Get samtools flagstat passing

software/samtools/flagstat/test/input/test.paired_end.sorted.bam

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+../../../../../tests/data/bam/test.paired_end.sorted.bam

software/samtools/flagstat/test/input/test.paired_end.sorted.bam.bai

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+../../../../../tests/data/bam/test.paired_end.sorted.bam.bai

software/samtools/flagstat/test/main.nf

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+#!/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()
+}

software/samtools/flagstat/test/nextflow.config

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+
+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
+    }
+}