From 40b887779be05953089d75ae84c7da1515ac95e2 Mon Sep 17 00:00:00 2001
From: jahn <jahn@mpusp.mpg.de>
Date: Thu, 24 Oct 2024 13:23:59 +0200
Subject: [PATCH] feat: added test to run GH actions

---
 .github/workflows/ci.yml | 2 --
 README.md                | 6 +++---
 conf/test.config         | 3 +++
 3 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index de80109..07de06d 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -28,10 +28,8 @@ jobs:
       matrix:
         NXF_VER:
           - "24.04.2"
-          - "latest-everything"
         profile:
           - "conda"
-          - "docker"
           - "singularity"
         test_name:
           - "test"
diff --git a/README.md b/README.md
index 590a2ac..8f4a551 100644
--- a/README.md
+++ b/README.md
@@ -60,17 +60,17 @@ The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool
 
 4. Test it on the minimal dataset included with this repository. Since `nf-core-crispriscreen` is not a canonical `nf-core` pipeline (yet), it is necessary to indicate the path to the pipeline folder after the `run` statement.
 
-   The generalized command to run the pipeline:
+   This is the generalized command to run the pipeline:
 
    ```console
    nextflow run <path/to/nf-core-crispriscreen> -profile <docker/singularity/podman/shifter/charliecloud/conda/institute> --input <sample_sheet> --fasta <fasta_file> --outdir <path/to/output>
    ```
 
-   The command to run the pipeline on the enclosed test data using `Singularity` (recommended):
+   This will run the pipeline on the enclosed test data using `Singularity` (recommended):
 
    ```console
    cd path/to/nf-core-crispriscreen
-   nextflow run ./ -profile singularity --input "assets/samplesheet.csv" --fasta "assets/library.fasta" --outdir "results"
+   nextflow run ./ -profile test,singularity --outdir ./results
    ```
 
    > - The pipeline comes with config profiles called `docker`, `singularity`, `podman`, `shifter`, `charliecloud` and `conda` which instruct the pipeline to use the named tool for software management. For example, `-profile test,docker`.
diff --git a/conf/test.config b/conf/test.config
index 23887a4..16bf769 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -26,4 +26,7 @@ params {
     max_cpus   = 2
     max_memory = '6.GB'
     max_time   = '6.h'
+
+    input = 'assets/samplesheet.csv'
+    fasta = 'assets/library.fasta'
 }