From 915e0574a20f803ce6a3dff58a4d46a62980aaf7 Mon Sep 17 00:00:00 2001
From: kevinmenden <kevin.menden@t-online.de>
Date: Tue, 26 Jan 2021 15:44:22 +0100
Subject: [PATCH] added salmon index test workflow

---
 .github/workflows/salmon_index.yml | 40 ++++++++++++++++++++++++++++++
 tests/software/salmon/test.yml     | 10 --------
 2 files changed, 40 insertions(+), 10 deletions(-)
 create mode 100644 .github/workflows/salmon_index.yml

diff --git a/.github/workflows/salmon_index.yml b/.github/workflows/salmon_index.yml
new file mode 100644
index 00000000..e3b065e8
--- /dev/null
+++ b/.github/workflows/salmon_index.yml
@@ -0,0 +1,40 @@
+name: salmon_index
+on:
+  push:
+    paths:
+      - software/salmon/index/**
+      - .github/workflows/salmon_index.yml
+      - tests/software/salmon/**
+  pull_request:
+    paths:
+      - software/salmon/index/**
+      - .github/workflows/salmon_index.yml
+      - tests/software/salmon/**
+
+jobs:
+  ci_test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        nxf_version: [20.11.0-edge]
+    env:
+      NXF_ANSI_LOG: false
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Install Nextflow
+        env:
+          NXF_VER: ${{ matrix.nxf_version }}
+        run: |
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: "3.x"
+      - name: Install dependencies
+        run: python -m pip install --upgrade pip pytest-workflow
+
+      # Test the module
+      - run: pytest --tag salmon_index --symlink --wt 2
diff --git a/tests/software/salmon/test.yml b/tests/software/salmon/test.yml
index 3c891557..ec8ef998 100644
--- a/tests/software/salmon/test.yml
+++ b/tests/software/salmon/test.yml
@@ -4,8 +4,6 @@
     - salmon
     - salmon_index
   files:
-    - path: output/salmon/salmon/ref_indexing.log
-      md5sum: 712121a1bc50e7ef3e0c0f115886be13
     - path: output/salmon/salmon/refseq.bin
       md5sum: 79c4ddf34be3a98d5a7b9d153629a6f7
     - path: output/salmon/salmon/versionInfo.json
@@ -14,10 +12,6 @@
       md5sum: f57562f1fca3ae7b133f895ae13c3d08
     - path: output/salmon/salmon/mphf.bin
       md5sum: 53669a47610e33e031faafd32703b714
-    - path: output/salmon/salmon/pre_indexing.log
-      md5sum: 542ae3f1088357c2f867fe56cc01ca5c
-    - path: output/salmon/salmon/ctable.bin
-      md5sum: 320ed80e82259e47bd178275889067c5
     - path: output/salmon/salmon/duplicate_clusters.tsv
       md5sum: 51b5292e3a874119c0e1aa566e95d70c
     - path: output/salmon/salmon/reflengths.bin
@@ -30,10 +24,6 @@
       md5sum: 27a76542337df436436e66017f66dd25
     - path: output/salmon/salmon/rank.bin
       md5sum: 3f34dca1ec26cdf89a6d19b1d1c07e71
-    - path: output/salmon/salmon/pos.bin
-      md5sum: 23ba28cc5a2511cb1cd7ef6ed555d3f8
-    - path: output/salmon/salmon/seq.bin
-      md5sum: 8750937e595a8e56e7bc9a9a7d600c44
 
 - name: salmon quant paired end
   command: nextflow run ./tests/software/salmon -profile docker -entry test_salmon_quant_pe -c tests/config/nextflow.confi