Merge branch 'preseq_test'

.github/workflows/preseq_lcextrap.yml

@@ -1,15 +1,15 @@
-name: phantompeakqualtools
+name: preseq_lcextrap
 on:
   push:
     paths:
-      - software/phantompeakqualtools/**
-      - .github/workflows/phantompeakqualtools.yml
-      - tests/software/phantompeakqualtools/**
+      - software/preseq/lcextrap/**
+      - .github/workflows/preseq_lcextrap.yml
+      - tests/software/preseq/**
   pull_request:
     paths:
-      - software/phantompeakqualtools/**
-      - .github/workflows/phantompeakqualtools.yml
-      - tests/software/phantompeakqualtools/**
+      - software/preseq/lcextrap/**
+      - .github/workflows/preseq_lcextrap.yml
+      - tests/software/preseq/**
 
 jobs:
   ci_test:
@@ -37,4 +37,4 @@ jobs:
         run: python -m pip install --upgrade pip pytest-workflow
 
       # Test the module
-      - run: pytest --tag phantompeakqualtools --symlink --wt 2
+      - run: pytest --tag preseq_lcextrap --symlink --wt 2

tests/software/phantompeakqualtools/main.nf

@@ -1,12 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { PHANTOMPEAKQUALTOOLS } from '../../../software/phantompeakqualtools/main.nf' addParams( options: [:] )
-
-workflow test_phantompeakqualtools {
-    def input = []
-    input = [ [ id:'test', single_end:true ], // meta map
-              [ file("${launchDir}/tests/data/bam/test.single_end.sorted.bam", checkIfExists: true) ] ]
-    PHANTOMPEAKQUALTOOLS ( input )
-}

tests/software/phantompeakqualtools/test.yml

@@ -1,9 +0,0 @@
-- name: Run phantompeakqualtools  test workflow
-  command: nextflow run ./tests/software/phantompeakqualtools/ -profile docker -entry test_phantompeakqualtools -c tests/config/nextflow.config
-  tags:
-    - phantompeakqualtools
-  files:
-    - path: output/phantompeakqualtools/test.spp.pdf
-    - path: output/phantompeakqualtools/test.spp.Rdata
-    - path: output/phantompeakqualtools/test.spp.out
-      md5sum: c18220e8082e695995edecc99235ec85

tests/software/preseq/main.nf

@@ -0,0 +1,32 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PRESEQ_LCEXTRAP as PRESEQ_LCEXTRAP_SE } from '../../../software/preseq/lcextrap/main.nf' addParams( options: [ publish_dir:'test_preseq_single_end' ] )
+include { PRESEQ_LCEXTRAP as PRESEQ_LCEXTRAP_PE } from '../../../software/preseq/lcextrap/main.nf' addParams( options: [ publish_dir:'test_preseq_paired_end' ] )
+
+/*
+ * Test with single-end data
+ */
+
+workflow test_preseq_single_end {
+
+    def input = []
+    input = [ [ id:'test', single_end:true ], // meta map
+              [ file('https://github.com/smithlabcode/preseq/raw/master/data/SRR1003759_5M_subset.mr', checkIfExists: true), ] ]
+    PRESEQ_LCEXTRAP_SE ( input )
+}
+
+/*
+ * Test with paired-end data
+ */
+
+workflow test_preseq_paired_end {
+
+    def input = []
+    input = [ [ id:'test', single_end:false ], // meta map
+              [ file('https://github.com/smithlabcode/preseq/raw/master/data/SRR1003759_5M_subset.mr', checkIfExists: true), ] ]
+
+    PRESEQ_LCEXTRAP_PE ( input )
+}
+

tests/software/preseq/test.yml

@@ -0,0 +1,21 @@
+- name: Run preseq single-end lcextrap
+  command: nextflow run ./tests/software/preseq -profile docker -entry test_preseq_single_end -c tests/config/nextflow.config
+  tags:
+    - preseq
+    - preseq_lcextrap
+
+  files:
+    - path: output/test_preseq_single_end/test.ccurve.txt
+      md5sum: 76ae04c8eaf19c94e3210bb69da38498
+    - path: output/test_preseq_single_end/test.command.log
+
+- name: Run preseq paired-end lcextrap
+  command: nextflow run ./tests/software/preseq -profile docker -entry test_preseq_paired_end -c tests/config/nextflow.config
+  tags:
+    - preseq
+    - preseq_lcextrap
+
+  files:
+    - path: output/test_preseq_paired_end/test.ccurve.txt
+      md5sum: 2836d2fabd2213f097fd7063db550276
+    - path: output/test_preseq_paired_end/test.command.log