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Add postprocessing option to hmmer/eslreformat#2061

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Sep 14, 2022
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Add postprocessing option to hmmer/eslreformat#2061
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@erikrikarddaniel erikrikarddaniel commented Sep 14, 2022

PR checklist

I've added a postprocessing config file option to the module to allow e.g. removal of gap characters, see discussion in #2053.

I'm unaware of naming (and other) conventions for this type of thing so please correct me! :-S

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the module conventions in the contribution docs
  • If necessary, include test data in your PR.
  • Remove all TODO statements.
  • Emit the versions.yml file.
  • Follow the naming conventions.
  • Follow the parameters requirements.
  • Follow the input/output options guidelines.
  • Add a resource label
  • Use BioConda and BioContainers if possible to fulfil software requirements.
  • Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
    • PROFILE=docker pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware
    • PROFILE=singularity pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware
    • PROFILE=conda pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware

d4straub
d4straub approved these changes Sep 14, 2022
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Looks good.
The syntax here is task.ext.anything.

Comment thread tests/modules/hmmer/eslreformat/nextflow.config Outdated
Comment thread modules/hmmer/eslreformat/main.nf Outdated
erikrikarddaniel and others added 2 commits September 14, 2022 18:36
@erikrikarddaniel @d4straub
Update tests/modules/hmmer/eslreformat/nextflow.config
768e4e7 
Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
@erikrikarddaniel @d4straub
Update modules/hmmer/eslreformat/main.nf
a16600f 
Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
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erikrikarddaniel commented Sep 14, 2022

Looks good. The syntax here is task.ext.anything.

Thanks!

@erikrikarddaniel erikrikarddaniel merged commit 885e724 into nf-core:master Sep 14, 2022
@erikrikarddaniel erikrikarddaniel deleted the postprocess-eslreformat branch September 14, 2022 16:44
matthdsm pushed a commit to matthdsm/nf-core-modules that referenced this pull request Sep 28, 2022
@erikrikarddaniel @d4straub @matthdsm
Add postprocessing option to hmmer/eslreformat (nf-core#2061)
3b356f8 
* Add postprocessing option to hmmer/eslreformat

* Update tests/modules/hmmer/eslreformat/nextflow.config

Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>

* Update modules/hmmer/eslreformat/main.nf

Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>

Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
pinin4fjords added a commit to pinin4fjords/nf-core-modules that referenced this pull request May 19, 2026
@pinin4fjords @claude
test(gedi/price): add real test using minimised chr19+chr22 fixtures
76b0994 
Replaces the stub-only PRICE test with an end-to-end test that runs
PRICE on a minimal cohort of four Ribo-seq samples (chr19+chr22,
protein-coding-only reference). The cohort produces 380 ORF calls;
snapshot captures the orfs.tsv line count for stability validation.

Fixtures published in nf-core/test-datasets PR nf-core#2061.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
delfiterradas pushed a commit to grst/modules that referenced this pull request May 19, 2026
@pinin4fjords @claude
feat(gedi): add gedi/indexgenome and gedi/price modules (nf-core#11693)
51af5cb 
* feat(gedi): add gedi/indexgenome and gedi/price modules

Adds two modules wrapping the GEDI / PRICE toolkit (`bioconda::gedi=1.0.6a`) for Ribo-seq translated-ORF discovery. PRICE (Erhard et al. 2018, doi:10.1038/nmeth.4631) calls translated ORFs from ribosome profiling data with near-cognate start codon detection.

`gedi/indexgenome` wraps `gedi -e IndexGenome`, producing the `.oml` genome index directory consumed by PRICE.

`gedi/price` wraps `bamlist2cit` + `gedi -e Price`, taking a cohort of Ribo-seq BAMs plus the genome index and emitting ORF predictions (`*.orfs.tsv` + `*.cit` + sidecars). One-shot across the cohort - PRICE is not per-sample.

Both modules use Wave-built community containers from `bioconda::gedi=1.0.6a`. The bioconda recipe was merged 2026-05-16; using Wave directly for now.

Source: nf-core/riboseq#174.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* refactor(gedi/indexgenome): use ${prefix} for the index output directory

Previously hard-coded the output directory as `price_index`. Switching to
`${prefix}` (default `${meta.id}`, overridable via `task.ext.prefix`) lets
callers control the directory name and matches the nf-core convention for
publishable directory outputs.

The default ${meta.id} keeps the directory keyed to the reference id, so
when `gedi/price` opens `${index}/${meta2.id}.oml`, the lookup still
resolves provided meta ids match (already the case in the test chain).

Snapshot regenerated: the index directory name in the output snapshot
changes from `price_index` to the test's `homo_sapiens_chr20` (its meta.id).

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* test(gedi/price): add real test using minimised chr19+chr22 fixtures

Replaces the stub-only PRICE test with an end-to-end test that runs
PRICE on a minimal cohort of four Ribo-seq samples (chr19+chr22,
protein-coding-only reference). The cohort produces 380 ORF calls;
snapshot captures the orfs.tsv line count for stability validation.

Fixtures published in nf-core/test-datasets PR nf-core#2061.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* fix(gedi/indexgenome): update meta.yml output name after ${prefix} refactor

The earlier `${prefix}` refactor (commit 0ca4c45) changed the index
output declaration from `path("price_index")` to `path("${prefix}")`,
but the meta.yml output entry still hard-coded `price_index` — causing
CI lint to flag `correct_meta_outputs: Module meta.yml does not match
main.nf`.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* style(gedi/indexgenome): collapse leftover alignment padding on index emit

After the `${prefix}` refactor (commit 0ca4c45) the index output line
was the only `tuple val(meta), path(...)` emit in the module, so the
52-space alignment padding it kept from when the path was `price_index`
no longer aligns with anything.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* fix(gedi): correct licence (GPL-3.0) and Gedi description in meta.yml

Two cross-cutting fixes from review of nf-core#11693:

- Licence was Apache-2.0 in both meta.yml files; the upstream repo
  erhard-lab/gedi is GPL-3.0. Corrected.
- "GEDI (Gene Expression Data Integration)" was unverified — the
  upstream README/wiki/paper don't expand the acronym that way.
  Replaced with the upstream one-liner phrasing. PRICE meta.yml also
  adds the verified PRICE expansion (Probabilistic Inference of Codon
  Activities by an EM algorithm) from the GEDI wiki.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* test(gedi/price): point fixtures at nf-core/test-datasets@modules

nf-core/test-datasets#2061 merged; fixtures now live on the modules branch.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

---------

Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
manascripts pushed a commit to manascripts/modules that referenced this pull request May 21, 2026
@pinin4fjords @claude @manascripts
feat(gedi): add gedi/indexgenome and gedi/price modules (nf-core#11693)
855a8e3 
* feat(gedi): add gedi/indexgenome and gedi/price modules

Adds two modules wrapping the GEDI / PRICE toolkit (`bioconda::gedi=1.0.6a`) for Ribo-seq translated-ORF discovery. PRICE (Erhard et al. 2018, doi:10.1038/nmeth.4631) calls translated ORFs from ribosome profiling data with near-cognate start codon detection.

`gedi/indexgenome` wraps `gedi -e IndexGenome`, producing the `.oml` genome index directory consumed by PRICE.

`gedi/price` wraps `bamlist2cit` + `gedi -e Price`, taking a cohort of Ribo-seq BAMs plus the genome index and emitting ORF predictions (`*.orfs.tsv` + `*.cit` + sidecars). One-shot across the cohort - PRICE is not per-sample.

Both modules use Wave-built community containers from `bioconda::gedi=1.0.6a`. The bioconda recipe was merged 2026-05-16; using Wave directly for now.

Source: nf-core/riboseq#174.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* refactor(gedi/indexgenome): use ${prefix} for the index output directory

Previously hard-coded the output directory as `price_index`. Switching to
`${prefix}` (default `${meta.id}`, overridable via `task.ext.prefix`) lets
callers control the directory name and matches the nf-core convention for
publishable directory outputs.

The default ${meta.id} keeps the directory keyed to the reference id, so
when `gedi/price` opens `${index}/${meta2.id}.oml`, the lookup still
resolves provided meta ids match (already the case in the test chain).

Snapshot regenerated: the index directory name in the output snapshot
changes from `price_index` to the test's `homo_sapiens_chr20` (its meta.id).

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* test(gedi/price): add real test using minimised chr19+chr22 fixtures

Replaces the stub-only PRICE test with an end-to-end test that runs
PRICE on a minimal cohort of four Ribo-seq samples (chr19+chr22,
protein-coding-only reference). The cohort produces 380 ORF calls;
snapshot captures the orfs.tsv line count for stability validation.

Fixtures published in nf-core/test-datasets PR nf-core#2061.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* fix(gedi/indexgenome): update meta.yml output name after ${prefix} refactor

The earlier `${prefix}` refactor (commit 0ca4c45) changed the index
output declaration from `path("price_index")` to `path("${prefix}")`,
but the meta.yml output entry still hard-coded `price_index` — causing
CI lint to flag `correct_meta_outputs: Module meta.yml does not match
main.nf`.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* style(gedi/indexgenome): collapse leftover alignment padding on index emit

After the `${prefix}` refactor (commit 0ca4c45) the index output line
was the only `tuple val(meta), path(...)` emit in the module, so the
52-space alignment padding it kept from when the path was `price_index`
no longer aligns with anything.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* fix(gedi): correct licence (GPL-3.0) and Gedi description in meta.yml

Two cross-cutting fixes from review of nf-core#11693:

- Licence was Apache-2.0 in both meta.yml files; the upstream repo
  erhard-lab/gedi is GPL-3.0. Corrected.
- "GEDI (Gene Expression Data Integration)" was unverified — the
  upstream README/wiki/paper don't expand the acronym that way.
  Replaced with the upstream one-liner phrasing. PRICE meta.yml also
  adds the verified PRICE expansion (Probabilistic Inference of Codon
  Activities by an EM algorithm) from the GEDI wiki.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* test(gedi/price): point fixtures at nf-core/test-datasets@modules

nf-core/test-datasets#2061 merged; fixtures now live on the modules branch.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

---------

Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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