Dowser lineages `igphyml` when using `r-enchantr=0.0.3` about airrflow HOT 9 CLOSED

I've checked within the enchantr 0.0.3 container and igphyml is installed in another path:

(base) [qeaga01@thanos test-raw]$ docker run -it quay.io/biocontainers/r-enchantr:0.0.3--r42hdfd78af_1
sh-5.0# /usr/local/share/igphyml/src/igphyml
sh: /usr/local/share/igphyml/src/igphyml: No such file or directory
sh-5.0# which igphyml
/usr/local/bin/igphyml
sh-5.0#

from airrflow.

This can be solved by changing the igphyml parameter

from airrflow.

Hi @ggabernet, thanks a lot for all the amazing work on nf-core/airrflow. I observed the same behavior with the test profile. Is there no way to fix this in the pipeline or mention it somewhere? I actually had to look for quite a while until I landed on this page.

from airrflow.

Hi @toobiwankenobi, glad that this pipeline can be helpful to other people too.
Which version of airrflow are you using, and which command did you use to launch the pipeline? In principle now the right path should be set by default, but let me know if it is not and I will fix it!

from airrflow.

Hi @ggabernet, see my specs below

N E X T F L O W ~ version 23.04.1
nf-core/airrflow v3.1.0-ga2a6099

nextflow run nf-core/airrflow -profile test,singularity

according to the documentation, the default is still /usr/local/share/igphyml/src/igphyml

from airrflow.

Hi @ggabernet ! I'm also testing airrflow now and ran into the same issue with running with -profile test,singularity. I checked the depot.galaxyproject.org-singularity-r-enchantr-0.1.2--r42hdfd78af_0.img image and igphyml path is /usr/local/bin/igphyml. However, running the test pipeline with "--igphyml /usr/local/bin/igphyml" does not prevent the error:

> processing file: _main.Rmd
>   |.................................                  |  64% [unnamed-chunk-3]
> Quitting from lines 136-216 [unnamed-chunk-3] (_main.Rmd)
> Error in `value[[3L]]()`:
> Backtrace:
>  1. dowser::getTrees(...)
> Warning messages:
> 1: replacing previous import 'data.table::last' by 'dplyr::last' when loading 'enchantr'
> 2: replacing previous import 'data.table::first' by 'dplyr::first' when loading 'enchantr'
> 3: replacing previous import 'data.table::between' by 'dplyr::between' when loading 'enchantr'

from airrflow.

nextflow run nf-core/airrflow -profile test,singularity --outdir output_test --skip_all_clones_report still crashes in the same process

from airrflow.

Hi. We are looking into this. The issue comes from the lineage tree generation, not the clone identification. If you want to skip that step, you should use --skip_lineage.

from airrflow.

Hi, sorry the documentation is wrong, this parameter default is updated both in the master and dev branch to match the container:

I think the error you are getting is related to something else but not the igphyml executable path. We are currently investigating this error.

I will fix the documentation regarding the default param now though!

from airrflow.