diff --git a/CHANGELOG.md b/CHANGELOG.md index ba88675..1f55818 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,7 +10,7 @@ Initial release of ferlab/postprocessing, created with the [nf-core](https://nf- ### `Added` ### `Fixed` -[#1]https://github.com/FelixAntoineLeSieur/Post-processing-Pipeline/pull/1 Fixed template schemas +[#1](https://github.com/FelixAntoineLeSieur/Post-processing-Pipeline/pull/1) Fixed template schemas ### `Dependencies` diff --git a/assets/schema_input.json b/assets/schema_input.json deleted file mode 100644 index 72a4e4a..0000000 --- a/assets/schema_input.json +++ /dev/null @@ -1,51 +0,0 @@ -{ - "$schema": "http://json-schema.org/draft-07/schema", - "$id": "https://raw.githubusercontent.com/ferlab/postprocessing/master/assets/schema_input.json", - "title": "ferlab/postprocessing pipeline - params.input schema", - "description": "Schema for the file provided with params.input", - "type": "array", - "items": { - "type": "object", - "properties": { - "familyID": { - "type": "string", - "errorMessage": "Sample name must be provided and cannot contain spaces", - "meta": ["id"] - }, - "sequencingType": { - "type": "string", - "pattern": "(WES|WGS)", - "errorMessage": "If the format is V2, the sequencing type (WES or WGS) will show in the 2nd column", - "meta": ["id"] - }, - "sample_1": { - "type": "string", - "format": "file-path", - "exists": true, - "pattern": "^\\S+\\.g(enome.)?vcf\\.gz$", - "errorMessage": "first GVCF sample must be provided and must have file extension 'genome.vcf.gz' or 'gvcf.gz'" - }, - "sample_2": { - "type": "string", - "format": "file-path", - "exists": true, - "pattern": "^\\S+\\.g(enome.)?vcf\\.gz$", - "errorMessage": "optional second GVCF sample must be provided and must have file extension 'genome.vcf.gz' or 'gvcf.gz'" - }, - "sample_3": { - "type": "string", - "format": "file-path", - "exists": true, - "pattern": "^\\S+\\.g(enome.)?vcf\\.gz$", - "errorMessage": "optional third GVCF sample must be provided and must have file extension 'genome.vcf.gz' or 'gvcf.gz'" - }, - "sample_4": { - "type": "string", - "format": "file-path", - "exists": true, - "pattern": "^\\S+\\.g(enome.)?vcf\\.gz$", - "errorMessage": "optional fourth GVCF sample must be provided and must have file extension 'genome.vcf.gz' or 'gvcf.gz'" - } - } - } -} diff --git a/nextflow_schema.json b/nextflow_schema.json index 616cb66..81b41c5 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -20,8 +20,7 @@ "pattern": "^\\S+\\.tsv$", "description": "Path to the .tsv sample file, of format V1 or V2, containing the Family ID and path to GVCF files", "help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row.", - "fa_icon": "fas fa-file-csv", - "schema": "assets/schema_input.json" + "fa_icon": "fas fa-file-csv" }, "outdir": { "type": "string", diff --git a/subworkflows/local/utils_nfcore_postprocessing_pipeline/main.nf b/subworkflows/local/utils_nfcore_postprocessing_pipeline/main.nf index 718e912..a42c2b4 100644 --- a/subworkflows/local/utils_nfcore_postprocessing_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_postprocessing_pipeline/main.nf @@ -80,6 +80,7 @@ workflow PIPELINE_INITIALISATION { // // Create channel from input file provided through params.input // + /* Channel .fromSamplesheet("input") .map { @@ -103,6 +104,7 @@ workflow PIPELINE_INITIALISATION { emit: samplesheet = ch_samplesheet versions = ch_versions + */ } /*