Modification from NF Language server #1779
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Warning Newer version of the nf-core template is available. Your pipeline is using an old version of the nf-core template: 3.0.2. For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation. |
main.nf
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| @@ -228,7 +228,7 @@ workflow NFCORE_SAREK { | |||
| versions = versions.mix(PREPARE_GENOME.out.versions) | |||
| versions = versions.mix(PREPARE_INTERVALS.out.versions) | |||
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| vep_fasta = (params.vep_include_fasta) ? fasta.map{ fasta -> [ [ id:fasta.baseName ], fasta ] } : [[id: 'null'], []] | |||
| vep_fasta = (params.vep_include_fasta) ? fasta.map{ fasta_ -> [ [ id:fasta_.baseName ], fasta_ ] } : [[id: 'null'], []] | |||
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why is the language server adding an underscore?
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because fasta is an already defined item, so we use _ after if the item is reused within the same scope or before is the item is dropped
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it hurts my eyes, but not going to argue with the language server
main.nf
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| @@ -228,7 +228,7 @@ workflow NFCORE_SAREK { | |||
| versions = versions.mix(PREPARE_GENOME.out.versions) | |||
| versions = versions.mix(PREPARE_INTERVALS.out.versions) | |||
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| vep_fasta = (params.vep_include_fasta) ? fasta.map{ fasta -> [ [ id:fasta.baseName ], fasta ] } : [[id: 'null'], []] | |||
| vep_fasta = (params.vep_include_fasta) ? fasta.map{ fasta_ -> [ [ id:fasta_.baseName ], fasta_ ] } : [[id: 'null'], []] | |||
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it hurts my eyes, but not going to argue with the language server
PR checklist
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).