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genomic-medicine-sweden · Oct 9, 2024 · 1c79c65 · 1c79c65
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diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml
@@ -2,7 +2,6 @@ name: Bug report
 description: Report something that is broken or incorrect
 labels: bug
 body:
-
   - type: textarea
     id: description
     attributes:

diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml
@@ -117,4 +117,3 @@ jobs:
           else
             echo "The pipeline can be downloaded successfully!"
           fi
-
diff --git a/.nf-core.yml b/.nf-core.yml
@@ -1,31 +1,31 @@
 bump_version: null
 lint:
   files_exist:
-  - CODE_OF_CONDUCT.md
-  - assets/nf-core-nallo_logo_light.png
-  - docs/README.md
-  - docs/images/nf-core-nallo_logo_light.png
-  - docs/images/nf-core-nallo_logo_dark.png
-  - .github/ISSUE_TEMPLATE/config.yml
-  - .github/workflows/awstest.yml
-  - .github/workflows/awsfulltest.yml
-  - conf/modules.config
+    - CODE_OF_CONDUCT.md
+    - assets/nf-core-nallo_logo_light.png
+    - docs/README.md
+    - docs/images/nf-core-nallo_logo_light.png
+    - docs/images/nf-core-nallo_logo_dark.png
+    - .github/ISSUE_TEMPLATE/config.yml
+    - .github/workflows/awstest.yml
+    - .github/workflows/awsfulltest.yml
+    - conf/modules.config
   files_unchanged:
-  - CODE_OF_CONDUCT.md
-  - assets/nf-core-nallo_logo_light.png
-  - docs/README.md
-  - docs/images/nf-core-nallo_logo_light.png
-  - docs/images/nf-core-nallo_logo_dark.png
-  - .github/ISSUE_TEMPLATE/bug_report.yml
-  - .github/CONTRIBUTING.md
-  - .prettierignore
+    - CODE_OF_CONDUCT.md
+    - assets/nf-core-nallo_logo_light.png
+    - docs/README.md
+    - docs/images/nf-core-nallo_logo_light.png
+    - docs/images/nf-core-nallo_logo_dark.png
+    - .github/ISSUE_TEMPLATE/bug_report.yml
+    - .github/CONTRIBUTING.md
+    - .prettierignore
   modules_config: false
   multiqc_config:
-  - report_comment
+    - report_comment
   nextflow_config:
-  - manifest.name
-  - manifest.homePage
-nf_core_version: 3.0.0
+    - manifest.name
+    - manifest.homePage
+nf_core_version: 3.0.1
 org_path: null
 repository_type: pipeline
 template:

diff --git a/CITATIONS.md b/CITATIONS.md
@@ -145,4 +145,3 @@
 - [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/)
 
   > Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675.
-  >
diff --git a/README.md b/README.md
@@ -2,7 +2,7 @@
 [![GitHub Actions Linting Status](https://github.com/genomic-medicine-sweden/nallo/actions/workflows/linting.yml/badge.svg)](https://github.com/genomic-medicine-sweden/nallo/actions/workflows/linting.yml)
 [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.13748210.svg)](https://doi.org/10.5281/zenodo.13748210)
-[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/)
+[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
 [![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/genomic-medicine-sweden/nallo)

diff --git a/assets/schema_input.json b/assets/schema_input.json
@@ -28,28 +28,28 @@
             "paternal_id": {
                 "oneOf": [
                     {
-                      "type": "integer",
-                      "enum": [0]
+                        "type": "integer",
+                        "enum": [0]
                     },
                     {
-                      "type": "string",
-                      "pattern": "^(\\S+)$"
+                        "type": "string",
+                        "pattern": "^(\\S+)$"
                     }
-                  ],
+                ],
                 "errorMessage": "Paternal ID must be provided and cannot contain spaces. If no paternal ID is available, use 0.",
                 "meta": ["paternal_id"]
             },
             "maternal_id": {
                 "oneOf": [
                     {
-                      "type": "integer",
-                      "enum": [0]
+                        "type": "integer",
+                        "enum": [0]
                     },
                     {
-                      "type": "string",
-                      "pattern": "^(\\S+)$"
+                        "type": "string",
+                        "pattern": "^(\\S+)$"
                     }
-                  ],
+                ],
                 "errorMessage": "Maternal ID must be provided and cannot contain spaces. If no maternal ID is available, use 0.",
                 "meta": ["maternal_id"]
             },

diff --git a/conf/base.config b/conf/base.config
@@ -10,7 +10,6 @@
 
 process {
 
-    // TODO nf-core: Check the defaults for all processes
     cpus   = { 1      * task.attempt }
     memory = { 6.GB   * task.attempt }
     time   = { 4.h    * task.attempt }

diff --git a/docs/usage.md b/docs/usage.md
@@ -320,7 +320,6 @@ Whilst the default requirements set within the pipeline will hopefully work for
 
 To change the resource requests, please see the [max resources](https://nf-co.re/docs/usage/configuration#max-resources) and [tuning workflow resources](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources) section of the nf-core website.
 
-
 ### Custom Containers
 
 In some cases you may wish to change which container a step of the pipeline uses for a particular tool. By default nf-core pipelines use containers and software from the [biocontainers](https://biocontainers.pro/) or [bioconda](https://bioconda.github.io/) projects. However in some cases the pipeline specified version maybe out of date.

diff --git a/modules.json b/modules.json
@@ -271,12 +271,12 @@
                 "nf-core": {
                     "utils_nextflow_pipeline": {
                         "branch": "master",
-                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
+                        "git_sha": "d20fb2a9cc3e2835e9d067d1046a63252eb17352",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "92de218a329bfc9a9033116eb5f65fd270e72ba3",
+                        "git_sha": "2fdce49d30c0254f76bc0f13c55c17455c1251ab",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfschema_plugin": {

diff --git a/nextflow.config b/nextflow.config
@@ -64,9 +64,6 @@ params {
 
     // References
     fasta                      = null
-    genome                     = null
-    igenomes_base              = 's3://ngi-igenomes/igenomes/'
-    igenomes_ignore            = true
 
     // MultiQC options
     multiqc_config             = null
@@ -221,8 +218,6 @@ podman.registry       = 'quay.io'
 singularity.registry  = 'quay.io'
 charliecloud.registry = 'quay.io'
 
-// Load igenomes.config if required
-includeConfig !params.igenomes_ignore ? 'conf/igenomes.config' : 'conf/igenomes_ignored.config'
 // Export these variables to prevent local Python/R libraries from conflicting with those in the container
 // The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container.
 // See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable.
@@ -273,7 +268,7 @@ manifest {
     mainScript      = 'main.nf'
     nextflowVersion = '!>=24.04.2'
     version         = '0.4.0dev'
-    doi             = ''
+    doi             = '10.5281/zenodo.13748210'
 }
 
 // Nextflow plugins
@@ -288,6 +283,29 @@ validation {
         command = "nextflow run $manifest.name -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
         fullParameter = "help_full"
         showHiddenParameter = "show_hidden"
+        beforeText = """
+                                  _                              _ _      _
+  __ _  ___ _ __   ___  _ __ ___ (_) ___      _ __ ___   ___  __| (_) ___(_)_ __   ___
+ / _` |/ _ \\ '_ \\ / _ \\| '_ ` _ \\| |/ __|____| '_ ` _ \\ / _ \\/ _` | |/ __| | '_ \\ / _ \\_____
+| (_| |  __/ | | | (_) | | | | | | | (_|_____| | | | | |  __/ (_| | | (__| | | | |  __/_____|
+ \\__, |\\___|_| |_|\\___/|_| |_| |_|_|\\___|    |_| |_| |_|\\___|\\__,_|_|\\___|_|_| |_|\\___|
+ |___/      _____  __| | ___ _ __    / / __   __ _| | | ___
+/ __\\ \\ /\\ / / _ \\/ _` |/ _ \\ '_ \\  / / '_ \\ / _` | | |/ _ \\
+\\__ \\\\ V  V /  __/ (_| |  __/ | | |/ /| | | | (_| | | | (_) |
+|___/ \\_/\\_/ \\___|\\__,_|\\___|_| |_/_/ |_| |_|\\__,_|_|_|\\___/
+
+"""
+        afterText = """${manifest.doi ? "* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { "  https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
+* The nf-core framework
+  https://doi.org/10.1038/s41587-020-0439-x
+
+* Software dependencies
+  https://github.com/${manifest.name}/blob/master/CITATIONS.md
+"""
+    }
+    summary {
+        beforeText = validation.help.beforeText
+        afterText = validation.help.afterText
     }
 }
 

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -225,20 +225,6 @@
                     "format": "file-path",
                     "exists": true
                 },
-                "validationFailUnrecognisedParams": {
-                    "type": "boolean",
-                    "fa_icon": "far fa-check-circle",
-                    "description": "Validation of parameters fails when an unrecognised parameter is found.",
-                    "hidden": true,
-                    "help_text": "By default, when an unrecognised parameter is found, it returns a warning."
-                },
-                "validationLenientMode": {
-                    "type": "boolean",
-                    "fa_icon": "far fa-check-circle",
-                    "description": "Validation of parameters in lenient more.",
-                    "hidden": true,
-                    "help_text": "Allows string values that are parseable as numbers or booleans. For further information see [JSONSchema docs](https://github.com/everit-org/json-schema#lenient-mode)."
-                },
                 "pipelines_testdata_base_path": {
                     "type": "string",
                     "fa_icon": "far fa-check-circle",
@@ -260,26 +246,6 @@
                     "pattern": "^.*\\.(fasta|fa|fna)(\\.gz)?$",
                     "format": "file-path",
                     "exists": true
-                },
-                "genome": {
-                    "type": "string",
-                    "description": "Name of iGenomes reference.",
-                    "help_text": "If using a reference genome configured in the pipeline using iGenomes, use this parameter to give the ID for the reference. This is then used to build the full paths for all required reference genome files e.g. `--genome GRCh38`. \n\nSee the [nf-core website docs](https://nf-co.re/usage/reference_genomes) for more details."
-                },
-                "igenomes_ignore": {
-                    "type": "boolean",
-                    "description": "Do not load the iGenomes reference config.",
-                    "fa_icon": "fas fa-ban",
-                    "hidden": true,
-                    "help_text": "Do not load `igenomes.config` when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in `igenomes.config`."
-                },
-                "igenomes_base": {
-                    "type": "string",
-                    "format": "directory-path",
-                    "description": "The base path to the igenomes reference files",
-                    "fa_icon": "fas fa-ban",
-                    "hidden": true,
-                    "default": "s3://ngi-igenomes/igenomes/"
                 }
             }
         },
@@ -412,11 +378,6 @@
                     "default": true,
                     "fa_icon": "fas fa-check-square",
                     "hidden": true
-                },
-                "monochromeLogs": {
-                    "type": "boolean",
-                    "hidden": true,
-                    "description": "Boolean whether to color nf-validation logs"
                 }
             }
         },
@@ -514,7 +475,7 @@
                 }
             },
             "required": ["preset"]
-        },
+        }
     },
     "allOf": [
         {