Homer (#330)

* started with homer

* added tests for homer annotatepeaks

* fix md5

* remove md5 sum

software/homer/annotatepeaks/meta.yml

@@ -0,0 +1,47 @@
+name: homer_annotatepeaks
+description: Annotate peaks with homer
+keywords:
+  - annotations
+  - peaks
+  - bed
+tools:
+  - cuatadapt:
+      description: |
+        HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis.
+      documentation: http://homer.ucsd.edu/homer/
+      doi: 10.1016/j.molcel.2010.05.004.
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - peaks:
+      type: file
+      description: The peak files in bed format
+      pattern: "*.bed"
+  - fasta:
+      type: file
+      description: Fasta file of reference genome
+      pattern: "*.fasta"
+  - gtf:
+      type: file
+      description: GTF file of reference genome
+      pattern: "*.gtf"
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - annotated_peaks:
+      type: file
+      description: The annotated peaks
+      pattern: "*annotatePeaks.txt"
+  - version:
+      type: file
+      description: File containing software version
+      pattern: "*.{version.txt}"
+authors:
+  - "@drpatelh"
+  - "@kevinmenden"

tests/config/pytest_software.yml

@@ -230,6 +230,10 @@ gunzip:
   - software/gunzip/**
   - tests/software/gunzip/**
 
+homer_annotatepeaks:
+  - software/homer/annotatepeaks/**
+  - tests/software/homer/annotatepeaks/**
+
 ivar_consensus:
   - software/ivar/consensus/**
   - tests/software/ivar/consensus/**

tests/software/homer/annotatepeaks/main.nf

@@ -0,0 +1,19 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { HOMER_ANNOTATEPEAKS } from '../../../../software/homer/annotatepeaks/main.nf' addParams( options: [:] )
+
+workflow test_homer_annotatepeaks {
+
+    def fasta = file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.fasta", checkIfExists: true)
+    def gtf = file("${launchDir}/tests/data/genomics/sarscov2/gtf/test_genome.gtf", checkIfExists: true)
+
+    def input = []
+    input = [ [ id:'test'],
+                file("${launchDir}/tests/data/genomics/sarscov2/bed/test.bed", checkIfExists: true) ]
+
+
+
+    HOMER_ANNOTATEPEAKS ( input, fasta, gtf)
+}

tests/software/homer/annotatepeaks/test.yml

@@ -0,0 +1,7 @@
+- name: homer annotatepeaks test_homer_annotatepeaks
+  command: nextflow run tests/software/homer/annotatepeaks -entry test_homer_annotatepeaks -c tests/config/nextflow.config
+  tags:
+    - homer
+    - homer_annotatepeaks
+  files:
+    - path: output/homer/test.annotatePeaks.txt