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Multiple fixes #45

Merged
merged 13 commits into from
May 29, 2024
Merged

Multiple fixes #45

merged 13 commits into from
May 29, 2024

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itrujnara
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Closes #35, closes #36, closes #38, closes #39, closes #40

Deduplicated code in get_orthologs.nf
Removed unnecessary channel population in report.nf
Improved parameter validation
Added information on downstream and a test_data link in usage.md
Removed some files from outdir, added parameter to enable others
Added timeout handling to Python requests

PR checklist

  • This comment contains a description of changes (with reason).
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).

@itrujnara itrujnara changed the title Multiple fixes [do not merge] Multiple fixes May 28, 2024
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github-actions bot commented May 28, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 824403c

+| ✅ 212 tests passed       |+
#| ❔  20 tests were ignored |#
!| ❗  10 tests had warnings |!

❗ Test warnings:

  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
  • pipeline_todos - TODO string in usage.md: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website.
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-05-28 16:14:01

JoseEspinosa
JoseEspinosa approved these changes May 28, 2024
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Very nice just a couple of suggestions

docs/usage.md Outdated Show resolved Hide resolved
docs/usage.md Outdated

While those options allow the pipeline to run its steps offline, the pipeline requires certain configuration files and container images that are downloaded from the internet. If you wish to run the pipeline on a machine without a connection, you can pre-download the required files with `nf-core download`. See [the nf-core tools documentation](https://nf-co.re/docs/nf-core-tools/pipelines/download) for details.

### Downstream analysis

Downstream analysis relies on online resources to obtain sequences and structures, and thus cannot be run offline. For your convenience, it will be automatically disabled if you enable `offline_run`. Note that in case some sequences or structures cannot be obtained, the corresponding ortholog will be excluded from the alignment and phylogeny. In particular, only the orthologs with both a sequence and a structure available will be retained if `use_structures` is enabled.
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Would be nice to first define what downstream analyses (not sure if should be plural) is/are

nextflow_schema.json Outdated Show resolved Hide resolved
subworkflows/local/get_orthologs.nf
@@ -36,16 +36,15 @@ workflow GET_ORTHOLOGS {
ch_eggnog = params.eggnog_path ? Channel.value(file(params.eggnog_path)) : Channel.empty()
ch_eggnog_idmap = params.eggnog_idmap_path ? Channel.value(file(params.eggnog_idmap_path)) : Channel.empty()

fasta_input = true
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Looks much nicer now ❤️

itrujnara and others added 3 commits May 28, 2024 18:10
@itrujnara @JoseEspinosa
Update docs/usage.md
8bb4dd0 
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
@itrujnara @JoseEspinosa
Update nextflow_schema.json
e61d529 
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
@itrujnara
Added brief explanation of downstream
824403c
luisas
luisas approved these changes May 29, 2024
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Amazing amazing job Igor!!

@itrujnara itrujnara changed the title [do not merge] Multiple fixes Multiple fixes May 29, 2024
@itrujnara itrujnara merged commit cb220ff into nf-core:dev May 29, 2024
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@JoseEspinosa JoseEspinosa JoseEspinosa approved these changes

@luisas luisas luisas approved these changes

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