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mapped BAM index not produced in high-throughput (ht) mode #74
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I think it may be being made, but not exported. Can you take a look in the working directory for ALIGN_CONSENSUS_BAM? |
thank you! yes it is there |
This is still an issue that needs fixing. |
Try adding this as a seperate config file for now:
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This should be fixed in the new dev version, so that the index file is actually exported. |
The index files weren't exported. I got the latest version of the dev branch: And ran |
@lauren-tjoeka. Odd the tests were passing. I was able to replicate. Looks like it's because of a space in the glob pattern. #80 should resolve this. |
Ah, didn't notice the space there. |
works great now! thank you! |
Description of the bug
Hi! I was expecting a mapped BAM index to be output alongside the final mapped BAM when running fastquorum in high-throughput mode. Perhaps I'm missing something from my params file (see below). If I'm not missing anything, it would be useful if this was implemented in a future release. Many thanks!
Command used and terminal output
Relevant files
System information
Nextflow version: nextflow/23.04.1
Hardware: HPC
Executor: slurm
Container engine: Singularity
OS: CentOS 7 (rip)
Version of nf-core/fastquorum (from MultiQC Report html): nf-core/fastquorum v1.0.1
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