From b95bd37780b3d9d11636360326e1e2f3e17d44ee Mon Sep 17 00:00:00 2001
From: sruthipsuresh <sruthiprabhasuresh@gmail.com>
Date: Tue, 12 Jan 2021 09:40:12 -0600
Subject: [PATCH] Added ucsc module

---
 .github/workflows/ucsc_bedgraphtobigwig.yml | 39 +++++++++++++++++++++
 tests/software/ucsc/main.nf                 | 15 ++++++++
 tests/software/ucsc/test.yml                |  7 ++++
 3 files changed, 61 insertions(+)
 create mode 100644 .github/workflows/ucsc_bedgraphtobigwig.yml
 create mode 100644 tests/software/ucsc/main.nf
 create mode 100644 tests/software/ucsc/test.yml

diff --git a/.github/workflows/ucsc_bedgraphtobigwig.yml b/.github/workflows/ucsc_bedgraphtobigwig.yml
new file mode 100644
index 00000000..11772d78
--- /dev/null
+++ b/.github/workflows/ucsc_bedgraphtobigwig.yml
@@ -0,0 +1,39 @@
+name: ucsc_bedgraphtobigwig
+on:
+  push:
+    paths:
+      - software/ucsc/bedgraphtobigwig/**
+      - .github/workflows/ucsc_bedgraphtobigwig.yml
+      - tests/software/ucsc/**
+  pull_request:
+    paths:
+      - software/ucsc/bedgraphtobigwig/**
+      - .github/workflows/ucsc_bedgraphtobigwig.yml
+      - tests/software/ucsc/**
+
+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 ucsc_bedgraphtobigwig --symlink --wt 2
diff --git a/tests/software/ucsc/main.nf b/tests/software/ucsc/main.nf
new file mode 100644
index 00000000..1613a707
--- /dev/null
+++ b/tests/software/ucsc/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { UCSC_BEDGRAPHTOBIGWIG  } from '../../../software/ucsc/bedgraphtobigwig/main.nf' addParams( options: [:] )
+
+workflow test_ucsc_bedgraphtobigwig {
+    def input = []
+    input = [ [ id:'test' ], // meta map
+              [ file('https://raw.githubusercontent.com/igvteam/igv.js/master/test/data/wig/bedgraph-example-uscs.bedgraph', checkIfExists: true) ] ]
+    UCSC_BEDGRAPHTOBIGWIG (
+        input,
+        file('https://raw.githubusercontent.com/igvteam/igv.js/master/test/data/wig/chrom.sizes', checkIfExists: true)
+        )
+}
diff --git a/tests/software/ucsc/test.yml b/tests/software/ucsc/test.yml
new file mode 100644
index 00000000..53be4e77
--- /dev/null
+++ b/tests/software/ucsc/test.yml
@@ -0,0 +1,7 @@
+- name: Run bedgraphtobigwig  test workflow
+  command: nextflow run ./tests/software/ucsc/ -profile docker -entry test_ucsc_bedgraphtobigwig -c tests/config/nextflow.config
+  tags:
+    - ucsc_bedgraphtobigwig
+  files:
+    - path: output/ucsc/test.bigWig
+      md5sum: 5346de25b01ecbff91b63178b3bfbeec