Fix GFFREAD #435

ftabaro · 2024-11-20T17:08:36Z

This pull request resolves #432. It fixes the call to GFFREAD by adding a second argument that is an empty list. In addition, this pull requests implement detection of gff file name and passes it as meta.id to GFFREAD generating a coherently named gtf output file.

PR checklist

If you've fixed a bug or added code that should be tested, add tests!
Make sure your code lints (nf-core lint).
Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).

nf-core-bot · 2024-11-20T17:09:17Z

Warning

Newer version of the nf-core template is available.

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JoseEspinosa

Thanks for the contribution @ftabaro!
I suggested several changes to your PR, if you could address them that would be great

subworkflows/local/prepare_genome.nf

JoseEspinosa

Awesome job! 🚀
Thanks!

JoseEspinosa

Just realised that the CHANGELOG.md has not been updated, could you please update it?

github-actions · 2024-11-25T16:39:59Z

`nf-core pipelines lint` overall result: Passed ✅ ⚠️

Posted for pipeline commit 705797c

+| ✅ 235 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   6 tests had warnings |!

❗ Test warnings:

pipeline_todos - TODO string in nextflow.config: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
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 base.config: Check the defaults for all processes
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

❔ Tests ignored:

nextflow_config - Config default ignored: params.bamtools_filter_pe_config
nextflow_config - Config default ignored: params.bamtools_filter_se_config

✅ Tests passed:

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nextflow_config - Found nf-schema plugin
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nextflow_config - Config timeline.enabled had correct value: true
nextflow_config - Config report.enabled had correct value: true
nextflow_config - Config trace.enabled had correct value: true
nextflow_config - Config dag.enabled had correct value: true
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nextflow_config - Lines for loading custom profiles found
nextflow_config - nextflow.config contains configuration profile test
nextflow_config - Config default value correct: params.fragment_size= 200
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nextflow_config - Config default value correct: params.aligner= bwa
nextflow_config - Config default value correct: params.broad_cutoff= 0.1
nextflow_config - Config default value correct: params.min_reps_consensus= 1
nextflow_config - Config default value correct: params.deseq2_vst= true
nextflow_config - Config default value correct: params.custom_config_version= master
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nextflow_config - Config default value correct: params.fingerprint_bins= 500000
nextflow_config - Config default value correct: params.max_multiqc_email_size= 25.MB
nextflow_config - Config default value correct: params.validate_params= true
nextflow_config - Config default value correct: params.pipelines_testdata_base_path= https://raw.githubusercontent.com/nf-core/test-datasets/
files_unchanged - .gitattributes matches the template
files_unchanged - .prettierrc.yml matches the template
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files_unchanged - .github/PULL_REQUEST_TEMPLATE.md matches the template
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readme - README Nextflow minimum version badge matched config. Badge: 24.04.2, Config: 24.04.2
readme - README Zenodo placeholder was replaced with DOI.
plugin_includes - No wrong validation plugin imports have been found
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (0 files)
schema_lint - Schema lint passed
schema_lint - Schema title + description lint passed
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merge_markers - No merge markers found in pipeline files
modules_json - Only installed modules found in modules.json
multiqc_config - assets/multiqc_config.yml found and not ignored.
multiqc_config - assets/multiqc_config.yml contains report_section_order
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base_config - conf/base.config found and not ignored.
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modules_config - BWA_MEM found in conf/modules.config and Nextflow scripts.
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modules_config - NFCORE_CHIPSEQ found in conf/modules.config and Nextflow scripts.
modules_config - NFCORE_CHIPSEQ found in conf/modules.config and Nextflow scripts.
modules_config - NFCORE_CHIPSEQ found in conf/modules.config and Nextflow scripts.
modules_config - BAM_REMOVE_ORPHANS found in conf/modules.config and Nextflow scripts.
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modules_config - SUBREAD_FEATURECOUNTS found in conf/modules.config and Nextflow scripts.
modules_config - ANNOTATE_BOOLEAN_PEAKS found in conf/modules.config and Nextflow scripts.
modules_config - DESEQ2_QC found in conf/modules.config and Nextflow scripts.
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modules_config - MULTIQC found in conf/modules.config and Nextflow scripts.
nfcore_yml - Repository type in .nf-core.yml is valid: pipeline
nfcore_yml - nf-core version in .nf-core.yml is set to the latest version: 3.0.2

Run details

nf-core/tools version 3.0.2
Run at 2024-11-25 21:16:08

JoseEspinosa

Awesome thanks! 🚀

ftabaro added 2 commits November 19, 2024 18:51

fix GFFREAD

cb1317e

Implement meta.id detection for GFFREAD

b775286

ftabaro added 2 commits November 21, 2024 10:23

remove whitespaces on line 74

16bf0bc

use gff basename for meta.id calculation

4aa51fe

JoseEspinosa requested changes Nov 25, 2024

View reviewed changes

implement suggestions

1abc2ff

JoseEspinosa approved these changes Nov 25, 2024

View reviewed changes

JoseEspinosa requested changes Nov 25, 2024

View reviewed changes

ftabaro and others added 2 commits November 25, 2024 18:01

update CHANGELOG.md

2a05331

Merge branch 'dev' into fix-gffread

705797c

JoseEspinosa approved these changes Nov 26, 2024

View reviewed changes

JoseEspinosa merged commit daadac3 into nf-core:dev Nov 26, 2024
16 checks passed

ftabaro mentioned this pull request Nov 28, 2024

correct merging error #437

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Fix GFFREAD #435

Fix GFFREAD #435

ftabaro commented Nov 20, 2024

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github-actions bot commented Nov 25, 2024 •

edited

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JoseEspinosa left a comment

Fix GFFREAD #435

Fix GFFREAD #435

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ftabaro commented Nov 20, 2024

PR checklist

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github-actions bot commented Nov 25, 2024 • edited Loading

nf-core pipelines lint overall result: Passed ✅ ⚠️

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✅ Tests passed:

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github-actions bot commented Nov 25, 2024 •

edited

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`nf-core pipelines lint` overall result: Passed ✅ ⚠️