From 46e4d35ec3aee932d63eeb8a451bed975b139011 Mon Sep 17 00:00:00 2001
From: drpatelh <drhpatel@gmail.com>
Date: Fri, 7 Aug 2020 15:12:03 +0100
Subject: [PATCH] Get samtools flagstat passing

---
 .../test/input/test.paired_end.sorted.bam     |  1 +
 .../test/input/test.paired_end.sorted.bam.bai |  1 +
 software/samtools/flagstat/test/main.nf       | 19 ++++++++++++++++++
 .../samtools/flagstat/test/nextflow.config    | 20 +++++++++++++++++++
 4 files changed, 41 insertions(+)
 create mode 120000 software/samtools/flagstat/test/input/test.paired_end.sorted.bam
 create mode 120000 software/samtools/flagstat/test/input/test.paired_end.sorted.bam.bai
 create mode 100755 software/samtools/flagstat/test/main.nf
 create mode 100644 software/samtools/flagstat/test/nextflow.config

diff --git a/software/samtools/flagstat/test/input/test.paired_end.sorted.bam b/software/samtools/flagstat/test/input/test.paired_end.sorted.bam
new file mode 120000
index 00000000..af606d91
--- /dev/null
+++ b/software/samtools/flagstat/test/input/test.paired_end.sorted.bam
@@ -0,0 +1 @@
+../../../../../tests/data/bam/test.paired_end.sorted.bam
\ No newline at end of file
diff --git a/software/samtools/flagstat/test/input/test.paired_end.sorted.bam.bai b/software/samtools/flagstat/test/input/test.paired_end.sorted.bam.bai
new file mode 120000
index 00000000..61a71557
--- /dev/null
+++ b/software/samtools/flagstat/test/input/test.paired_end.sorted.bam.bai
@@ -0,0 +1 @@
+../../../../../tests/data/bam/test.paired_end.sorted.bam.bai
\ No newline at end of file
diff --git a/software/samtools/flagstat/test/main.nf b/software/samtools/flagstat/test/main.nf
new file mode 100755
index 00000000..f41a0d86
--- /dev/null
+++ b/software/samtools/flagstat/test/main.nf
@@ -0,0 +1,19 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SAMTOOLS_FLAGSTAT } from '../main.nf'
+
+workflow test {
+
+    def input = []
+    input = [ [ id:'test', single_end:false ], // meta map
+              file("${baseDir}/input/test.paired_end.sorted.bam", checkIfExists: true),
+              file("${baseDir}/input/test.paired_end.sorted.bam.bai", checkIfExists: true) ]
+
+    SAMTOOLS_FLAGSTAT ( input, [:] )
+}
+
+workflow {
+    test()
+}
diff --git a/software/samtools/flagstat/test/nextflow.config b/software/samtools/flagstat/test/nextflow.config
new file mode 100644
index 00000000..44b62ed8
--- /dev/null
+++ b/software/samtools/flagstat/test/nextflow.config
@@ -0,0 +1,20 @@
+
+params {
+    outdir = "output/"
+    publish_dir_mode = "copy"
+    conda = false
+}
+
+profiles {
+    conda  {
+        params.conda = true
+    }
+    docker {
+        docker.enabled = true
+        docker.runOptions = '-u \$(id -u):\$(id -g)'
+    }
+    singularity {
+        singularity.enabled = true
+        singularity.autoMounts = true
+    }
+}