Just wanted to say that this pipeline looks really exciting, and I hope I find a reason to use it sometime in the near future. Thanks for creating this! 🙏 🎉

Thanks David! We're looking forward to your feedback

Hey Igor, the pipeline failed on the full size tests on release: https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/4EwADRgiHxhNc8

Hi! This pipeline didn't get a template update with tools 3.0.0 due to an incorrectly formatted

.nf-core.yml

file. Please check the [nf-core/tools documentation](https://nf-co.re/tools) for the correct format. Once you changed that in your

dev

branch you can get a template sync PR by starting the sync GHA action with your pipeline name as an input https://github.com/nf-core/tools/actions/workflows/sync.yml

Hi all. Thank you for the pipeline, it seems very lovely! I wanted to mention an issue I was having, and check I'm not doing something wrong. My use case is running the pipeline with a number of uniprot ids some of which will be viruses and maybe not return much from the orthology search (which is ok) and others will be standard human genes which I hope will. I ran into this python error in this process:

Caused by:
  Process `NFCORE_REPORTHO:REPORTHO:GET_ORTHOLOGS:FETCH_INSPECTOR_GROUP_ONLINE (OXDA_RHOTO)` terminated with an error exit status (1)

The error:

INFO:    Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred
  Traceback (most recent call last):
    File "/usr/local/lib/python3.11/site-packages/requests/models.py", line 971, in json
      return complexjson.loads(self.text, **kwargs)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/usr/local/lib/python3.11/json/__init__.py", line 346, in loads
      return _default_decoder.decode(s)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/usr/local/lib/python3.11/json/decoder.py", line 337, in decode
      obj, end = self.raw_decode(s, idx=_w(s, 0).end())
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/usr/local/lib/python3.11/json/decoder.py", line 355, in raw_decode
      raise JSONDecodeError("Expecting value", s, err.value) from None
  json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
  
  During handling of the above exception, another exception occurred:
  
  Traceback (most recent call last):
    File "/users/diasfrazer/cpugh/.nextflow/assets/nf-core/reportho/bin/fetch_inspector_group.py", line 39, in <module>
      main()
    File "/users/diasfrazer/cpugh/.nextflow/assets/nf-core/reportho/bin/fetch_inspector_group.py", line 35, in main
      fetch_inspector_by_id(sys.argv[1], sys.argv[2])
    File "/users/diasfrazer/cpugh/.nextflow/assets/nf-core/reportho/bin/fetch_inspector_group.py", line 21, in fetch_inspector_by_id
      json = res.json()
             ^^^^^^^^^^
    File "/usr/local/lib/python3.11/site-packages/requests/models.py", line 975, in json
      raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)
  requests.exceptions.JSONDecodeError: Expecting value: line 1 column 1 (char 0)

But then I go to the work directory and run command.run and somehow don't get the same error, so I'm not sure what could be causing it!

cpugh@login1:/nfs/scratch02/diasfrazer/cpugh/orthoplace_work/08/c440060e49ff7ee0ed1cdacc961b7c$ source .command.run 
INFO:    Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred
INFO:    Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred
[1]+  Done                    ( set -o pipefail; ( nxf_launch | tee .command.out ) 3>&1 1>&2 2>&3 | tee .command.err )

Thank you very much for the help in advance!

Hi everyone, I've made a logo for the pipeline, which will join the official docs with the 1.1 release. Speaking of it, we are about 80% done with the core new functionalities, so we should be able to release it within a few weeks.

@Igor Trujnara What is the rationale behind the pirate/treasure map? We can probably simplify the design

image.png

image.png

I've made 3 alternative versions along with the tiny icons for testing. They look OK for me at 128x128 but please double-check me.

I like REALLY like the map

mainly because it still has the reference to the function of the pipeline

btw, your first design is not in vain, you can still order cools stickers with that 😉

I will still keep it for decorative purposes, not sure where exactly I can put it

Other than in the merch store

you can still have it in the Readme of the pipeline, no?

btw, I think your pirate has two left hands. Literally 😅

If anyone is interested in reportho merch, go vote on the designs in #C07RJS9BMRU

Hi everyone, I have a major design consideration that I have discussed with some people but I want to talk to as many people as possible before committing. I thought that maintaining and adding downstream modules (alignment + phylogeny) will be tricky, and redundant with the other pipelines in the ecosystem. Because of that, I would like to remove that part of the pipeline entirely, and instead add a daisy-chain module into #C05LZ7EAYGK. What do you think about this?

By the way, I don't think we have any pipeline specific to phylogeny reconstruction, but I don't have the resources to fill this gap

To all those who had issues with the downstream (cc @Charlie Pugh) You can now use the newest revision on the

dev

branch – it has no MSA modules so all related bugs should be gone. The #C05LZ7EAYGK chain will be added in due course (not guaranteed for 1.1, sorry). Do let me know if you find any further issues.

Hackathon time! If you've seen the project description and you're (even potentially) interested in joining the hackathon project, please react to this message. I will not be able to join on Monday morning. I'm ready to do a project meeting on Tuesday, and you're obviously free to discuss things without me on Monday.

Version 1.1.0 is now live! We have added the option to merge IDs based on sequence and increased the number of sequence sources. We have decided to let go of the MSA and phylogeny subworkflows, and we will replace them with a link to #C05LZ7EAYGK in a future version. Please let me know ASAP if you encounter any issues!

Automated release messages failed, so here they are: mastodon https://mstdn.science/@nf_core/115502484035441768 🟦 https://bsky.app/profile/nf-co.re/post/3m4xgziopyc2k Fix incoming with the 3.5.0 #CE5LG7WMB release

just saw that this pipeline has

master

and

main

please just pick one to avoid confusion 🙂

I wanted to change to

main

with the next release, my plan was to release 1.2 to

main

, make it default, and then remove

master

. Is this sound or will it break something in the process?

sounds fine I think.

Hi @mashehu, since we are in transition, could you please trigger the security patch to both

master

and

main

just in case?