Sofia Stamouli

`Local copy of module does not match remote` Fixing this first.

https://github.com/DiltheyLab/MetaMaps/issues/74#issuecomment-2230111994 I close this PR for the time being.

Good point, it was already a draft.

Yes the data are the same. Tried to upload them but the file is too big. Can be found [here](url). [ganon_GHA.zip](https://github.com/pirovc/ganon/files/14310755/ganon_GHA.zip) Results by running ganon 2 through GHA [ganon_local.zip](https://github.com/pirovc/ganon/files/14310796/ganon_local.zip) Results...

This is the db used. [test-db-ganon.zip](https://github.com/pirovc/ganon/files/14312797/test-db-ganon.zip)

Thank you for looking into that. Yes, the data is correct. Regarding the command, I clone this[ branch](https://github.com/genomic-medicine-sweden/taxprofiler/tree/update_ganon) and then I run: `nextflow run main.nf -profile hasta,dev_prio,test,singularity --run_ganon --outdir test_ganon_output`

Sorry, I misread your comment above. Both commands: ``` #!/bin/bash -euo pipefail dbprefix=$(find -L . -name '*.*ibf' | sed 's/\.h\?ibf$//') ganon \ classify \ --db-prefix ${dbprefix%%.*ibf} \ \ --threads 2...

``` #!/bin/bash -euo pipefail dbprefix=$(find -L . -name '*.*ibf' | sed 's/\.h\?ibf$//') ganon \ classify \ --db-prefix ${dbprefix%%.*ibf} \ \ --threads 2 \ --output-prefix 2612_pe_ERR5766176_db1.ganon \ --paired-reads ERX5474932_ERR5766176_1.fastq.gz ERX5474932_ERR5766176_2.fastq.gz 2>&1...

Thanks for your reply. We only updated the module and we did not change anything in taxprofiler. Is this what you mean if the `fastq` files are as expected?

Sorry for my late reply. [2612_se_ERR5766180_db1.ganon.log](https://github.com/pirovc/ganon/files/14435798/2612_se_ERR5766180_db1.ganon.log) [2612_pe_ERR5766176_db1.ganon.log](https://github.com/pirovc/ganon/files/14435866/2612_pe_ERR5766176_db1.ganon.log)