Merging template updates #103
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Ok, this is good to be merged once the nfcore schema changes are included into the new template. |
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@maxulysse I am having problems with the logo - apparently it clashes with the template. Do you see whats the problem? |
We changed the logo a little to have a white background so that it shows up on GitHub with dark mode. Just run |
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ok great now it passed |
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it seems the last test in the CI doesn't complete even everything is done already: |
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Looks like you have a few lint warnings that should probably be cleared up:
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ewels
requested changes
Mar 24, 2021
conf/test.config
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| @@ -44,4 +44,6 @@ params { | |||
| input_sheet_dda = 'https://raw.githubusercontent.com/nf-core/test-datasets/diaproteomics/dda_sheet.tsv' | |||
| input = 'https://raw.githubusercontent.com/nf-core/test-datasets/diaproteomics/sample_sheet.tsv' | |||
| unimod = 'https://raw.githubusercontent.com/nf-core/test-datasets/diaproteomics/unimod.xml' | |||
| // Ignore `--input` as otherwise the parameter validation will throw an error | |||
| schema_ignore_params = 'genomes,input_paths,input' | |||
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As with other review, I don't think that you're using input_paths (or genomes?)
conf/test_full.config
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| @@ -41,4 +41,6 @@ params { | |||
| unimod = 'https://raw.githubusercontent.com/nf-core/test-datasets/diaproteomics/unimod.xml' | |||
| input_sheet_dda = 'https://raw.githubusercontent.com/nf-core/test-datasets/diaproteomics/dda_sheet_full.tsv' | |||
| irts = 'https://raw.githubusercontent.com/nf-core/test-datasets/diaproteomics/irt_sheet_full.tsv' | |||
| // Ignore `--input` as otherwise the parameter validation will throw an error | |||
| schema_ignore_params = 'genomes,input_paths,input' | |||
nextflow.config
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| @@ -85,6 +84,9 @@ params { | |||
| config_profile_description = false | |||
| config_profile_contact = false | |||
| config_profile_url = false | |||
| validate_params = true | |||
| show_hidden_params = false | |||
| schema_ignore_params = 'genomes,input_paths' | |||
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Probably don't need this?
Also, input should technically be null if not set by default instead of false (though not sure that it makes any difference at this point).
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As with mhcquant, I think that you can strip all mention of genomes, right?
Co-authored-by: Phil Ewels <[email protected]>
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@ewels - Alright everything passed, but I guess I wait to include the 1.13.3 template updates still |
ewels
requested changes
Mar 31, 2021
nextflow.config
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| @@ -85,6 +84,9 @@ params { | |||
| config_profile_description = false | |||
| config_profile_contact = false | |||
| config_profile_url = false | |||
| validate_params = true | |||
| show_hidden_params = false | |||
| schema_ignore_params = 'genomes,input_paths' | |||
There was a problem hiding this comment.
As with mhcquant, I think that you can strip all mention of genomes, right?
ewels
requested changes
Mar 31, 2021
nextflow_schema.json
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Comment on lines
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| "igenomes_ignore": { | ||
| "type": "boolean", |
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ah ok, now I got it I though it was about igenomes_base which was already deleted
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the parameter group "reference_genome_options" will be emtpy though... and if I remove the whole parameter group linting fails.
ewels
approved these changes
Mar 31, 2021
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PR checklist
scrape_software_versions.pynf-core lint .).nextflow run . -profile test,docker).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).