Merge pull request #17 from phac-nml/release-0.1.0

Release 0.1.0

CHANGELOG.md

@@ -3,7 +3,7 @@
 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).
 
-## [0.1.0]
+## [0.1.0] - 2024-08-19
 
 Initial release of the arboratornf pipeline to be used for running [Arborator](https://github.com/phac-nml/arborator) under Nextflow.
 

README.md

@@ -21,8 +21,8 @@ The columns of the samplesheet are defined as follows:
 
 The names of each metadata column (metadata_partition, and metadata_1..metadata_8) are provided using the following parameters:
 
-- metadata_partition_name: The name of the metadata_partition column (for example: "outbreak").
-- metadata_1_header..metadata_8_header: The name of each individual metadata column (for example: "organism" or "source").
+- `--metadata_partition_name`: The name of the metadata_partition column (for example: "outbreak").
+- `--metadata_1_header..metadata_8_header`: The name of each individual metadata column (for example: "organism" or "source").
 
 Entries in the `metadata_partition` column in the sample sheet, as well as the name provided by the `metadata_partition_name` parameter, must contain only the following characters alphanumeric, `_`, `.`, and `-` characters.
 
@@ -36,6 +36,15 @@ Furthermore, the structure of the sample sheet is programmatically defined in [a
 
 The mandatory parameters are `--input`, which specifies the samplesheet as described above, and `--output`, which specifies the output results directory. You may wish to provide `-profile singularity` to specify the use of singularity containers and `-r [branch]` to specify which GitHub branch you would like to run. Metadata-related parameters are described above in [Input](#input).
 
+## Optional
+
+The optional parameters are as follows:
+
+### Arborator
+
+- `--ar_config`: The Arborator-specific config file for specifying the operations used when summarizing metadata and how such metadata should be displayed in the output.
+- `--ar_thresholds`: The clustering thresholds used by Arborator. These thresholds must be provided as a list of integers.
+
 Further parameters (defaults from nf-core) are defined in [nextflow_schema.json](nextflow_schema.json).
 
 # Running
@@ -48,6 +57,8 @@ nextflow run phac-nml/arboratornf -profile singularity -r main -latest --input a
 
 Where the `samplesheet.csv` is structured as specified in the [Input](#input) section and `parameters.yaml` provides parameters for renaming metadata column headers, which may either be specified individually on the command line or collectively in a parameters file.
 
+Additional details on usage of the pipeline are found in [docs/usage.md](docs/usage.md).
+
 # Output
 
 A JSON-formatted file for loading metadata into IRIDA Next is output by this pipeline. The format of this JSON-formatted file is specified in our [Pipeline Standards for the IRIDA Next JSON](https://github.com/phac-nml/pipeline-standards#32-irida-next-json). This JSON-formatted file is written directly within the `--outdir` provided to the pipeline with the name `iridanext.output.json.gz` (ex: `[outdir]/iridanext.output.json.gz`).
@@ -66,7 +77,8 @@ An example of the what the contents of the IRIDA Next JSON-formatted file looks
             },
             {
                 "path": "arborator/cluster_summary.tsv"
-            }
+            },
+            // ...
         ],
         "samples": {
 
@@ -84,6 +96,8 @@ Within the `files` section of this JSON-formatted file, all of the output paths
 
 The `arborator/metadata.included.tsv` and `arborator/metadata.excluded.tsv` output files summarize which samples were analyzed and which were not. Samples that contain missing data for the `metadata_partition` column will not be included in analysis and will be reported in the `arborator/metadata.excluded.tsv` output file.
 
+Additional details on output files are found in [docs/output.md](docs/output.md).
+
 ## Test profile
 
 To run with the test profile, please do:

tests/pipelines/main.nf.test

@@ -1,5 +1,5 @@
 nextflow_pipeline {
-    name "Integration Tests for Cluster Splitting"
+    name "Integration Tests for Arborator pipeline"
     script "main.nf"
 
     test("Small-scale test of full pipeline"){