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modify template to use nf-validation plugin for parameter validation #2300

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Merged
mirpedrol merged 11 commits into from
Jun 13, 2023
Merged

modify template to use nf-validation plugin for parameter validation #2300

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b634573
validate pipeline parameters with nf-validation
mirpedrol Jun 5, 2023
df79197
fix ch_input
mirpedrol Jun 5, 2023
6e4c582
add parameter defaults to schema to avoid printing them with paramete…
mirpedrol Jun 5, 2023
2cf0814
check if input file exists
mirpedrol Jun 5, 2023
0519307
update nf-validation to v0.2.1
mirpedrol Jun 7, 2023
81595ec
check paths exist with schema
mirpedrol Jun 7, 2023
e749f08
add comment about creating a channel with fromSamplesheet
mirpedrol Jun 7, 2023
d9b7b27
print help before initialise
mirpedrol Jun 7, 2023
e36fdbf
fix trailing whitespaces
mirpedrol Jun 7, 2023
44a7c7d
Apply suggestions from code review
mirpedrol Jun 9, 2023
7af5f95
do not check if multiqc_config exists
mirpedrol Jun 9, 2023
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -12,6 +12,7 @@
- Remove `aws_tower` profile ([#2287])(https://github.com/nf-core/tools/pull/2287)
- Fixed the Slack report to include the pipeline name ([#2291](https://github.com/nf-core/tools/pull/2291))
- Fix link in the MultiQC report to point to exact version of output docs ([#2298](https://github.com/nf-core/tools/pull/2298))
- Remove schema validation from `lib` folder and use Nextflow [nf-validation plugin](https://nextflow-io.github.io/nf-validation/) instead ([#1771](https://github.com/nf-core/tools/pull/1771/))

### Download

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2 changes: 0 additions & 2 deletions nf_core/lint/files_exist.py
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Expand Up @@ -52,7 +52,6 @@ def files_exist(self):
docs/README.md
docs/usage.md
lib/nfcore_external_java_deps.jar
lib/NfcoreSchema.groovy
lib/NfcoreTemplate.groovy
lib/Utils.groovy
lib/WorkflowMain.groovy
Expand Down Expand Up @@ -161,7 +160,6 @@ def files_exist(self):
[os.path.join("docs", "README.md")],
[os.path.join("docs", "usage.md")],
[os.path.join("lib", "nfcore_external_java_deps.jar")],
[os.path.join("lib", "NfcoreSchema.groovy")],
[os.path.join("lib", "NfcoreTemplate.groovy")],
[os.path.join("lib", "Utils.groovy")],
[os.path.join("lib", "WorkflowMain.groovy")],
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2 changes: 0 additions & 2 deletions nf_core/lint/files_unchanged.py
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Expand Up @@ -40,7 +40,6 @@ def files_unchanged(self):
docs/images/nf-core-PIPELINE_logo_dark.png
docs/README.md'
lib/nfcore_external_java_deps.jar
lib/NfcoreSchema.groovy
lib/NfcoreTemplate.groovy
['LICENSE', 'LICENSE.md', 'LICENCE', 'LICENCE.md'], # NB: British / American spelling

Expand Down Expand Up @@ -105,7 +104,6 @@ def files_unchanged(self):
[os.path.join("docs", "images", f"nf-core-{short_name}_logo_dark.png")],
[os.path.join("docs", "README.md")],
[os.path.join("lib", "nfcore_external_java_deps.jar")],
[os.path.join("lib", "NfcoreSchema.groovy")],
[os.path.join("lib", "NfcoreTemplate.groovy")],
]
files_partial = [
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8 changes: 4 additions & 4 deletions nf_core/lint/nextflow_config.py
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Expand Up @@ -62,11 +62,11 @@ def nextflow_config(self):
* Should always be set to default value:
``https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}``

* ``params.show_hidden_params``
* ``params.validationShowHiddenParams``

* Determines whether boilerplate params are showed by schema. Set to ``false`` by default

* ``params.schema_ignore_params``
* ``params.validationSchemaIgnoreParams``

* A comma separated string of inputs the schema validation should ignore.

Expand Down Expand Up @@ -130,8 +130,8 @@ def nextflow_config(self):
["process.time"],
["params.outdir"],
["params.input"],
["params.show_hidden_params"],
["params.schema_ignore_params"],
["params.validationShowHiddenParams"],
["params.validationSchemaIgnoreParams"],
]
# Throw a warning if these are missing
config_warn = [
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