correction via prettier

mskcc · Dec 31, 2022 · 0a8b606 · 0a8b606
1 parent e3e9a7f
commit 0a8b606
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Showing 3 changed files with 41 additions and 83 deletions.
diff --git a/.nf-core.yml b/.nf-core.yml
@@ -1,29 +1,29 @@
 repository_type: pipeline
 lint:
   files_exist:
-  - CODE_OF_CONDUCT.md
-  - assets/nf-core-forte_logo_light.png
-  - docs/images/nf-core-forte_logo_light.png
-  - docs/images/nf-core-forte_logo_dark.png
-  - .github/ISSUE_TEMPLATE/config.yml
-  - .github/workflows/awstest.yml
-  - .github/workflows/awsfulltest.yml
-  - .github/ISSUE_TEMPLATE/bug_report.yml
-  - .github/workflows/branch.yml
-  - .github/workflows/ci.yml
-  - .github/workflows/linting_comment.yml
-  - .github/workflows/linting.yml
-  - conf/igenomes.config
+    - CODE_OF_CONDUCT.md
+    - assets/nf-core-forte_logo_light.png
+    - docs/images/nf-core-forte_logo_light.png
+    - docs/images/nf-core-forte_logo_dark.png
+    - .github/ISSUE_TEMPLATE/config.yml
+    - .github/workflows/awstest.yml
+    - .github/workflows/awsfulltest.yml
+    - .github/ISSUE_TEMPLATE/bug_report.yml
+    - .github/workflows/branch.yml
+    - .github/workflows/ci.yml
+    - .github/workflows/linting_comment.yml
+    - .github/workflows/linting.yml
+    - conf/igenomes.config
   nextflow_config:
-  - manifest.name
-  - manifest.homePage
-  - process.cpus
-  - process.memory
-  - process.time
-  - custom_config
+    - manifest.name
+    - manifest.homePage
+    - process.cpus
+    - process.memory
+    - process.time
+    - custom_config
   multiqc_config:
-  - report_comment
+    - report_comment
   files_unchanged:
-  - .github/ISSUE_TEMPLATE/bug_report.yml
+    - .github/ISSUE_TEMPLATE/bug_report.yml
   readme:
-  - nextflow_badge
+    - nextflow_badge
diff --git a/modules.json b/modules.json
@@ -8,114 +8,82 @@
                     "arriba": {
                         "branch": "master",
                         "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
                         "git_sha": "8022c68e7403eecbd8ba9c49496f69f8c49d50f0",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "fastp": {
                         "branch": "master",
                         "git_sha": "1e49f31e93c56a3832833eef90a02d3cde5a3f7e",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "gatk4/bedtointervallist": {
                         "branch": "master",
                         "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "gatk4/createsequencedictionary": {
                         "branch": "master",
                         "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "gunzip": {
                         "branch": "master",
                         "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "multiqc": {
                         "branch": "master",
                         "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "picard/collecthsmetrics": {
                         "branch": "master",
                         "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "picard/collectrnaseqmetrics": {
                         "branch": "master",
                         "git_sha": "54f28e020daf9215ab000da7af3b273e85639855",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "samtools/bam2fq": {
                         "branch": "master",
                         "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "samtools/index": {
                         "branch": "master",
                         "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "star/align": {
                         "branch": "master",
                         "git_sha": "cf5b9c30a2adacc581793afb79fae5f5b50bed01",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "star/genomegenerate": {
                         "branch": "master",
                         "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "ucsc/gtftogenepred": {
                         "branch": "master",
                         "git_sha": "511909dedab2a9955f2c3eae88abd3733edfd349",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "umitools/dedup": {
                         "branch": "master",
                         "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "umitools/extract": {
                         "branch": "master",
                         "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     }
                 }
             },
@@ -124,4 +92,4 @@
             }
         }
     }
-}
+}
diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -10,10 +10,7 @@
             "type": "object",
             "fa_icon": "fas fa-terminal",
             "description": "Define where the pipeline should find input data and save output data.",
-            "required": [
-                "input",
-                "outdir"
-            ],
+            "required": ["input", "outdir"],
             "properties": {
                 "input": {
                     "type": "string",
@@ -114,14 +111,7 @@
                     "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": {