Added new tests, todo: fix md5sums

tests/software/bedtools/complement/main.nf

@@ -9,7 +9,7 @@ workflow test_bedtools_complement {
     def input = []
     input = [ [ id:'test'],
               file("${launchDir}/tests/data/bed/A.bed", checkIfExists: true),
-              file("${launchDir}/tests/data/bed/genome.sizes", checkIfExists: true) ] //metamap
+              file("${launchDir}/tests/data/bed/genome.sizes", checkIfExists: true) ]
 
     BEDTOOLS_COMPLEMENT( input )
 }

tests/software/bedtools/genomecov/main.nf

@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BEDTOOLS_GENOMECOV } from '../../../../software/bedtools/genomecov/main.nf' addParams( options: [:] )
+
+
+workflow test_bedtools_genomecov {
+    def input = []
+    input = [ [ id:'test'],
+              file("${launchDir}/tests/data/bam/test.paired_end.name.sorted.bam", checkIfExists: true) ]
+
+    BEDTOOLS_GENOMECOV( input )
+}
+

tests/software/bedtools/genomecov/test.yml

@@ -0,0 +1,8 @@
+- name: bedtools genomecov
+  command: nextflow run ./tests/software/bedtools/genomecov -entry test_bedtools_genomecov -c tests/config/nextflow.config
+  tags:
+    - bedtools
+    - bedtools_genomecov
+  files:
+    - path: output/bedtools/test.bed
+      md5sum: cc1bb317886e7df0a942b56f8a320d9c

tests/software/bedtools/intersect/main.nf

@@ -0,0 +1,16 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BEDTOOLS_INTERSECT } from '../../../../software/bedtools/intersect/main.nf' addParams( options: [:] )
+
+
+workflow test_bedtools_intersect {
+    def input = []
+    input = [ [ id:'test'],
+              file("${launchDir}/tests/data/bed/A.bed", checkIfExists: true),
+              file("${launchDir}/tests/data/bed/B.bed", checkIfExists: true) ]
+
+    BEDTOOLS_INTERSECT( input )
+}
+

tests/software/bedtools/intersect/test.yml

@@ -0,0 +1,8 @@
+- name: bedtools intersect
+  command: nextflow run ./tests/software/bedtools/intersect -entry test_bedtools_intersect -c tests/config/nextflow.config
+  tags:
+    - bedtools
+    - bedtools_intersect
+  files:
+    - path: output/bedtools/test.intersect.bed
+      md5sum: cc1bb317886e7df0a942b56f8a320d9c

tests/software/bedtools/merge/main.nf

@@ -0,0 +1,16 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BEDTOOLS_MERGE } from '../../../../software/bedtools/merge/main.nf' addParams( options: [:] )
+
+
+workflow test_bedtools_merge {
+    def input = []
+    input = [ [ id:'test'],
+              file("${launchDir}/tests/data/bed/A.bed", checkIfExists: true) ]
+
+    BEDTOOLS_MERGE( input )
+}
+
+

tests/software/bedtools/merge/test.yml

@@ -0,0 +1,8 @@
+- name: bedtools merge
+  command: nextflow run ./tests/software/bedtools/merge -entry test_bedtools_merge -c tests/config/nextflow.config
+  tags:
+    - bedtools
+    - bedtools_merge
+  files:
+    - path: output/bedtools/test.merged.bed
+      md5sum: 13e5a3b254fac35fe0da0c92cbaf1761

tests/software/bedtools/slop/main.nf

@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BEDTOOLS_SLOP } from '../../../../software/bedtools/slop/main.nf' addParams( options: [args: '-l 15 r 30'] )
+
+
+workflow test_bedtools_slop {
+    def input = []
+    input = [ [ id:'test'],
+              file("${launchDir}/tests/data/bed/A.bed", checkIfExists: true) ]
+
+    BEDTOOLS_SLOP( input )
+
+}

tests/software/bedtools/slop/test.yml

@@ -0,0 +1,8 @@
+- name: bedtools slop
+  command: nextflow run ./tests/software/bedtools/slop -entry test_bedtools_slop -c tests/config/nextflow.config
+  tags:
+    - bedtools
+    - bedtools_complement
+  files:
+    - path: output/bedtools/test.slop.bed
+      md5sum: 55a43973abb1a08ac57290ff44f6c502

tests/software/bedtools/sort/main.nf

@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BEDTOOLS_SORT } from '../../../../software/bedtools/sort/main.nf' addParams( options: [:] )
+
+
+workflow test_bedtools_sort {
+    def input = []
+    input = [ [ id:'test'],
+              file("${launchDir}/tests/data/bed/A.bed", checkIfExists: true) ]
+
+    BEDTOOLS_SORT( input )
+
+}

tests/software/bedtools/sort/test.yml

@@ -0,0 +1,8 @@
+- name: bedtools sort
+  command: nextflow run ./tests/software/bedtools/sort -entry test_bedtools_sort -c tests/config/nextflow.config
+  tags:
+    - bedtools
+    - bedtools_sort
+  files:
+    - path: output/bedtools/test.sort.bed
+      md5sum: 4279202e33fcce3d19f420f1b27fddee