From cb39fcb91540c57bd376fdd7a520c2e89bdebb95 Mon Sep 17 00:00:00 2001
From: sruthipsuresh <sruthiprabhasuresh@gmail.com>
Date: Tue, 12 Jan 2021 08:41:09 -0600
Subject: [PATCH] Added preseq module and workflow

---
 .github/workflows/preseq_lcextrap.yml | 40 +++++++++++++++++++++++++++
 tests/software/preseq/main.nf         | 33 ++++++++++++++++++++++
 tests/software/preseq/test.yml        | 21 ++++++++++++++
 3 files changed, 94 insertions(+)
 create mode 100644 .github/workflows/preseq_lcextrap.yml
 create mode 100644 tests/software/preseq/main.nf
 create mode 100644 tests/software/preseq/test.yml

diff --git a/.github/workflows/preseq_lcextrap.yml b/.github/workflows/preseq_lcextrap.yml
new file mode 100644
index 00000000..33443f5e
--- /dev/null
+++ b/.github/workflows/preseq_lcextrap.yml
@@ -0,0 +1,40 @@
+name: preseq_lcextrap
+on:
+  push:
+    paths:
+      - software/preseq/lcextrap/**
+      - .github/workflows/preseq_lcextrap.yml
+      - tests/software/preseq/**
+  pull_request:
+    paths:
+      - software/preseq/lcextrap/**
+      - .github/workflows/preseq_lcextrap.yml
+      - tests/software/preseq/**
+
+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 preseq_lcextrap --symlink --wt 2
diff --git a/tests/software/preseq/main.nf b/tests/software/preseq/main.nf
new file mode 100644
index 00000000..421c79ba
--- /dev/null
+++ b/tests/software/preseq/main.nf
@@ -0,0 +1,33 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PRESEQ_LCEXTRAP as PRESEQ_LCEXTRAP_SE } from '../../../software/preseq/lcextrap/main.nf' addParams( options: [ publish_dir:'test_preseq_single_end' ] )
+include { PRESEQ_LCEXTRAP as PRESEQ_LCEXTRAP_PE } from '../../../software/preseq/lcextrap/main.nf' addParams( options: [ publish_dir:'test_preseq_paired_end' ] )
+
+/*
+ * Test with single-end data
+ */
+
+workflow test_preseq_single_end {
+
+    def input = []
+    input = [ [ id:'test', single_end:true ], // meta map
+              [ file('https://github.com/smithlabcode/preseq/raw/master/data/SRR1106616_5M_subset.bam', checkIfExists: true), ] ]
+
+    PRESEQ_LCEXTRAP_SE ( input )
+}
+
+/*
+ * Test with paired-end data
+ */
+
+workflow test_preseq_paired_end {
+
+    def input = []
+    input = [ [ id:'test', single_end:false ], // meta map
+              [ file('https://github.com/smithlabcode/preseq/raw/master/data/SRR1106616_5M_subset.bam', checkIfExists: true), ] ]
+
+    PRESEQ_LCEXTRAP_PE ( input )
+}
+
diff --git a/tests/software/preseq/test.yml b/tests/software/preseq/test.yml
new file mode 100644
index 00000000..67dd27f0
--- /dev/null
+++ b/tests/software/preseq/test.yml
@@ -0,0 +1,21 @@
+- name: Run preseq single-end lcextrap
+  command: nextflow run ./tests/software/preseq -profile docker -entry test_preseq_single_end -c tests/config/nextflow.config
+  tags:
+    - preseq
+    - preseq_lcextrap
+
+  files:
+    - path: output/test_preseq_single_end/test.ccurve.txt
+    - path: output/test_preseq_single_end/test.command.log
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+
+- name: Run preseq paired-end lcextrap
+  command: nextflow run ./tests/software/preseq -profile docker -entry test_preseq_paired_end -c tests/config/nextflow.config
+  tags:
+    - preseq
+    - preseq_lcextrap
+
+  files:
+    - path: output/test_preseq_paired_end/test.ccurve.txt
+    - path: output/test_preseq_paired_end/test.log
+      md5sum: 66b339780630fc1aa72dcfbd0a4490fd