Merge pull request #8 from Sage-Bionetworks-Workflows/bwmac/orca-254/…

…report_config

[ORCA-254] Adds information for output files and Tower reports

README.md

@@ -52,6 +52,16 @@ On release, automated continuous integration tests run the pipeline on a full-si
    nextflow run sage/dcqc --input samplesheet.csv --outdir <OUTDIR> --genome GRCh37 -profile <docker/singularity/podman/shifter/charliecloud/conda/institute>
    ```
 
+## Special Considerations for Running `nf-dcqc` on Nextflow Tower
+
+`nf-dcqc` leverages the reports feature when executed on Tower. This is done by pointing Tower to the generated `output.csv` file which is saved to `params.outdir` after a successful run. By default, the `outdir` for the workflow is set to a local directory called `results`. This does not work on Nextflow Tower runs, as you will not have access to the `results` directory once the job has completed. Thus, the `outdir` should be set to an S3 bucket location that the Tower workspace you are using has access to. For example, in the `pipeline parameters` for a Tower run, you can provide YAML such as:
+
+```yaml
+outdir: s3://example-project-tower-bucket/dcqc_output
+```
+
+From the reports tab within your workflow run, you can view and download the generated `output.csv` file.
+
 ## Credits
 
 sage/dcqc was originally written by Bruno Grande <[email protected]>.

docs/output.md

@@ -15,6 +15,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 - [FastQC](#fastqc) - Raw read QC
 - [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline
 - [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution
+- [QC Results Files](#qc-results-files) - QC results generated by the pipeline
 
 ### FastQC
 
@@ -66,3 +67,11 @@ Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQ
 </details>
 
 [Nextflow](https://www.nextflow.io/docs/latest/tracing.html) provides excellent functionality for generating various reports relevant to the running and execution of the pipeline. This will allow you to troubleshoot errors with the running of the pipeline, and also provide you with other information such as launch commands, run times and resource usage.
+
+### QC Results Files
+
+<details markdown="1">
+<summary>Output files</summary>
+
+- `output.csv`: The original input CSV file updated to include the QC results for each file.
+- `suites.json`: A JSON file containing summary information for all QC tests performed.