Fix a bunch of stuff in GitHub Actions test workflows

.github/workflows/cutadapt.yml

@@ -1,8 +1,9 @@
 name: cutadapt
 on:
-  push: {}
+  push:
+    paths: software/cutadapt/**
   pull_request:
-    paths: software/cutadapt/*
+    paths: software/cutadapt/**
 
 jobs:
   run_ci_test:
@@ -12,13 +13,6 @@ jobs:
     steps:
       - uses: actions/checkout@v2
 
-      - name: Checkout submodules
-        shell: bash
-        run: |
-          auth_header="$(git config --local --get http.https://github.com/.extraheader)"
-          git submodule sync --recursive
-          git -c "http.extraheader=$auth_header" -c protocol.version=2 submodule update --init --force --recursive --depth=1
-
       - name: Install Nextflow
         run: |
           wget -qO- get.nextflow.io | bash

.github/workflows/docker.yml

@@ -14,7 +14,7 @@ jobs:
     steps:
 
       # Check out the repo
-      - uses: actions/checkout@v1
+      - uses: actions/checkout@v2
 
       # Find the tool wrappers that changed
       # Annoyingly, matrix can't take dynamic variables

.github/workflows/fastqc.yml

@@ -12,9 +12,7 @@ jobs:
       NXF_ANSI_LOG: false
     steps:
 
-    # Check out the repository
     - uses: actions/checkout@v1
-      submodules: true
 
     - name: Install Nextflow
       run: |

.github/workflows/lint-code.yml

@@ -36,7 +36,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out repository
-        uses: actions/checkout@v1
+        uses: actions/checkout@v2
 
       - name: Install NodeJS
         uses: actions/setup-node@v1

.github/workflows/samtools_index.yml

@@ -1,8 +1,9 @@
 name: samtools index
 on:
-  push: {}
+  push:
+    paths: software/samtools/index/**
   pull_request:
-    paths: software/samtools/index*
+    paths: software/samtools/index/**
 
 jobs:
   run_ci_test:
@@ -11,9 +12,7 @@ jobs:
       NXF_ANSI_LOG: false
     steps:
 
-    # Check out the repository
+    - uses: actions/checkout@v2
-    - uses: actions/checkout@v1
-      submodules: true
 
     - name: Install Nextflow
       run: |

.github/workflows/samtools_sort.yml

@@ -1,8 +1,9 @@
 name: samtools sort
 on:
-  push: {}
+  push:
+    paths: software/samtools/sort**
   pull_request:
-    paths: software/samtools/sort*
+    paths: software/samtools/sort**
 
 jobs:
   run_ci_test:
@@ -11,9 +12,7 @@ jobs:
       NXF_ANSI_LOG: false
     steps:
 
-    # Check out the repository
+    - uses: actions/checkout@v2
-    - uses: actions/checkout@v1
-      submodules: true
 
     - name: Install Nextflow
       run: |

.github/workflows/tcoffee.yml

@@ -1,8 +1,9 @@
 name: tcoffee
 on:
-  push: {}
+  push:
+    paths: software/tcoffee/**
   pull_request:
-    paths: software/tcoffee/*
+    paths: software/tcoffee/**
 
 jobs:
   run_ci_test:
@@ -11,14 +12,7 @@ jobs:
       NXF_ANSI_LOG: false
     steps:
 
-    # Check out the repository
     - uses: actions/checkout@v2
-    - name: Checkout submodules
-      shell: bash
-      run: |
-          auth_header="$(git config --local --get http.https://github.com/.extraheader)"
-          git submodule sync --recursive
-          git -c "http.extraheader=$auth_header" -c protocol.version=2 submodule update --init --force --recursive --depth=1
 
     - name: Install Nextflow
       run: |

.github/workflows/trim_galore.yml

@@ -1,8 +1,9 @@
 name: Trim Galore!
 on:
-  push: {}
+  push:
+    paths: software/trim_galore/**
   pull_request:
-    paths: software/trim_galore/*
+    paths: software/trim_galore/**
 
 jobs:
   run_ci_test:
@@ -11,9 +12,7 @@ jobs:
       NXF_ANSI_LOG: false
     steps:
 
-    # Check out the repository
+    - uses: actions/checkout@v2
-    - uses: actions/checkout@v1
-      submodules: true
 
     - name: Install Nextflow
       run: |