ci: Get rid of software folder

.github/workflows/bwa_index.yml

@@ -0,0 +1,36 @@
+name: bwa_index
+on:
+    push:
+        paths:
+            - software/bwa/index/**
+            - .github/workflows/bwa_index.yml
+            - tests/software/bwa/**
+    pull_request:
+        paths:
+            - software/bwa/index/**
+            - .github/workflows/bwa_index.yml
+            - tests/software/bwa/**
+
+jobs:
+    ci_test:
+        runs-on: ubuntu-latest
+        env:
+            NXF_ANSI_LOG: false
+        steps:
+            - uses: actions/checkout@v2
+
+            - name: Install Nextflow
+              run: |
+                  export NXF_VER="20.07.1"
+                  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 bwa_index --symlink --wt 2

.github/workflows/bwa_mem.yml

@@ -3,12 +3,12 @@ on:
   push:
     paths:
       - software/bwa/mem/**
-      - .github/workflows/software/bwa_mem.yml
+      - .github/workflows/bwa_mem.yml
       - tests/software/bwa/**
   pull_request:
     paths:
       - software/bwa/mem/**
-      - .github/workflows/software/bwa_mem.yml
+      - .github/workflows/bwa_mem.yml
       - tests/software/bwa/**
 
 jobs:

.github/workflows/picard_collectmultiplemetrics.yml

@@ -3,12 +3,12 @@ on:
   push:
     paths:
       - software/picard/collectmultiplemetrics/**
-      - .github/workflows/software/picard_collectmultiplemetrics.yml
+      - .github/workflows/picard_collectmultiplemetrics.yml
       - tests/software/picard/**
   pull_request:
     paths:
       - software/picard/collectmultiplemetrics/**
-      - .github/workflows/software/picard_collectmultiplemetrics.yml
+      - .github/workflows/picard_collectmultiplemetrics.yml
       - tests/software/picard/**
 
 jobs:

.github/workflows/picard_markduplicates.yml

@@ -3,12 +3,12 @@ on:
   push:
     paths:
       - software/picard/markduplicates/**
-      - .github/workflows/software/picard_markduplicates.yml
+      - .github/workflows/picard_markduplicates.yml
       - tests/software/picard/**
   pull_request:
     paths:
       - software/picard/markduplicates/**
-      - .github/workflows/software/picard_markduplicates.yml
+      - .github/workflows/picard_markduplicates.yml
       - tests/software/picard/**
 
 jobs:

.github/workflows/picard_mergesamfiles.yml

@@ -3,12 +3,12 @@ on:
   push:
     paths:
       - software/picard/mergesamfiles/**
-      - .github/workflows/software/picard_mergesamfiles.yml
+      - .github/workflows/picard_mergesamfiles.yml
       - tests/software/picard/**
   pull_request:
     paths:
       - software/picard/mergesamfiles/**
-      - .github/workflows/software/picard_mergesamfiles.yml
+      - .github/workflows/picard_mergesamfiles.yml
       - tests/software/picard/**
 
 jobs:

.github/workflows/samtools_flagstat.yml

@@ -3,12 +3,12 @@ on:
   push:
     paths:
       - software/samtools/flagstat/**
-      - .github/workflows/software/samtools_flagstat.yml
+      - .github/workflows/samtools_flagstat.yml
       - tests/software/samtools/**
   pull_request:
     paths:
       - software/samtools/flagstat/**
-      - .github/workflows/software/samtools_flagstat.yml
+      - .github/workflows/samtools_flagstat.yml
       - tests/software/samtools/**
 
 jobs:

.github/workflows/samtools_idxstats.yml

@@ -3,12 +3,12 @@ on:
   push:
     paths:
       - software/samtools/idxstats/**
-      - .github/workflows/software/samtools_idxstats.yml
+      - .github/workflows/samtools_idxstats.yml
       - tests/software/samtools/**
   pull_request:
     paths:
       - software/samtools/idxstats/**
-      - .github/workflows/software/samtools_idxstats.yml
+      - .github/workflows/samtools_idxstats.yml
       - tests/software/samtools/**
 
 jobs:

.github/workflows/samtools_index.yml

@@ -3,12 +3,12 @@ on:
   push:
     paths:
       - software/samtools/index/**
-      - .github/workflows/software/samtools_index.yml
+      - .github/workflows/samtools_index.yml
       - tests/software/samtools/**
   pull_request:
     paths:
       - software/samtools/index/**
-      - .github/workflows/software/samtools_index.yml
+      - .github/workflows/samtools_index.yml
       - tests/software/samtools/**
 
 jobs:

.github/workflows/samtools_sort.yml

@@ -3,12 +3,12 @@ on:
   push:
     paths:
       - software/samtools/sort/**
-      - .github/workflows/software/samtools_sort.yml
+      - .github/workflows/samtools_sort.yml
       - tests/software/samtools/**
   pull_request:
     paths:
       - software/samtools/sort/**
-      - .github/workflows/software/samtools_sort.yml
+      - .github/workflows/samtools_sort.yml
       - tests/software/samtools/**
 
 jobs:

.github/workflows/samtools_stats.yml

@@ -3,12 +3,12 @@ on:
   push:
     paths:
       - software/samtools/stats/**
-      - .github/workflows/software/software/samtools_stats.yml
+      - .github/workflows/software/samtools_stats.yml
       - tests/software/samtools/**
   pull_request:
     paths:
       - software/samtools/stats/**
-      - .github/workflows/software/software/samtools_stats.yml
+      - .github/workflows/software/samtools_stats.yml
       - tests/software/samtools/**
 
 jobs:

.github/workflows/software/bwa_index.yml

@@ -1,36 +0,0 @@
-name: bwa_index
-on:
-  push:
-    paths:
-      - software/bwa/index/**
-      - .github/workflows/software/bwa_index.yml
-      - tests/software/bwa/**
-  pull_request:
-    paths:
-      - software/bwa/index/**
-      - .github/workflows/software/bwa_index.yml
-      - tests/software/bwa/**
-
-jobs:
-  ci_test:
-    runs-on: ubuntu-latest
-    env:
-      NXF_ANSI_LOG: false
-    steps:
-      - uses: actions/checkout@v2
-
-      - name: Install Nextflow
-        run: |
-          export NXF_VER="20.07.1"
-          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 bwa_index --symlink --wt 2

.github/workflows/trimgalore.yml

@@ -3,12 +3,12 @@ on:
   push:
     paths:
       - software/trimgalore/**
-      - .github/workflows/software/trimgalore.yml
+      - .github/workflows/trimgalore.yml
       - tests/software/trimgalore/**
   pull_request:
     paths:
       - software/trimgalore/**
-      - .github/workflows/software/trimgalore.yml
+      - .github/workflows/trimgalore.yml
       - tests/software/trimgalore/**
 
 jobs: