From 0a04c96357554aa1171b4ba7d3d019cb38a63515 Mon Sep 17 00:00:00 2001
From: sruthipsuresh <sruthiprabhasuresh@gmail.com>
Date: Tue, 12 Jan 2021 09:13:37 -0600
Subject: [PATCH] Added module, TODO data

---
 .github/workflows/stringtie.yml   | 40 +++++++++++++++++++++++++++++++
 tests/software/stringtie/main.nf  | 36 ++++++++++++++++++++++++++++
 tests/software/stringtie/test.yml | 24 +++++++++++++++++++
 3 files changed, 100 insertions(+)
 create mode 100644 .github/workflows/stringtie.yml
 create mode 100644 tests/software/stringtie/main.nf
 create mode 100644 tests/software/stringtie/test.yml

diff --git a/.github/workflows/stringtie.yml b/.github/workflows/stringtie.yml
new file mode 100644
index 00000000..f650dfae
--- /dev/null
+++ b/.github/workflows/stringtie.yml
@@ -0,0 +1,40 @@
+name: stringtie
+on:
+  push:
+    paths:
+      - software/stringtie/**
+      - .github/workflows/stringtie.yml
+      - tests/software/stringtie/**
+  pull_request:
+    paths:
+      - software/stringtie/**
+      - .github/workflows/stringtie.yml
+      - tests/software/stringtie/**
+
+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: ${{ matrix.nxf_version }}
+        run: |
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: "3.x"
+      - name: Install dependencies
+        run: python -m pip install --upgrade pip pytest-workflow
+
+      # Test the module
+      - run: pytest --tag stringtie --symlink --wt 2
diff --git a/tests/software/stringtie/main.nf b/tests/software/stringtie/main.nf
new file mode 100644
index 00000000..1a5bdbdd
--- /dev/null
+++ b/tests/software/stringtie/main.nf
@@ -0,0 +1,36 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { STRINGTIE as STRINGTIE_F } from '../../../software/stringtie/main.nf'  addParams( options: [ publish_dir:'test_forward' ] )
+include { STRINGTIE as STRINGTIE_R } from '../../../software/stringtie/main.nf'  addParams( options: [ publish_dir:'test_reverse' ] )
+
+/*
+ * Test with forward strandedness
+ */
+workflow test_stringtie_forward {
+
+    def input = []
+    input = [ [ id:'test', strandedness:'forward' ], // meta map
+              [ file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true) ] ]
+
+    STRINGTIE_F (
+                    input,
+                     file("${launchDir}/tests/data/gff/a.gtf", checkIfExists: true)
+                     )
+}
+
+/*
+ * Test with reverse strandedness
+ */
+workflow test_stringtie_reverse {
+
+    def input = []
+    input = [ [ id:'test', strandedness:'reverse' ], // meta map
+              [ file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true) ] ]
+
+    STRINGTIE_R (
+                    input,
+                     file("${launchDir}/tests/data/gff/a.gtf", checkIfExists: true)
+                     )
+}
diff --git a/tests/software/stringtie/test.yml b/tests/software/stringtie/test.yml
new file mode 100644
index 00000000..34de5570
--- /dev/null
+++ b/tests/software/stringtie/test.yml
@@ -0,0 +1,24 @@
+- name: Run stringtie forward strand test workflow
+  command: nextflow run ./tests/software/stringtie/ -profile docker -entry test_stringtie_forward -c tests/config/nextflow.config
+  tags:
+    - stringtie
+  files:
+    - path: output/test_forward/test.ballgown
+    - path: output/test_forward/test.gene_abundance.txt
+    - path: output/test_forward/test.transcripts.gtf
+      md5sum: f1b5baa8d94f86e499556a4ec419a75a
+    - path: output/test_forward/test.coverage.gtf
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+
+
+- name: Run stringtie reverse strand test workflow
+  command: nextflow run ./tests/software/stringtie/ -profile docker -entry test_stringtie_reverse -c tests/config/nextflow.config
+  tags:
+    - stringtie
+  files:
+    - path: output/test_reverse/test.ballgown
+    - path: output/test_reverse/test.gene_abundance.txt
+    - path: output/test_reverse/test.transcripts.gtf
+      md5sum: cb0367e5f98f19fcc2043d248deb513c
+    - path: output/test_reverse/test.coverage.gtf
+      md5sum: d41d8cd98f00b204e9800998ecf8427e