diff --git a/modules.json b/modules.json index 4eb434b..10816e9 100644 --- a/modules.json +++ b/modules.json @@ -8,82 +8,114 @@ "atlasgeneannotationmanipulation/gtf2featureannotation": { "branch": "master", "git_sha": "04bc484c987b523ea5420ed6bbc1fdc6d8aef751", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bedtools/complement": { "branch": "master", "git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bedtools/getfasta": { "branch": "master", "git_sha": "cdcdd5e3d806f0ff3983c40c69e0b07bb44ec299", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bedtools/intersect": { "branch": "master", "git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bedtools/merge": { "branch": "master", "git_sha": "a5377837fe9013bde89de8689829e83e84086536", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bedtools/slop": { "branch": "master", "git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bedtools/sort": { "branch": "master", "git_sha": "571a5feac4c9ce0a8df0bc15b94230e7f3e8db47", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bedtools/subtract": { "branch": "master", "git_sha": "3b248b84694d1939ac4bb33df84bf6233a34d668", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "cat/cat": { "branch": "master", "git_sha": "9437e6053dccf4aafa022bfd6e7e9de67e625af8", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "deseq2/differential": { "branch": "master", "git_sha": "4699a675cfc36b3c3f53926afd5dc1cf2e6a780e", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "gawk": { "branch": "master", "git_sha": "cf3ed075695639b0a0924eb0901146df1996dc08", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "gnu/sort": { "branch": "master", "git_sha": "ca199cfe5aa4f1ea3c41302158f0af2cfaa58957", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "gunzip": { "branch": "master", "git_sha": "3a5fef109d113b4997c9822198664ca5f2716208", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "multiqc": { "branch": "master", "git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "samtools/faidx": { "branch": "master", "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "samtools/reheader": { "branch": "master", "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] } } }, @@ -92,20 +124,19 @@ "utils_nextflow_pipeline": { "branch": "master", "git_sha": "3aa0aec1d52d492fe241919f0c6100ebf0074082", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "utils_nfcore_pipeline": { "branch": "master", "git_sha": "1b6b9a3338d011367137808b49b923515080e3ba", - "installed_by": ["subworkflows"] - }, - "utils_nfschema_plugin": { - "branch": "master", - "git_sha": "bbd5a41f4535a8defafe6080e00ea74c45f4f96c", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] } } } } } -} +} \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nfschema_plugin/main.nf b/subworkflows/nf-core/utils_nfschema_plugin/main.nf deleted file mode 100644 index 4994303..0000000 --- a/subworkflows/nf-core/utils_nfschema_plugin/main.nf +++ /dev/null @@ -1,46 +0,0 @@ -// -// Subworkflow that uses the nf-schema plugin to validate parameters and render the parameter summary -// - -include { paramsSummaryLog } from 'plugin/nf-schema' -include { validateParameters } from 'plugin/nf-schema' - -workflow UTILS_NFSCHEMA_PLUGIN { - - take: - input_workflow // workflow: the workflow object used by nf-schema to get metadata from the workflow - validate_params // boolean: validate the parameters - parameters_schema // string: path to the parameters JSON schema. - // this has to be the same as the schema given to `validation.parametersSchema` - // when this input is empty it will automatically use the configured schema or - // "${projectDir}/nextflow_schema.json" as default. This input should not be empty - // for meta pipelines - - main: - - // - // Print parameter summary to stdout. This will display the parameters - // that differ from the default given in the JSON schema - // - if(parameters_schema) { - log.info paramsSummaryLog(input_workflow, parameters_schema:parameters_schema) - } else { - log.info paramsSummaryLog(input_workflow) - } - - // - // Validate the parameters using nextflow_schema.json or the schema - // given via the validation.parametersSchema configuration option - // - if(validate_params) { - if(parameters_schema) { - validateParameters(parameters_schema:parameters_schema) - } else { - validateParameters() - } - } - - emit: - dummy_emit = true -} - diff --git a/subworkflows/nf-core/utils_nfschema_plugin/meta.yml b/subworkflows/nf-core/utils_nfschema_plugin/meta.yml deleted file mode 100644 index f7d9f02..0000000 --- a/subworkflows/nf-core/utils_nfschema_plugin/meta.yml +++ /dev/null @@ -1,35 +0,0 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json -name: "utils_nfschema_plugin" -description: Run nf-schema to validate parameters and create a summary of changed parameters -keywords: - - validation - - JSON schema - - plugin - - parameters - - summary -components: [] -input: - - input_workflow: - type: object - description: | - The workflow object of the used pipeline. - This object contains meta data used to create the params summary log - - validate_params: - type: boolean - description: Validate the parameters and error if invalid. - - parameters_schema: - type: string - description: | - Path to the parameters JSON schema. - This has to be the same as the schema given to the `validation.parametersSchema` config - option. When this input is empty it will automatically use the configured schema or - "${projectDir}/nextflow_schema.json" as default. The schema should not be given in this way - for meta pipelines. -output: - - dummy_emit: - type: boolean - description: Dummy emit to make nf-core subworkflows lint happy -authors: - - "@nvnieuwk" -maintainers: - - "@nvnieuwk" diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test deleted file mode 100644 index 842dc43..0000000 --- a/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test +++ /dev/null @@ -1,117 +0,0 @@ -nextflow_workflow { - - name "Test Subworkflow UTILS_NFSCHEMA_PLUGIN" - script "../main.nf" - workflow "UTILS_NFSCHEMA_PLUGIN" - - tag "subworkflows" - tag "subworkflows_nfcore" - tag "subworkflows/utils_nfschema_plugin" - tag "plugin/nf-schema" - - config "./nextflow.config" - - test("Should run nothing") { - - when { - - params { - test_data = '' - } - - workflow { - """ - validate_params = false - input[0] = workflow - input[1] = validate_params - input[2] = "" - """ - } - } - - then { - assertAll( - { assert workflow.success } - ) - } - } - - test("Should validate params") { - - when { - - params { - test_data = '' - outdir = 1 - } - - workflow { - """ - validate_params = true - input[0] = workflow - input[1] = validate_params - input[2] = "" - """ - } - } - - then { - assertAll( - { assert workflow.failed }, - { assert workflow.stdout.any { it.contains('ERROR ~ Validation of pipeline parameters failed!') } } - ) - } - } - - test("Should run nothing - custom schema") { - - when { - - params { - test_data = '' - } - - workflow { - """ - validate_params = false - input[0] = workflow - input[1] = validate_params - input[2] = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json" - """ - } - } - - then { - assertAll( - { assert workflow.success } - ) - } - } - - test("Should validate params - custom schema") { - - when { - - params { - test_data = '' - outdir = 1 - } - - workflow { - """ - validate_params = true - input[0] = workflow - input[1] = validate_params - input[2] = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json" - """ - } - } - - then { - assertAll( - { assert workflow.failed }, - { assert workflow.stdout.any { it.contains('ERROR ~ Validation of pipeline parameters failed!') } } - ) - } - } -} diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config deleted file mode 100644 index 0907ac5..0000000 --- a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config +++ /dev/null @@ -1,8 +0,0 @@ -plugins { - id "nf-schema@2.1.0" -} - -validation { - parametersSchema = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json" - monochromeLogs = true -} \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json deleted file mode 100644 index 3228406..0000000 --- a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json +++ /dev/null @@ -1,96 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft-07/schema", - "$id": "https://raw.githubusercontent.com/./master/nextflow_schema.json", - "title": ". pipeline parameters", - "description": "", - "type": "object", - "$defs": { - "input_output_options": { - "title": "Input/output options", - "type": "object", - "fa_icon": "fas fa-terminal", - "description": "Define where the pipeline should find input data and save output data.", - "required": ["outdir"], - "properties": { - "validate_params": { - "type": "boolean", - "description": "Validate parameters?", - "default": true, - "hidden": true - }, - "outdir": { - "type": "string", - "format": "directory-path", - "description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.", - "fa_icon": "fas fa-folder-open" - }, - "test_data_base": { - "type": "string", - "default": "https://raw.githubusercontent.com/nf-core/test-datasets/modules", - "description": "Base for test data directory", - "hidden": true - }, - "test_data": { - "type": "string", - "description": "Fake test data param", - "hidden": true - } - } - }, - "generic_options": { - "title": "Generic options", - "type": "object", - "fa_icon": "fas fa-file-import", - "description": "Less common options for the pipeline, typically set in a config file.", - "help_text": "These options are common to all nf-core pipelines and allow you to customise some of the core preferences for how the pipeline runs.\n\nTypically these options would be set in a Nextflow config file loaded for all pipeline runs, such as `~/.nextflow/config`.", - "properties": { - "help": { - "type": "boolean", - "description": "Display help text.", - "fa_icon": "fas fa-question-circle", - "hidden": true - }, - "version": { - "type": "boolean", - "description": "Display version and exit.", - "fa_icon": "fas fa-question-circle", - "hidden": true - }, - "logo": { - "type": "boolean", - "default": true, - "description": "Display nf-core logo in console output.", - "fa_icon": "fas fa-image", - "hidden": true - }, - "singularity_pull_docker_container": { - "type": "boolean", - "description": "Pull Singularity container from Docker?", - "hidden": true - }, - "publish_dir_mode": { - "type": "string", - "default": "copy", - "description": "Method used to save pipeline results to output directory.", - "help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.", - "fa_icon": "fas fa-copy", - "enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"], - "hidden": true - }, - "monochrome_logs": { - "type": "boolean", - "description": "Use monochrome_logs", - "hidden": true - } - } - } - }, - "allOf": [ - { - "$ref": "#/$defs/input_output_options" - }, - { - "$ref": "#/$defs/generic_options" - } - ] -}