybe it will resolve the issue of the missing outputs). However, as these are paths...

Ok, please what about the targets. I have tried: `--cnvkit_targets /path/to/my_cnvkit_targets.bed` and it ended up with: ``` WARN: The following invalid input values have been detected: * --cnvkit_targets: /home/ahmed/NGS/Twist_HumanCoreExome-RefSeq_hg38/cnvkit_targets.bed ```

Hello, @maxulysse thanks a lot for the hint. It worked but I still need to tweak a bit using the cnvkit parameters. Please, could you let me know where can...

Hello, Sorry for posting again but unfortunately I thought the issue was solved but it turns out that it doesn't. Actually, I still have the same missing files with cnvkit,...

Thanks a lot for the feedback @FriederikeHanssen. As I am already using cnvkit "manually", may be I can share the tools sequence that works perfectly for my germline wes-based cnv...

Hi @lescai Please, find attached the .command.log from the `cnvkit batch` work folder and the .nextflow.log of the corresponding run: [.command.log](https://github.com/nf-core/sarek/files/14311117/default.command.log) [.nextflow.log](https://github.com/nf-core/sarek/files/14311142/default.nextflow.log) Please, are you using your own intervals and...