From d4c9b9e15d17199e005b4bc3d6e4475e008a40b3 Mon Sep 17 00:00:00 2001 From: kevinmenden Date: Mon, 3 May 2021 14:19:38 +0200 Subject: [PATCH 1/2] fix camelCase params warnings --- nf_core/pipeline-template/lib/NfcoreSchema.groovy | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/nf_core/pipeline-template/lib/NfcoreSchema.groovy b/nf_core/pipeline-template/lib/NfcoreSchema.groovy index d591b434c3..52ee730432 100644 --- a/nf_core/pipeline-template/lib/NfcoreSchema.groovy +++ b/nf_core/pipeline-template/lib/NfcoreSchema.groovy @@ -112,8 +112,14 @@ class NfcoreSchema { } // unexpected params def params_ignore = params.schema_ignore_params.split(',') + 'schema_ignore_params' - if (!expectedParams.contains(specifiedParam) && !params_ignore.contains(specifiedParam)) { - unexpectedParams.push(specifiedParam) + def expectedParamsLowerCase = expectedParams.collect{ it.replace("-", "").toLowerCase() } + def specifiedParamLowerCase = specifiedParam.replace("-", "").toLowerCase() + if (!expectedParams.contains(specifiedParam) && !params_ignore.contains(specifiedParam) && !expectedParamsLowerCase.contains(specifiedParamLowerCase)) { + // Temporarily remove camelCase/camel-case params #1035 + def unexpectedParamsLowerCase = unexpectedParams.collect{ it.replace("-", "").toLowerCase()} + if (!unexpectedParamsLowerCase.contains(specifiedParamLowerCase)){ + unexpectedParams.push(specifiedParam) + } } } From d59b7dbad58c3775c82843b7c59dcaf7ae724d7b Mon Sep 17 00:00:00 2001 From: kevinmenden Date: Mon, 3 May 2021 14:21:41 +0200 Subject: [PATCH 2/2] update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index ada9702873..d11f81b4d3 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -16,6 +16,7 @@ * Ignore permission errors for setting up requests cache directories to allow starting with an invalid or read-only HOME directory * New lint test to check if params in `nextflow config` are mentioned in `main.nf` [[#1038](https://github.com/nf-core/tools/issues/1038)] * New modules lint test comparing the `functions.nf` file to the template version +* Added temporary fix to remove warnings about params that get converted from camelCase to camel-case [[#1035](https://github.com/nf-core/tools/issues/1035)] ### Template