From c72146c931bbada00cfee68c6b27970594d1cc39 Mon Sep 17 00:00:00 2001
From: mapo9 <mark.polster@qbic.uni-tuebingen.de>
Date: Thu, 16 May 2024 08:55:07 +0200
Subject: [PATCH] sc rnaseq tests

---
 .github/workflows/ci.yml     |  1 +
 conf/test_rnaseq_bulk.config |  2 +-
 conf/test_rnaseq_sc.config   | 31 +++++++++++++++++++++++++++++++
 nextflow.config              |  1 +
 4 files changed, 34 insertions(+), 1 deletion(-)
 create mode 100644 conf/test_rnaseq_sc.config

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 84d26cb5..6a3ffa98 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -63,6 +63,7 @@ jobs:
             "test_clontech_umi",
             "test_nebnext_umi",
             "test_rnaseq_bulk",
+            "test_rnaseq_sc",
           ]
       fail-fast: false
     steps:
diff --git a/conf/test_rnaseq_bulk.config b/conf/test_rnaseq_bulk.config
index 2dd6740e..83d0eaf2 100644
--- a/conf/test_rnaseq_bulk.config
+++ b/conf/test_rnaseq_bulk.config
@@ -4,7 +4,7 @@
  * -------------------------------------------------
  * Defines bundled input files and everything required
  * to run a fast and simple test. Use as follows:
- *   nextflow run nf-core/airrflow -profile test_10x_sc,<docker/singularity>
+ *   nextflow run nf-core/airrflow -profile test_rnaseq_bulk,<docker/singularity>
  */
 
 params {
diff --git a/conf/test_rnaseq_sc.config b/conf/test_rnaseq_sc.config
new file mode 100644
index 00000000..0ca7618f
--- /dev/null
+++ b/conf/test_rnaseq_sc.config
@@ -0,0 +1,31 @@
+/*
+ * -------------------------------------------------
+ *  Nextflow config file for running tests
+ * -------------------------------------------------
+ * Defines bundled input files and everything required
+ * to run a fast and simple test. Use as follows:
+ *   nextflow run nf-core/airrflow -profile test_rnaseq_sc,<docker/singularity>
+ */
+
+params {
+    config_profile_name = 'Test single-cell RNA-seq based workflow using TRUST4'
+    config_profile_description = 'Minimal test dataset to check pipeline function with raw single-cell RNA-seq data'
+
+    // Limit resources so that this can run on GitHub Actions
+    max_cpus = 2
+    max_memory = 6.GB
+    max_time = 48.h
+
+    // params
+    mode = 'fastq'
+    library_generation_method = 'trust4'
+    clonal_threshold = 0
+    barcode_read = R1
+    umi_position = R1
+    read_format = "bc:0:15,um:16:27"
+    skip_lineage = True
+
+    // Input data
+    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/testdata-rnaseq/sc_rnaseq_metadata.tsv'
+    coord_fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/testdata-rnaseq/IMGT+C.fa'
+}
diff --git a/nextflow.config b/nextflow.config
index 7db8af95..4384b769 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -307,6 +307,7 @@ profiles {
     test_clontech_umi { includeConfig 'conf/test_clontech_umi.config' }
     test_nebnext_umi { includeConfig 'conf/test_nebnext_umi.config' }
     test_rnaseq_bulk { includeConfig 'conf/test_rnaseq_bulk.config' }
+    test_rnaseq_sc { includeConfig 'conf/test_rnaseq_sc.config' }
     nebnext_umi_tcr { includeConfig 'conf/nebnext_umi_tcr.config' }
     nebnext_umi_bcr { includeConfig 'conf/nebnext_umi_bcr.config' }
     clontech_umi_bcr { includeConfig 'conf/clontech_umi_bcr.config' }