Add samtools stats commands

software/samtools/stats/meta.yml

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+name: samtools_stats
+description: Produces comprehensive statistics from SAM/BAM/CRAM file
+keywords:
+    - statistics
+    - counts
+    - bam
+    - sam
+    - cram
+tools:
+    - samtools:
+        description: |
+            SAMtools is a set of utilities for interacting with and post-processing
+            short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.
+            These files are generated as output by short read aligners like BWA.
+        homepage: http://www.htslib.org/
+        documentation: hhttp://www.htslib.org/doc/samtools.html
+        doi: 10.1093/bioinformatics/btp352
+params:
+    - outdir:
+        type: string
+        description: |
+            The pipeline's output directory. By default, the module will
+            output files into `$params.outdir/<SOFTWARE>`
+    - publish_dir_mode:
+        type: string
+        description: |
+            Value for the Nextflow `publishDir` mode parameter.
+            Available: symlink, rellink, link, copy, copyNoFollow, move.
+    - conda:
+        type: boolean
+        description: |
+            Run the module with Conda using the software specified
+            via the `conda` directive
+input:
+    - meta:
+        type: map
+        description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+    - bam:
+        type: file
+        description: BAM/CRAM/SAM file
+        pattern: "*.{bam,cram,sam}"
+    - bai:
+        type: file
+        description: Index for BAM/CRAM/SAM file
+        pattern: "*.{bai,crai,sai}"
+    - options:
+        type: map
+        description: |
+            Groovy Map containing module options for passing command-line arguments and
+            output file paths.
+output:
+    - meta:
+        type: map
+        description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+    - stats:
+        type: file
+        description: File containing samtools stats output
+        pattern: "*.{stats}"
+    - version:
+        type: file
+        description: File containing software version
+        pattern: "*.{version.txt}"
+authors:
+    - "@drpatelh"

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

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

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

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

software/samtools/stats/test/main.nf

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+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SAMTOOLS_STATS } 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_STATS ( input, [:] )
+}
+
+workflow {
+    test()
+}

software/samtools/stats/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
+    }
+}