Fixed test and removed phantompeak tests

.github/workflows/phantompeakqualtools.yml

@@ -1,40 +0,0 @@
-name: phantompeakqualtools
-on:
-  push:
-    paths:
-      - software/phantompeakqualtools/**
-      - .github/workflows/phantompeakqualtools.yml
-      - tests/software/phantompeakqualtools/**
-  pull_request:
-    paths:
-      - software/phantompeakqualtools/**
-      - .github/workflows/phantompeakqualtools.yml
-      - tests/software/phantompeakqualtools/**
-
-jobs:
-  ci_test:
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        nxf_version: [20.07.1, ""]
-    env:
-      NXF_ANSI_LOG: false
-    steps:
-      - uses: actions/checkout@v2
-
-      - name: Install Nextflow
-        env:
-          NXF_VER: ${{ matrix.nxf_version }}
-        run: |
-          wget -qO- get.nextflow.io | bash
-          sudo mv nextflow /usr/local/bin/
-
-      - name: Set up Python
-        uses: actions/setup-python@v2
-        with:
-          python-version: "3.x"
-      - name: Install dependencies
-        run: python -m pip install --upgrade pip pytest-workflow
-
-      # Test the module
-      - run: pytest --tag phantompeakqualtools --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/test.yml

@@ -8,6 +8,7 @@
     - path: output/test_preseq_single_end/test.ccurve.txt
       md5sum: 5253ffcfd4b6162851631efdbfe16f92
     - path: output/test_preseq_single_end/test.command.log
+      md5sum: ad83871098825d36d267e375c2b46f01
 
 - name: Run preseq paired-end lcextrap
   command: nextflow run ./tests/software/preseq -profile docker -entry test_preseq_paired_end -c tests/config/nextflow.config
@@ -18,4 +19,5 @@
   files:
     - path: output/test_preseq_paired_end/test.ccurve.txt
       md5sum: 66b339780630fc1aa72dcfbd0a4490fd
-    - path: output/test_preseq_paired_end/test.command.log
+    - path: output/test_preseq_paired_end/test.log
+      md5sum: d41d8cd98f00b204e9800998ecf8427e