Merge branch 'TEMPLATE' into dev

sanger-tol · Jul 12, 2023 · f8ae514 · f8ae514
2 parents 9e64c21 + ee55f5d
commit f8ae514
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diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml
@@ -2,53 +2,53 @@ name: Bug report
 description: Report something that is broken or incorrect
 labels: bug
 body:
-- type: textarea
-  id: description
-  attributes:
-    label: Description of the bug
-    description: A clear and concise description of what the bug is.
-  validations:
-    required: true
-- type: textarea
-  id: command_used
-  attributes:
-    label: Command used and terminal output
-    description: Steps to reproduce the behaviour. Please paste the command you used
-      to launch the pipeline and the output from your terminal.
-    render: console
-    placeholder: '$ nextflow run ...
-
-
-      Some output where something broke
-
-      '
-- type: textarea
-  id: files
-  attributes:
-    label: Relevant files
-    description: 'Please drag and drop the relevant files here. Create a `.zip` archive
-      if the extension is not allowed.
-
-      Your verbose log file `.nextflow.log` is often useful _(this is a hidden file
-      in the directory where you launched the pipeline)_ as well as custom Nextflow
-      configuration files.
-
-      '
-- type: textarea
-  id: system
-  attributes:
-    label: System information
-    description: '* Nextflow version _(eg. 22.10.1)_
-
-      * Hardware _(eg. HPC, Desktop, Cloud)_
-
-      * Executor _(eg. slurm, local, awsbatch)_
-
-      * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud,
-      or Apptainer)_
-
-      * OS _(eg. CentOS Linux, macOS, Linux Mint)_
-
-      * Version of sanger-tol/sequencecomposition _(eg. 1.1, 1.5, 1.8.2)_
-
-      '
+  - type: textarea
+    id: description
+    attributes:
+      label: Description of the bug
+      description: A clear and concise description of what the bug is.
+    validations:
+      required: true
+  - type: textarea
+    id: command_used
+    attributes:
+      label: Command used and terminal output
+      description: Steps to reproduce the behaviour. Please paste the command you used
+        to launch the pipeline and the output from your terminal.
+      render: console
+      placeholder: "$ nextflow run ...
+
+
+        Some output where something broke
+
+        "
+  - type: textarea
+    id: files
+    attributes:
+      label: Relevant files
+      description: "Please drag and drop the relevant files here. Create a `.zip` archive
+        if the extension is not allowed.
+
+        Your verbose log file `.nextflow.log` is often useful _(this is a hidden file
+        in the directory where you launched the pipeline)_ as well as custom Nextflow
+        configuration files.
+
+        "
+  - type: textarea
+    id: system
+    attributes:
+      label: System information
+      description: "* Nextflow version _(eg. 22.10.1)_
+
+        * Hardware _(eg. HPC, Desktop, Cloud)_
+
+        * Executor _(eg. slurm, local, awsbatch)_
+
+        * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud,
+        or Apptainer)_
+
+        * OS _(eg. CentOS Linux, macOS, Linux Mint)_
+
+        * Version of sanger-tol/sequencecomposition _(eg. 1.1, 1.5, 1.8.2)_
+
+        "
diff --git a/.nf-core.yml b/.nf-core.yml
@@ -1,24 +1,24 @@
 repository_type: pipeline
 lint:
   files_exist:
-  - CODE_OF_CONDUCT.md
-  - assets/multiqc_config.yml
-  - assets/nf-core-sequencecomposition_logo_light.png
-  - conf/igenomes.config
-  - docs/images/nf-core-sequencecomposition_logo_light.png
-  - docs/images/nf-core-sequencecomposition_logo_dark.png
-  - .github/ISSUE_TEMPLATE/config.yml
-  - .github/workflows/awstest.yml
-  - .github/workflows/awsfulltest.yml
+    - CODE_OF_CONDUCT.md
+    - assets/multiqc_config.yml
+    - assets/nf-core-sequencecomposition_logo_light.png
+    - conf/igenomes.config
+    - docs/images/nf-core-sequencecomposition_logo_light.png
+    - docs/images/nf-core-sequencecomposition_logo_dark.png
+    - .github/ISSUE_TEMPLATE/config.yml
+    - .github/workflows/awstest.yml
+    - .github/workflows/awsfulltest.yml
   files_unchanged:
-  - LICENSE
-  - .github/CONTRIBUTING.md
-  - .github/ISSUE_TEMPLATE/bug_report.yml
-  - .github/workflows/linting.yml
-  - assets/sendmail_template.txt
-  - lib/NfcoreTemplate.groovy
+    - LICENSE
+    - .github/CONTRIBUTING.md
+    - .github/ISSUE_TEMPLATE/bug_report.yml
+    - .github/workflows/linting.yml
+    - assets/sendmail_template.txt
+    - lib/NfcoreTemplate.groovy
   nextflow_config:
-  - manifest.name
-  - manifest.homePage
+    - manifest.name
+    - manifest.homePage
   multiqc_config:
-  - report_comment
+    - report_comment
diff --git a/CITATION.cff b/CITATION.cff
@@ -4,21 +4,21 @@
 cff-version: 1.2.0
 title: sanger-tol/sequencecomposition v1.0.0 - Apophis
 message: >-
-  If you use this software, please cite it using the
-  metadata from this file.
+    If you use this software, please cite it using the
+    metadata from this file.
 type: software
 authors:
-  - given-names: Matthieu
-    family-names: Muffato
-    affiliation: Wellcome Sanger Institute
-    orcid: "https://orcid.org/0000-0002-7860-3560"
-  - given-names: Priyanka
-    family-names: Surana
-    orcid: "https://orcid.org/0000-0002-7167-0875"
-    affiliation: Wellcome Sanger Institute
+    - given-names: Matthieu
+      family-names: Muffato
+      affiliation: Wellcome Sanger Institute
+      orcid: "https://orcid.org/0000-0002-7860-3560"
+    - given-names: Priyanka
+      family-names: Surana
+      orcid: "https://orcid.org/0000-0002-7167-0875"
+      affiliation: Wellcome Sanger Institute
 identifiers:
-  - type: doi
-    value: 10.5281/zenodo.7155169
+    - type: doi
+      value: 10.5281/zenodo.7155169
 repository-code: "https://github.com/sanger-tol/sequencecomposition"
 license: MIT
 commit: TODO

diff --git a/modules.json b/modules.json
@@ -8,40 +8,30 @@
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "fastawindows": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "gunzip": {
                         "branch": "master",
                         "git_sha": "e06548bfa36ee31869b81041879dd6b3a83b1d57",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "tabix/bgzip": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "tabix/tabix": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     }
                 }
             }
         }
     }
-}
+}
diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -10,11 +10,7 @@
             "type": "object",
             "fa_icon": "fas fa-terminal",
             "description": "Define where the pipeline should find input data and save output data.",
-            "required": [
-                "outdir",
-                "window_size_info",
-                "selected_fw_output"
-            ],
+            "required": ["outdir", "window_size_info", "selected_fw_output"],
             "properties": {
                 "fasta": {
                     "type": "string",
@@ -171,14 +167,7 @@
                     "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"
-                    ],
+                    "enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"],
                     "hidden": true
                 },
                 "email_on_fail": {

diff --git a/pipeline_template.yml b/pipeline_template.yml
@@ -1,3 +1,3 @@
 prefix: sanger-tol
 skip:
-- igenomes
+  - igenomes