diff --git a/CHANGELOG.md b/CHANGELOG.md index be9d451..3beb8f3 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -6,6 +6,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## v1.0.3 - Fixed an issue where pool grouping for multiqc wasn't properly performed on pipeline resume +- Revert the default configs base to the nf-core configs in preparation of converting nf-cmgg/configs to a private repo ## v1.0.2 diff --git a/main.nf b/main.nf index 03da35b..c4ee01e 100644 --- a/main.nf +++ b/main.nf @@ -29,7 +29,7 @@ params { input: Path // The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure. - outdir: Path + outdir: String // Email address for completion summary. email: String? diff --git a/nextflow.config b/nextflow.config index 95e77bb..585ac66 100644 --- a/nextflow.config +++ b/nextflow.config @@ -20,8 +20,8 @@ params { config_profile_name = null config_profile_description = null - custom_config_version = 'main' - custom_config_base = "https://raw.githubusercontent.com/nf-cmgg/configs/${params.custom_config_version}" + custom_config_version = 'master' + custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}" config_profile_contact = null config_profile_url = null diff --git a/workflows/sampletracking.nf b/workflows/sampletracking.nf index 42be045..04720a3 100644 --- a/workflows/sampletracking.nf +++ b/workflows/sampletracking.nf @@ -258,7 +258,7 @@ workflow SAMPLETRACKING { softwareVersionsToYAML(topic_versions.versions_file) .mix(topic_versions_string) .collectFile( - storeDir: "${outdir.toUriString()}/pipeline_info", + storeDir: "${outdir}/pipeline_info", name: 'nf_cmgg_sampletracking_software_mqc_versions.yml', sort: true, newLine: true,