Merge pull request #6 from CenterForMedicalGeneticsGhent/dev

Release PR v1.0.1
nf-cmgg · Jun 19, 2023 · ddccaa7 · ddccaa7
2 parents ef940a3 + e85c85d
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diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml
@@ -2,54 +2,54 @@ 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 CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx _(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 CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx _(eg. 1.1, 1.5,
+        1.8.2)_
+
+        "
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -47,4 +47,4 @@ jobs:
         uses: mikepenz/action-junit-report@v3
         if: always() # always run even if the previous step fails
         with:
-          report_paths: "default.xml"
+          report_paths: "default.xml"
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,6 +3,17 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## v1.0.1 - Helpful Apprentice - [19 June 2023]
+
+### New features
+
+1. Added a gender metrics output file (can be turned off by using `--no_metrics`)
+2. Added a new field to the samplesheet (`gender`). This optional field is used for the generation of the metrics file. The gender will be determined by the pipeline if this field is empty.
+
+### Improvements
+
+1. Added parameter information to the docs
+
 ## v1.0.0 - Clumsy Apprentice - [22 May 2023]
 
 Initial release of CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx, created with the [nf-core](https://nf-co.re/) template.
diff --git a/README.md b/README.md
@@ -27,6 +27,8 @@ nextflow run CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx \
    --outdir <OUTDIR>
 ```
 
+See the [parameters](docs/parameters.md) documentation for more information on all the options.
+
 > **Warning:**
 > Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those
 > provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_;

diff --git a/assets/samplesheet.csv b/assets/samplesheet.csv
@@ -1,3 +1,3 @@
-cram,crai
-https://raw.githubusercontent.com/CenterForMedicalGeneticsGhent/nf-cmgg-test-datasets/main/data/genomics/homo_sapiens/illumina/cram/test.cram,,
-https://raw.githubusercontent.com/CenterForMedicalGeneticsGhent/nf-cmgg-test-datasets/main/data/genomics/homo_sapiens/illumina/cram/test2.cram,https://raw.githubusercontent.com/CenterForMedicalGeneticsGhent/nf-cmgg-test-datasets/main/data/genomics/homo_sapiens/illumina/cram/test2.cram.crai
+cram,crai,gender
+https://raw.githubusercontent.com/CenterForMedicalGeneticsGhent/nf-cmgg-test-datasets/main/data/genomics/homo_sapiens/illumina/cram/test.cram,,male
+https://raw.githubusercontent.com/CenterForMedicalGeneticsGhent/nf-cmgg-test-datasets/main/data/genomics/homo_sapiens/illumina/cram/test2.cram,https://raw.githubusercontent.com/CenterForMedicalGeneticsGhent/nf-cmgg-test-datasets/main/data/genomics/homo_sapiens/illumina/cram/test2.cram.crai,
diff --git a/assets/schema_input.json b/assets/schema_input.json
@@ -3,18 +3,26 @@
     "$id": "https://raw.githubusercontent.com/CenterForMedicalGeneticsGhent/nf-cmgg-wisecondorx/master/assets/schema_input.json",
     "title": "Samplesheet validation schema",
     "description": "Schema for the samplesheet used in this pipeline",
-    "type": "object",
-    "properties": {
-        "cram": {
-            "type": "string",
-            "pattern": "^\\S+\\.(b|cr)am$",
-            "format": "file-path"
+    "type": "array",
+    "items": {
+        "type": "object",
+        "properties": {
+            "cram": {
+                "type": "string",
+                "pattern": "^\\S+\\.(b|cr)am$",
+                "format": "file-path"
+            },
+            "crai": {
+                "type": "string",
+                "pattern": "^\\S+\\.(b|cr)ai$",
+                "format": "file-path"
+            },
+            "gender": {
+                "type": "string",
+                "pattern": "^(male|female)$",
+                "meta": ["gender"]
+            }
         },
-        "crai": {
-            "type": "string",
-            "pattern": "^\\S+\\.(b|cr)ai$",
-            "format": "file-path"
-        }
-    },
-    "required": ["cram"]
+        "required": ["cram"]
+    }
 }
diff --git a/docs/output.md b/docs/output.md
@@ -10,13 +10,15 @@ The directories listed below will be created in the results directory after the
 results/
 ├── multiqc_reports
 ├── pipeline_info
+├── metrics.txt
 └── WisecondorX_09052023.npz
 ```
 
 ## Pipeline overview
 
 The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes data using the following steps:
 
+- SampleGender (ngs-bits) - Determine the gender from a BAM/CRAM file
 - WiseCondorX convert - Convert CRAM/BAM files to NPZ files
 - WiseCondorX newref- Create a new reference from all NPZ files
 - MultiQC- Aggregate report describing results and QC from the whole pipeline