From 724fa227f7567facc276542cfbdde864e29c0b85 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=BAlia=20Mir?= Date: Sat, 1 Oct 2022 12:35:05 +0000 Subject: [PATCH 01/11] Add new directory --- modules/nf-core/.gitkeep | 0 1 file changed, 0 insertions(+), 0 deletions(-) create mode 100644 modules/nf-core/.gitkeep diff --git a/modules/nf-core/.gitkeep b/modules/nf-core/.gitkeep new file mode 100644 index 00000000..e69de29b From 6fc7cb185bd6dc0dc0ffe624aa823abeda4b7066 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= Date: Sat, 1 Oct 2022 12:40:05 +0000 Subject: [PATCH 02/11] restructure modules folder --- modules/{ => nf-core}/fastqc/main.nf | 0 modules/{ => nf-core}/fastqc/meta.yml | 0 modules/{ => nf-core}/multiqc/main.nf | 0 modules/{ => nf-core}/multiqc/meta.yml | 0 4 files changed, 0 insertions(+), 0 deletions(-) rename modules/{ => nf-core}/fastqc/main.nf (100%) rename modules/{ => nf-core}/fastqc/meta.yml (100%) rename modules/{ => nf-core}/multiqc/main.nf (100%) rename modules/{ => nf-core}/multiqc/meta.yml (100%) diff --git a/modules/fastqc/main.nf b/modules/nf-core/fastqc/main.nf similarity index 100% rename from modules/fastqc/main.nf rename to modules/nf-core/fastqc/main.nf diff --git a/modules/fastqc/meta.yml b/modules/nf-core/fastqc/meta.yml similarity index 100% rename from modules/fastqc/meta.yml rename to modules/nf-core/fastqc/meta.yml diff --git a/modules/multiqc/main.nf b/modules/nf-core/multiqc/main.nf similarity index 100% rename from modules/multiqc/main.nf rename to modules/nf-core/multiqc/main.nf diff --git a/modules/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml similarity index 100% rename from modules/multiqc/meta.yml rename to modules/nf-core/multiqc/meta.yml From 6cd7161de5b59678bafef6994a91acf4d4ccbacb Mon Sep 17 00:00:00 2001 From: mashehu Date: Fri, 25 Nov 2022 13:33:41 +0000 Subject: [PATCH 03/11] Update .nf-core.yml --- .nf-core.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.nf-core.yml b/.nf-core.yml index f0b10750..7f9a6f74 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -1 +1,2 @@ repository_type: modules +org_path: nf-core From 190cf37171e27900bb9f257c1688e98ad38adb2a Mon Sep 17 00:00:00 2001 From: mashehu Date: Mon, 28 Nov 2022 14:19:25 +0000 Subject: [PATCH 04/11] add fakeqc --- modules/nf-core/fakeqc/main.nf | 0 modules/nf-core/fakeqc/meta.yml | 1 + 2 files changed, 1 insertion(+) create mode 100644 modules/nf-core/fakeqc/main.nf create mode 100644 modules/nf-core/fakeqc/meta.yml diff --git a/modules/nf-core/fakeqc/main.nf b/modules/nf-core/fakeqc/main.nf new file mode 100644 index 00000000..e69de29b diff --git a/modules/nf-core/fakeqc/meta.yml b/modules/nf-core/fakeqc/meta.yml new file mode 100644 index 00000000..8b137891 --- /dev/null +++ b/modules/nf-core/fakeqc/meta.yml @@ -0,0 +1 @@ + From debda59c06896bdd65adae895c6b06a70ef5afd0 Mon Sep 17 00:00:00 2001 From: mashehu Date: Mon, 28 Nov 2022 14:19:43 +0000 Subject: [PATCH 05/11] add fakeqc --- modules/nf-core/fakeqc/main.nf | 1 + 1 file changed, 1 insertion(+) diff --git a/modules/nf-core/fakeqc/main.nf b/modules/nf-core/fakeqc/main.nf index e69de29b..8b137891 100644 --- a/modules/nf-core/fakeqc/main.nf +++ b/modules/nf-core/fakeqc/main.nf @@ -0,0 +1 @@ + From f3aa0c0bb7fcc5a84f80c633a2af7ca4cb206e5f Mon Sep 17 00:00:00 2001 From: mashehu Date: Wed, 29 Mar 2023 08:35:28 +0000 Subject: [PATCH 06/11] add yaml-schema --- yaml-schema.json | 146 +++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 146 insertions(+) create mode 100644 yaml-schema.json diff --git a/yaml-schema.json b/yaml-schema.json new file mode 100644 index 00000000..24516d54 --- /dev/null +++ b/yaml-schema.json @@ -0,0 +1,146 @@ +{ + "$schema": "http://json-schema.org/draft-07/schema", + "title": "Meta yaml", + "description": "Validate the meta yaml file for an nf-core module", + "type": "object", + "properties": { + "name": { + "type": "string", + "description": "Name of the module" + }, + "description": { + "type": "string", + "description": "Description of the module" + }, + "keywords": { + "type": "array", + "description": "Keywords for the module", + "items": { + "type": "string" + }, + "minItems": 3 + }, + "authors": { + "type": "array", + "description": "Authors of the module", + "items": { + "type": "string" + } + }, + "input": { + "type": "array", + "description": "Input channels for the module", + + "items": { + "type": "object", + "patternProperties": { + ".*": { + "type": "object", + "properties": { + "type": { + "type": "string", + "description": "Type of the input channel", + "enum": ["map", "file", "directory", "string", "integer", "float"] + }, + "description": { + "type": "string", + "description": "Description of the input channel" + }, + "pattern": { + "type": "string", + "description": "Pattern of the input channel, given in Java glob syntax" + }, + "default": { + "type": ["string", "number", "boolean", "array", "object"], + "description": "Default value for the input channel" + } + }, + "required": ["type", "description"] + } + } + } + }, + "output": { + "type": "array", + "description": "Output channels for the module", + "items": { + "type": "object", + "patternProperties": { + ".*": { + "type": "object", + "properties": { + "type": { + "type": "string", + "description": "Type of the output channel", + "enum": ["map", "file", "directory", "string", "integer", "float"] + }, + "description": { + "type": "string", + "description": "Description of the output channel" + }, + "pattern": { + "type": "string", + "description": "Pattern of the input channel, given in Java glob syntax" + } + }, + "required": ["type", "description"] + } + } + } + }, + "tools": { + "type": "array", + "description": "Tools used by the module", + "items": { + "type": "object", + "patternProperties": { + ".*": { + "type": "object", + "properties": { + "description": { + "type": "string", + "description": "Description of the output channel" + }, + "homepage": { + "type": "string", + "description": "Homepage of the tool", + "pattern": "^(http|https)://.*$" + }, + "documentation": { + "type": "string", + "description": "Documentation of the tool", + "pattern": "^(http|https)://.*$" + }, + "tool_dev_url": { + "type": "string", + "description": "URL of the development version of the tool's documentation", + "pattern": "^(http|https)://.*$" + }, + "doi": { + "type": "string", + "description": "DOI of the tool", + "pattern": "^10.\\d{4,9}\\/[^,]+$" + }, + "licence": { + "type": ["array", "string"], + "description": "Licence of the tool", + "items": { + "type": "string" + }, + "uniqueItems": true + } + }, + "required": ["description"], + "anyOf": [ + { "required": ["homepage"] }, + { "required": ["documentation"] }, + { "required": ["tool_dev_url"] }, + { "required": ["doi"] } + ] + } + } + } + } + }, + "required": ["name", "description", "keywords", "authors", "output", "tools"] +} \ No newline at end of file From 313e461906848c842b6317a6300e851cb37cc0d1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= Date: Tue, 18 Apr 2023 10:50:22 +0000 Subject: [PATCH 07/11] change org_path --- .nf-core.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.nf-core.yml b/.nf-core.yml index 7f9a6f74..23f2f93f 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -1,2 +1,2 @@ repository_type: modules -org_path: nf-core +org_path: nf-core-test From 47dd9808858533cd1957e8da67967084751d4b76 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= Date: Tue, 18 Apr 2023 10:54:11 +0000 Subject: [PATCH 08/11] modify nf-core directory name --- modules/{nf-core => nf-core-test}/.gitkeep | 0 modules/{nf-core => nf-core-test}/fakeqc/main.nf | 0 modules/{nf-core => nf-core-test}/fakeqc/meta.yml | 0 modules/{nf-core => nf-core-test}/fastqc/main.nf | 0 modules/{nf-core => nf-core-test}/fastqc/meta.yml | 0 modules/{nf-core => nf-core-test}/multiqc/main.nf | 0 modules/{nf-core => nf-core-test}/multiqc/meta.yml | 0 7 files changed, 0 insertions(+), 0 deletions(-) rename modules/{nf-core => nf-core-test}/.gitkeep (100%) rename modules/{nf-core => nf-core-test}/fakeqc/main.nf (100%) rename modules/{nf-core => nf-core-test}/fakeqc/meta.yml (100%) rename modules/{nf-core => nf-core-test}/fastqc/main.nf (100%) rename modules/{nf-core => nf-core-test}/fastqc/meta.yml (100%) rename modules/{nf-core => nf-core-test}/multiqc/main.nf (100%) rename modules/{nf-core => nf-core-test}/multiqc/meta.yml (100%) diff --git a/modules/nf-core/.gitkeep b/modules/nf-core-test/.gitkeep similarity index 100% rename from modules/nf-core/.gitkeep rename to modules/nf-core-test/.gitkeep diff --git a/modules/nf-core/fakeqc/main.nf b/modules/nf-core-test/fakeqc/main.nf similarity index 100% rename from modules/nf-core/fakeqc/main.nf rename to modules/nf-core-test/fakeqc/main.nf diff --git a/modules/nf-core/fakeqc/meta.yml b/modules/nf-core-test/fakeqc/meta.yml similarity index 100% rename from modules/nf-core/fakeqc/meta.yml rename to modules/nf-core-test/fakeqc/meta.yml diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core-test/fastqc/main.nf similarity index 100% rename from modules/nf-core/fastqc/main.nf rename to modules/nf-core-test/fastqc/main.nf diff --git a/modules/nf-core/fastqc/meta.yml b/modules/nf-core-test/fastqc/meta.yml similarity index 100% rename from modules/nf-core/fastqc/meta.yml rename to modules/nf-core-test/fastqc/meta.yml diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core-test/multiqc/main.nf similarity index 100% rename from modules/nf-core/multiqc/main.nf rename to modules/nf-core-test/multiqc/main.nf diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core-test/multiqc/meta.yml similarity index 100% rename from modules/nf-core/multiqc/meta.yml rename to modules/nf-core-test/multiqc/meta.yml From f1ca213d83be53cb2acecba54395b094516be452 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= Date: Fri, 21 Apr 2023 12:14:26 +0000 Subject: [PATCH 09/11] fix dir type in multiqc meta.yml --- modules/nf-core-test/multiqc/meta.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core-test/multiqc/meta.yml b/modules/nf-core-test/multiqc/meta.yml index bf3a27fe..d385b4d2 100644 --- a/modules/nf-core-test/multiqc/meta.yml +++ b/modules/nf-core-test/multiqc/meta.yml @@ -31,7 +31,7 @@ output: description: MultiQC report file pattern: "multiqc_report.html" - data: - type: dir + type: directory description: MultiQC data dir pattern: "multiqc_data" - plots: From db18ba6a427f17cb925eb18ba733de138f4f1cde Mon Sep 17 00:00:00 2001 From: mashehu Date: Tue, 25 Apr 2023 12:11:06 +0000 Subject: [PATCH 10/11] move yam-schema.json file into modules dir --- yaml-schema.json => modules/yaml-schema.json | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename yaml-schema.json => modules/yaml-schema.json (100%) diff --git a/yaml-schema.json b/modules/yaml-schema.json similarity index 100% rename from yaml-schema.json rename to modules/yaml-schema.json From e22f845e5ca42ca743dad4dbf250479aeae32f0f Mon Sep 17 00:00:00 2001 From: nf-core_bot Date: Tue, 9 May 2023 16:10:35 +0200 Subject: [PATCH 11/11] remove quay.io/ prefix --- modules/nf-core-test/fastqc/main.nf | 2 +- modules/nf-core-test/multiqc/main.nf | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/nf-core-test/fastqc/main.nf b/modules/nf-core-test/fastqc/main.nf index 05730368..7777e0aa 100644 --- a/modules/nf-core-test/fastqc/main.nf +++ b/modules/nf-core-test/fastqc/main.nf @@ -5,7 +5,7 @@ process FASTQC { conda (params.enable_conda ? "bioconda::fastqc=0.11.9" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0' : - 'quay.io/biocontainers/fastqc:0.11.9--0' }" + 'biocontainers/fastqc:0.11.9--0' }" input: tuple val(meta), path(reads) diff --git a/modules/nf-core-test/multiqc/main.nf b/modules/nf-core-test/multiqc/main.nf index b0831b5d..c6d1fe52 100644 --- a/modules/nf-core-test/multiqc/main.nf +++ b/modules/nf-core-test/multiqc/main.nf @@ -4,7 +4,7 @@ process MULTIQC { conda (params.enable_conda ? 'bioconda::multiqc=1.12' : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/multiqc:1.12--pyhdfd78af_0' : - 'quay.io/biocontainers/multiqc:1.12--pyhdfd78af_0' }" + 'biocontainers/multiqc:1.12--pyhdfd78af_0' }" input: path multiqc_files, stageAs: "?/*"