Dev > main: first release

.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. 23.04.0)_
-
-      * 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 nf-cmgg/sampletracking _(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. 23.04.0)_
+
+        * 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 nf-cmgg/sampletracking _(eg. 1.1, 1.5, 1.8.2)_
+
+        "

.nf-core.yml

@@ -1,24 +1,24 @@
 lint:
   files_exist:
-  - CODE_OF_CONDUCT.md
-  - assets/nf-core-sampletracking_logo_light.png
-  - docs/images/nf-core-sampletracking_logo_light.png
-  - docs/images/nf-core-sampletracking_logo_dark.png
-  - .github/ISSUE_TEMPLATE/config.yml
-  - .github/workflows/awstest.yml
-  - .github/workflows/awsfulltest.yml
+    - CODE_OF_CONDUCT.md
+    - assets/nf-core-sampletracking_logo_light.png
+    - docs/images/nf-core-sampletracking_logo_light.png
+    - docs/images/nf-core-sampletracking_logo_dark.png
+    - .github/ISSUE_TEMPLATE/config.yml
+    - .github/workflows/awstest.yml
+    - .github/workflows/awsfulltest.yml
   files_unchanged:
-  - CODE_OF_CONDUCT.md
-  - assets/nf-core-sampletracking_logo_light.png
-  - docs/images/nf-core-sampletracking_logo_light.png
-  - docs/images/nf-core-sampletracking_logo_dark.png
-  - .github/ISSUE_TEMPLATE/bug_report.yml
+    - CODE_OF_CONDUCT.md
+    - assets/nf-core-sampletracking_logo_light.png
+    - docs/images/nf-core-sampletracking_logo_light.png
+    - docs/images/nf-core-sampletracking_logo_dark.png
   multiqc_config:
-  - report_comment
+    - report_comment
   nextflow_config:
-  - manifest.name
-  - manifest.homePage
+    - manifest.name
+    - manifest.homePage
 repository_type: pipeline
 template:
   prefix: nf-cmgg
-  skip: []
+  skip:
+    - igenomes

assets/multiqc_config.yml

@@ -1,5 +1,5 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-cmgg/sampletracking/tree/dev" target="_blank">nf-cmgg/sampletracking</a>
+  This report has been generated by the <a href="https://github.com/nf-cmgg/sampletracking/releases/tag/1.0" target="_blank">nf-cmgg/sampletracking</a>
   analysis pipeline.
 report_section_order:
   "nf-cmgg-sampletracking-methods-description":

assets/samplesheet.csv

@@ -1,3 +1,3 @@
-sample,fastq_1,fastq_2
-SAMPLE_PAIRED_END,/path/to/fastq/files/AEG588A1_S1_L002_R1_001.fastq.gz,/path/to/fastq/files/AEG588A1_S1_L002_R2_001.fastq.gz
-SAMPLE_SINGLE_END,/path/to/fastq/files/AEG588A4_S4_L003_R1_001.fastq.gz,
+sample  ,pool  ,sample_bam                                                                                                               ,sample_bam_index ,snp_fastq_1                                                                                                     ,snp_fastq_2                                                                                                     ,snp_bam                                                                                                                                 ,snp_bam_index
+sample1 ,pool1 ,https://github.com/nf-core/test-datasets/blob/modules/data/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam ,                 ,                                                                                                                ,                                                                                                                ,https://github.com/nf-core/test-datasets/blob/modules/data/genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam
+sample2 ,pool1 ,https://github.com/nf-core/test-datasets/raw/modules/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam ,                 ,https://github.com/nf-core/test-datasets/raw/modules/data/genomics/homo_sapiens/illumina/fastq/test2_1.fastq.gz ,https://github.com/nf-core/test-datasets/raw/modules/data/genomics/homo_sapiens/illumina/fastq/test2_2.fastq.gz ,                                                                                                                                        ,

assets/schema_input.json

@@ -11,23 +11,62 @@
                 "type": "string",
                 "pattern": "^\\S+$",
                 "errorMessage": "Sample name must be provided and cannot contain spaces",
-                "meta": ["id"]
+                "meta": ["id", "samplename"],
+                "unique": true
             },
-            "fastq_1": {
+            "pool": {
+                "type": "string",
+                "pattern": "^\\S+$",
+                "default": "sampletracking_pool",
+                "meta": ["pool"],
+                "errorMessage": "Pool name must be provided and cannot contain spaces"
+            },
+            "sample_bam": {
+                "type": "string",
+                "format": "file-path",
+                "exists": true,
+                "errorMessage": "Sample BAM/CRAM file must be provided, cannot contain spaces and must have extension '.bam' or '.cram'"
+            },
+            "sample_bam_index": {
+                "type": "string",
+                "format": "file-path",
+                "exists": true,
+                "errorMessage": "Sample BAM/CRAM index file must be provided, cannot contain spaces and must have extension '.bai' or '.csi'"
+            },
+            "snp_fastq_1": {
                 "type": "string",
                 "format": "file-path",
                 "exists": true,
                 "pattern": "^\\S+\\.f(ast)?q\\.gz$",
                 "errorMessage": "FastQ file for reads 1 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
             },
-            "fastq_2": {
+            "snp_fastq_2": {
                 "type": "string",
                 "format": "file-path",
                 "exists": true,
                 "pattern": "^\\S+\\.f(ast)?q\\.gz$",
                 "errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
+            },
+            "snp_bam": {
+                "type": "string",
+                "format": "file-path",
+                "exists": true,
+                "errorMessage": "snp BAM/CRAM file must be provided, cannot contain spaces and must have extension '.bam' or '.cram'"
+            },
+            "snp_bam_index": {
+                "type": "string",
+                "format": "file-path",
+                "exists": true,
+                "errorMessage": "snp BAM/CRAM index file must be provided, cannot contain spaces and must have extension '.bai' or '.csi'"
             }
         },
-        "required": ["sample", "fastq_1"]
+        "AnyOf": [
+            {
+                "required": ["sample", "sample_bam", "snp_fastq_1", "snp_fastq_2"]
+            },
+            {
+                "required": ["sample", "sample_bam", "snp_bam"]
+            }
+        ]
     }
 }