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nf-core

Hello, I have an issue with the MultiQC report for the bacass pipeline. This report includes a barplot showing the features found using Prokka or Bakta. But, when running multiple samples together this barplot only summarizes a single sample. No barplots are created for any other samples in the run. Is there a way to fix this?

Likely relevant: <https://multiqc.info/docs/usage/troubleshooting/#not-enough-samples-found|https://multiqc.info/docs/usage/troubleshooting/#not-enough-samples-found>

Hello!! this might fix it :thinking_face:: <https://github.com/MultiQC/MultiQC/issues/482>

Good try! But no - that issue is 7 years old and was fixed 7 years ago, so doubt it :blush: 

Very likely the pipeline (or user via config + ext.args) needs to pass -d to avoid having identical sample names 

ok, I'm going to do a deeper check :sweat_smile:. New issue incoming

<@U073YKKU2DP> - some more information would help here. eg. A screenshot at least, but best of all the sample sheet and command. So that we can see the filenames, sample IDs and replicate the same behaviour. 

5003_samplesheet.csv

image.png

<@UE4L64T4G> I've attached a screenshot of the issue as well as the sample sheet I used. Here is the command:
```nextflow run '<https://github.com/nf-core/bacass>' \
		 -name assembly_5003_v_2_2_0 \
		 -params-file '<https://api.cloud.seqera.io/ephemeral/basOu4sIAtjgbfK-HSXL3Q.json>' \
		 -with-tower \
		 -r 2.2.0 \
		 -profile docker```
Thanks!

Fix will be available in `dev` branch: <https://github.com/nf-core/bacass/pull/134>  Thanks for reporting :raised_hands: , and thanks for the clue <@UE4L64T4G>

I'd forgotten that option. Does it also work using <https://multiqc.info/docs/getting_started/config/#using-log-filenames-as-sample-names> ?

```use_filename_as_sample_name:
  - prokka```

I think `prokka_fn_snames` predates this more generic method, we should probably remove it if the above works.

It wokred as well :party_parrot:. This approach is much better, thanks :raised_hands:

Great, thanks for checking! <https://github.com/MultiQC/MultiQC/issues/2571>

<@U073YKKU2DP> Fix is now available in `dev`  branch : <https://github.com/nf-core/bacass/tree/dev>

<@U0293V7GCCV> Thank you! Is there an estimate on when this fix will be available on the `master`branch?

We will try to make a release soon. In the mean time you can use the `dev`version by adding `-r dev` to your nextflow run command:
```# Example
nextflow run '<https://github.com/nf-core/bacass>' \
		 -name assembly_5003_v_2_2_0 \
		 -params-file '<https://api.cloud.seqera.io/ephemeral/basOu4sIAtjgbfK-HSXL3Q.json>' \
		 -with-tower \
		 -r dev \
		 -profile docker```


bakta_full_samplesheet.csv

<@U0293V7GCCV> <@UE4L64T4G> I am running into an issue in version 2.3.0 where only 1 sample is annotated with bakta when the path to a full bakta database is specified. Multiple samples assemble successfully when running the pipeline, but only one sample is annotated after. This problem does not occur when downloading the light database using the `baktadb_download = true` and `baktadb_download_args = --type light` parameters. Is there a fix for this?
```nextflow run '<https://github.com/nf-core/bacass>' \
		 -name bakta_full_test_4 \
		 -params-file '<https://api.cloud.seqera.io/ephemeral/fkpFh52VEXF2NV6LC8amcg.json>' \
		 -with-tower \
		 -r 2.3.0 \
		 -profile docker```
