This might be a nextflow bug. When looking at the workflow error to do with sample name collision (similar to #108), I've tracked down the issue to this .command.sh:
Either the --output parameter should be PS036_3scattered.bam or the --input parameter should be PS044.markdup.sorted.bam and the --output should then be PS044_3scattered.bam
Nextflow had this under the PS044 sample, so likely the latter case (wrong staging?).
Description of the bug
This might be a nextflow bug. When looking at the workflow error to do with sample name collision (similar to #108), I've tracked down the issue to this .command.sh:
Either the --output parameter should be PS036_3scattered.bam or the --input parameter should be PS044.markdup.sorted.bam and the --output should then be PS044_3scattered.bam Nextflow had this under the PS044 sample, so likely the latter case (wrong staging?).
Command used and terminal output
Relevant files
tissues_batch2.csv
System information
Nextflow version 23.10.1 build 5891 (conda) Local executor on Desktop Ubuntu 22.04.3, rnavar v 1.0.0, docker containers