add comments

.github/workflows/ncbench.yml

@@ -71,6 +71,7 @@ jobs:
       - name: Upload to zenodo
         id: upload_zenodo
         env:
+          # ATTENTION: Use SANDBOX TOKEN during development: ${{ secrets.NCBENCH_CI_TOKEN_SANDBOX }}
           ACCESS_TOKEN: ${{ secrets.NCBENCH_CI_TOKEN_SANDBOX }} # ${{ secrets.ZENODO_DEPOSIT }}
           PIPELINE_VERSION: ${{ env.PIPELINE_VERSION }}
         run: python .github/workflows/upload.py

.github/workflows/set_ncbench_config.sh

@@ -1,5 +1,9 @@
 #!/bin/bash
 
+# This script updates the config.yml in the NCBench repository.
+# The config file is needed to trigger the subsequent benchmarking workflow.
+# For each variant caller and each input file a new entry needs to be created.
+
 declare -A variant_callers=(
     ["deepvariant"]="NA12878_%sM.deepvariant.vcf.gz"
     ["freebayes"]="NA12878_%sM.freebayes.vcf.gz"

.github/workflows/upload.py

@@ -2,6 +2,17 @@
 import os
 import json
 
+'''
+This scripts collects all variant calling files and uploads them to Zenodo.
+1. A new Zenodo entry is created
+2. All files are uploaded
+3. Meta data is added: Pipeline version, authors
+4. Entry is published.
+
+ATTENTION: Use sandbox links during development! They are set in each affected line as comment.
+            If you need to use the production Zenodo links, turn off publishing (see bottom).
+'''
+
 headers = {"Content-Type": "application/json"}
 access_token = os.environ["ACCESS_TOKEN"]
 params = {"access_token": access_token}

README.md

@@ -94,6 +94,14 @@ To see the results of an example test run with a full size dataset refer to the
 For more details about the output files and reports, please refer to the
 [output documentation](https://nf-co.re/sarek/output).
 
+## Benchmarking
+
+On each release, the pipeline is run on 3 full size tests:
+
+- `test_full` runs tumor-normal data for one patient from the SEQ2C consortium
+- `test_full_germline` runs a WGS 30X Genome-in-a-Bottle(NA12878) dataset
+- `test_full_germline_ncbench_agilent` runs two WES samples with 75M and 200M reads (data available [here](https://github.com/ncbench/ncbench-workflow#contributing-callsets)). The results are uploaded to Zenodo, evaluated against a truth dataset, and results are made available via the [NCBench dashboard](https://ncbench.github.io/report/report.html#).
+
 ## Credits
 
 Sarek was originally written by Maxime U Garcia and Szilveszter Juhos at the [National Genomics Infastructure](https://ngisweden.scilifelab.se) and [National Bioinformatics Infastructure Sweden](https://nbis.se) which are both platforms at [SciLifeLab](https://scilifelab.se), with the support of [The Swedish Childhood Tumor Biobank (Barntumörbanken)](https://ki.se/forskning/barntumorbanken).