Merge pull request #1228 from nf-core/readme_usage

Make README usage consistent with docs/usage.md

Author: pinin4fjords

.github/workflows/ci.yml

@@ -256,7 +256,7 @@ jobs:
     if: always()
     steps:
       - name: All tests ok
-        if: ${{ !contains(needs.*.result, 'failure') }}
+        if: ${{ success() }}
         run: exit 0
       - name: One or more tests failed
         if: ${{ contains(needs.*.result, 'failure') }}

CHANGELOG.md

@@ -35,6 +35,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [PR #1241](https://github.com/nf-core/rnaseq/pull/1241) - Add nf-test tests to deseq2_qc
 - [PR #1242](https://github.com/nf-core/rnaseq/pull/1242) - Use dupradar from nf-core/modules
 - [PR #1244](https://github.com/nf-core/rnaseq/pull/1244) - Add gtf2bed tests
+- [PR #1228](https://github.com/nf-core/rnaseq/pull/1228) - Change CI/CD testing logic to pass if no nf-tests have been ran
 
 ### Parameters
 

README.md

@@ -80,9 +80,10 @@ Now, you can run the pipeline using:
 
 ```bash
 nextflow run nf-core/rnaseq \
-    --input samplesheet.csv \
+    --input <SAMPLESHEET> \
     --outdir <OUTDIR> \
-    --genome GRCh37 \
+    --gtf <GTF> \
+    --fasta <GENOME FASTA> \
     -profile <docker/singularity/.../institute>
 ```
 

docs/usage.md

@@ -213,8 +213,6 @@ nextflow run \
     --outdir <OUTDIR> \
     --gtf <GTF> \
     --fasta <GENOME FASTA> \
-    --igenomes_ignore \
-    --genome null \
     -profile docker
 ```