SL-13 Add param to turn off DEXSeq.gff output save #31

claire-prince · 2022-11-24T11:19:30Z

Hi,

There is currently no param that disables saving the output DEXSeq.gff. This PR adds a param called skip_dexseq_gff_save to the nextflow.config, and included this param in the modules.config to skip saving DEXSeq.gff if this param is specified.

PR checklist

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 pipeline conventions in the contribution docs- [ ] If necessary, also make a PR on the nf-core/rnasplice branch on the nf-core/test-datasets repository.
Make sure your code lints (nf-core lint).
Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
Usage Documentation in docs/usage.md is updated.
Output Documentation in docs/output.md is updated.
CHANGELOG.md is updated.
README.md is updated (including new tool citations and authors/contributors).

bensouthgate

Could we specify it using the enabled flag so it looks something like: enabled: params.save_dexseq_annotation and the dexseq annotation is saved when set to true?

claire-prince · 2022-11-25T16:39:16Z

Thanks, I have now changed the config files to specify using enabled as suggested.

bensouthgate

Looks good but not passing ECLint or nf-core lint.

github-actions · 2022-12-02T15:17:01Z

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

Posted for pipeline commit 0a8233c

+| ✅ 157 tests passed       |+
!| ❗  59 tests had warnings |!

❗ Test warnings:

pipeline_todos - TODO string in nextflow.config: Specify your pipeline's command line flags
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 WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
pipeline_todos - TODO string in ci.yml: You can customise CI pipeline run tests as required
pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
schema_description - No description provided in schema for parameter: gff
schema_description - No description provided in schema for parameter: rmats
schema_description - No description provided in schema for parameter: rmats_splice_diff_cutoff
schema_description - No description provided in schema for parameter: rmats_paired_stats
schema_description - No description provided in schema for parameter: rmats_read_len
schema_description - No description provided in schema for parameter: rmats_novel_splice_site
schema_description - No description provided in schema for parameter: rmats_min_intron_len
schema_description - No description provided in schema for parameter: rmats_max_exon_len
schema_description - No description provided in schema for parameter: dexseq_exon
schema_description - No description provided in schema for parameter: save_dexseq_annotation
schema_description - No description provided in schema for parameter: gff_dexseq
schema_description - No description provided in schema for parameter: alignment_quality
schema_description - No description provided in schema for parameter: aggregation
schema_description - No description provided in schema for parameter: deu_lfc_denominator
schema_description - No description provided in schema for parameter: edger_exon
schema_description - No description provided in schema for parameter: dexseq_dtu
schema_description - No description provided in schema for parameter: dtu_txi
schema_description - No description provided in schema for parameter: dtu_lfc_denominator
schema_description - No description provided in schema for parameter: min_samps_feature_expr
schema_description - No description provided in schema for parameter: min_samps_feature_prop
schema_description - No description provided in schema for parameter: min_samps_gene_expr
schema_description - No description provided in schema for parameter: min_feature_expr
schema_description - No description provided in schema for parameter: min_feature_prop
schema_description - No description provided in schema for parameter: min_gene_expr
schema_description - No description provided in schema for parameter: suppa
schema_description - No description provided in schema for parameter: suppa_per_local_event
schema_description - No description provided in schema for parameter: suppa_per_isoform
schema_description - No description provided in schema for parameter: suppa_tpm
schema_description - No description provided in schema for parameter: generateevents_pool_genes
schema_description - No description provided in schema for parameter: generateevents_localevents
schema_description - No description provided in schema for parameter: generateevents_boundary
schema_description - No description provided in schema for parameter: generateevents_threshold
schema_description - No description provided in schema for parameter: generateevents_exon_length
schema_description - No description provided in schema for parameter: psiperevent_total_filter
schema_description - No description provided in schema for parameter: diffsplice_local_event
schema_description - No description provided in schema for parameter: diffsplice_isoform
schema_description - No description provided in schema for parameter: diffsplice_method
schema_description - No description provided in schema for parameter: diffsplice_area
schema_description - No description provided in schema for parameter: diffsplice_lower_bound
schema_description - No description provided in schema for parameter: diffsplice_gene_correction
schema_description - No description provided in schema for parameter: diffsplice_paired
schema_description - No description provided in schema for parameter: diffsplice_alpha
schema_description - No description provided in schema for parameter: diffsplice_median
schema_description - No description provided in schema for parameter: diffsplice_tpm_threshold
schema_description - No description provided in schema for parameter: diffsplice_nan_threshold
schema_description - No description provided in schema for parameter: clusterevents_local_event
schema_description - No description provided in schema for parameter: clusterevents_isoform
schema_description - No description provided in schema for parameter: clusterevents_sigthreshold
schema_description - No description provided in schema for parameter: clusterevents_dpsithreshold
schema_description - No description provided in schema for parameter: clusterevents_eps
schema_description - No description provided in schema for parameter: clusterevents_metric
schema_description - No description provided in schema for parameter: clusterevents_separation
schema_description - No description provided in schema for parameter: clusterevents_min_pts
schema_description - No description provided in schema for parameter: clusterevents_method

✅ Tests passed:

files_exist - File found: .gitattributes
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files_exist - File found: LICENSE or LICENSE.md or LICENCE or LICENCE.md
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nextflow_config - Config variable found: manifest.name
nextflow_config - Config variable found: manifest.nextflowVersion
nextflow_config - Config variable found: manifest.description
nextflow_config - Config variable found: manifest.version
nextflow_config - Config variable found: manifest.homePage
nextflow_config - Config variable found: timeline.enabled
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nextflow_config - Config variable found: dag.enabled
nextflow_config - Config variable found: process.cpus
nextflow_config - Config variable found: process.memory
nextflow_config - Config variable found: process.time
nextflow_config - Config variable found: params.outdir
nextflow_config - Config variable found: params.input
nextflow_config - Config variable found: params.show_hidden_params
nextflow_config - Config variable found: params.schema_ignore_params
nextflow_config - Config variable found: manifest.mainScript
nextflow_config - Config variable found: timeline.file
nextflow_config - Config variable found: trace.file
nextflow_config - Config variable found: report.file
nextflow_config - Config variable found: dag.file
nextflow_config - Config variable (correctly) not found: params.version
nextflow_config - Config variable (correctly) not found: params.nf_required_version
nextflow_config - Config variable (correctly) not found: params.container
nextflow_config - Config variable (correctly) not found: params.singleEnd
nextflow_config - Config variable (correctly) not found: params.igenomesIgnore
nextflow_config - Config variable (correctly) not found: params.name
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 - Config dag.file ended with .html
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nextflow_config - Config manifest.version ends in dev: '1.0dev'
nextflow_config - Config params.custom_config_version is set to master
nextflow_config - Config params.custom_config_base is set to https://raw.githubusercontent.com/nf-core/configs/master
nextflow_config - Lines for loading custom profiles found
files_unchanged - .gitattributes matches the template
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files_unchanged - LICENSE matches the template
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files_unchanged - .github/workflows/branch.yml matches the template
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files_unchanged - .github/workflows/linting.yml matches the template
files_unchanged - assets/email_template.html matches the template
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files_unchanged - lib/NfcoreTemplate.groovy matches the template
files_unchanged - .gitignore matches the template
files_unchanged - .prettierignore matches the template
files_unchanged - pyproject.toml matches the template
actions_ci - '.github/workflows/ci.yml' is triggered on expected events
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readme - README Nextflow minimum version badge matched config. Badge: 21.10.3, Config: 21.10.3
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pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (158 files)
schema_lint - Schema lint passed
schema_lint - Schema title + description lint passed
schema_lint - Input mimetype lint passed: 'text/csv'
schema_params - Schema matched params returned from nextflow config
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
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actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: linting.yml
merge_markers - No merge markers found in pipeline files
modules_json - Only installed modules found in modules.json
multiqc_config - 'assets/multiqc_config.yml' follows the ordering scheme of the minimally required plugins.
multiqc_config - 'assets/multiqc_config.yml' contains a matching 'report_comment'.
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modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'

Run details

nf-core/tools version 2.6
Run at 2022-12-02 17:39:03

claire-prince · 2022-12-02T15:17:12Z

Thanks, have now fixed the typo causing this.

SL-13 Add param to turn off DEXSeq.gff output save

f802837

bensouthgate requested changes Nov 25, 2022

View reviewed changes

SL-13 Specify dexseq annotation param using enabled

50f2025

bensouthgate requested changes Dec 2, 2022

View reviewed changes

Fix missing comma

7c45b88

claireprince added 2 commits December 2, 2022 17:31

Fix trailing whitespace in modules.config

930586d

Update nextflow.schema.json with save_dexseq_annotation param

0a8233c

bensouthgate merged commit f7f134f into nf-core:dev Dec 6, 2022

jma1991 deleted the SL-13-param-to-disable-DEXSeq.gff-output branch March 15, 2023 22:00

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nf-core lint overall result: Passed ✅ ⚠️

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