From e0b1d62b8ae20e4d9ae1f61f14cd39b484d7df86 Mon Sep 17 00:00:00 2001
From: Ksenia Krasheninnikova <kk16@sanger.ac.uk>
Date: Wed, 11 Oct 2023 11:16:53 +0100
Subject: [PATCH] CI testing

---
 .github/workflows/ci.yml |  9 +++++----
 assets/test_github.yaml  | 17 +++++++++++++++++
 conf/test_github.config  | 33 +++++++++++++++++++++++++++++++++
 3 files changed, 55 insertions(+), 4 deletions(-)
 create mode 100644 assets/test_github.yaml
 create mode 100644 conf/test_github.config

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 2d62c8fb..8373ba89 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -35,9 +35,10 @@ jobs:
         with:
           version: "${{ matrix.NXF_VER }}"
 
+      - name: Download test data
+            run: |
+                curl https://darwin.cog.sanger.ac.uk/genomeassembly_test_data.tar.gz | tar xzf -
+
       - name: Run pipeline with test data
-        # TODO nf-core: You can customise CI pipeline run tests as required
-        # For example: adding multiple test runs with different parameters
-        # Remember that you can parallelise this by using strategy.matrix
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
+          nextflow run ${GITHUB_WORKSPACE} -profile test_github,docker --outdir ./results
diff --git a/assets/test_github.yaml b/assets/test_github.yaml
new file mode 100644
index 00000000..e988a52d
--- /dev/null
+++ b/assets/test_github.yaml
@@ -0,0 +1,17 @@
+dataset:
+  id: baUndUnlc1
+  illumina_10X:
+    reads: /home/runner/work/genomeassembly/genomessembly/Undibacterium_unclassified/genomic_data/baUndUnlc1/10x/
+  pacbio:
+    reads:
+      - reads: /home/runner/work/genomeassembly/genomessembly/Undibacterium_unclassified/genomic_data/baUndUnlc1/pacbio/fasta/HiFi.reads.fasta
+  HiC:
+    reads:
+      - reads: /home/runner/work/genomeassembly/genomessembly/Undibacterium_unclassified/genomic_data/baUndUnlc1/hic-arima2/41741_2#7.sub.cram
+hic_motif: GATC,GANTC,CTNAG,TTAA
+busco:
+  lineage: bacteria_odb10
+mito:
+  species: Caradrina clavipalpis
+  min_length: 15000
+  code: 5
diff --git a/conf/test_github.config b/conf/test_github.config
new file mode 100644
index 00000000..6f42f079
--- /dev/null
+++ b/conf/test_github.config
@@ -0,0 +1,33 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Nextflow config file for running minimal tests
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Defines input files and everything required to run a fast and simple pipeline test.
+
+    Use as follows:
+        nextflow run sanger-tol/genomeassembly -profile test,<docker/singularity> --outdir <OUTDIR>
+
+----------------------------------------------------------------------------------------
+*/
+
+params {
+    config_profile_name        = 'Github test profile'
+    config_profile_description = 'Minimal test dataset to check pipeline function'
+
+    max_cpus   = 2
+    max_memory = '6.GB'
+    max_time   = '6.h'
+    // Limit resources so that this can run on GitHub Actions
+
+    // Input data
+    input = "${projectDir}/assets/test_github.yaml"
+    bed_chunks_polishing = 2
+    polishing_on = true
+    hifiasm_hic_on = true
+}
+
+// Set up of the scffolding eipeline
+withName: 'YAHS' {
+    // Skip the initial assembly error correction step
+    ext.args = '-r 1000,2000,5000'
+}