From c94bb567176d0ce8e2316bd4d7926c763dfecf2f Mon Sep 17 00:00:00 2001
From: earx <eascarrunz.dev@mailfence.com>
Date: Thu, 17 Apr 2025 11:17:01 +0200
Subject: [PATCH 01/18] implement image caching with setup-buildx-action;
 update cache and checkout actions to v4

---
 .github/workflows/main.yml | 24 +++++++++++++-----------
 build_all.sh               | 13 +++++++++++--
 2 files changed, 24 insertions(+), 13 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index b850f59..24df40a 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -51,22 +51,24 @@ jobs:
       - name: Install Nextflow
         if: ${{ steps.cache-nextflow.outputs.cache-hit != 'true' }}
         run: cat .github/workflows/install_nextflow_v24.10.5.sh | bash && mv nextflow /usr/local/bin && chmod +x /usr/local/bin/nextflow
+        
+      # Check-out the repo under $GITHUB_WORKSPACE so that the job can access it
+      - uses: actions/checkout@v3
 
       # Build/cache containers
-      - name: Cache containers
-        id: cache-containers
-        uses: actions/cache@v3
+      - name: Set up Docker Buildx
+        uses: docker/setup-build-action@v3
+
+      - name: Cache Docker layers
+        uses: actions/cache@v4
         with:
-          key: ${{ runner.os }}-containers
-          path: /var/lib/docker/overlay2
+          path: /tmp/.buildx-cache
+          key: ${{ runner.os }}-buildx-${{ github.sha }}
           restore-keys: |
-            ${{ runner.os }}-containers
-      - name: Build Containers
-        if: ${{ steps.cache-containers.outputs.cache-hit != 'true'}}
-        run: bash build_all.sh
+            ${{ runner.os }}-buildx-
 
-      # Check-out the repo under $GITHUB_WORKSPACE so that the job can access it
-      - uses: actions/checkout@v3
+      - name: Build images
+        run: bash build_all.sh github_action
 
       # Run test(s)
       - name: test short single
diff --git a/build_all.sh b/build_all.sh
index 08285b2..ed8da65 100755
--- a/build_all.sh
+++ b/build_all.sh
@@ -1,5 +1,7 @@
 #!/usr/bin/env sh
 
+build_mode=$1
+
 # get architecture
 arch=$(uname -m)
 # set architecture to docker buildx
@@ -11,6 +13,8 @@ for dir in docker/*
 do 
     cd ${dir}
     imgname=$(echo $dir | rev | cut -d/ -f1 | rev)
+
+    echo ██████████████████▓▒░   Building ${imgname}   ░▒▓██████████████████
     
     # Reditools2 does not compile on arm64, force using amd64 compilation
     if [[ $dir =~ "reditools2" ]];then
@@ -19,8 +23,13 @@ do
             docker_arch_option=" --platform linux/amd64"
         fi
     fi
-    
-    docker build ${docker_arch_option} -t ${imgname} .
+
+    # Check "github_action" mode to enable cache
+    if [[ ${build_mode} == 'github_action' ]]; then
+        docker buildx build --cache-from type=local,src=/tmp/.buildx-cache --cache-to type=local,dest=/tmp/.buildx-cache ${docker_arch_option} -t ${imgname} .
+    else
+        docker build ${docker_arch_option} -t ${imgname} .
+    fi
     
     # back to the original working directory
     cd $wd

From 6fc6195d1e6fcd9fef0f8e386896b0cf52877c32 Mon Sep 17 00:00:00 2001
From: earx <eascarrunz.dev@mailfence.com>
Date: Thu, 17 Apr 2025 11:18:20 +0200
Subject: [PATCH 02/18] fix typo

---
 .github/workflows/main.yml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 24df40a..0b3d7d5 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -24,12 +24,12 @@ jobs:
     steps:
 
       - name: Get the code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         
       # Install/cache OpenJDK
       - name: Cache OpenJDK
         id: cache-openjdk
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: /usr/lib/jvm/java-11-openjdk-amd64
           key: ${{ runner.os }}-openjdk-11
@@ -42,7 +42,7 @@ jobs:
       # Install/cache Nextflow
       - name: Cache Nextflow
         id: cache-nextflow
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: /usr/local/bin/nextflow
           key: ${{ runner.os }}-nextflow
@@ -53,11 +53,11 @@ jobs:
         run: cat .github/workflows/install_nextflow_v24.10.5.sh | bash && mv nextflow /usr/local/bin && chmod +x /usr/local/bin/nextflow
         
       # Check-out the repo under $GITHUB_WORKSPACE so that the job can access it
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       # Build/cache containers
       - name: Set up Docker Buildx
-        uses: docker/setup-build-action@v3
+        uses: docker/setup-buildx-action@v3
 
       - name: Cache Docker layers
         uses: actions/cache@v4

From cdff5f788821724417a2ebb3ea9f263ffccbb0f0 Mon Sep 17 00:00:00 2001
From: earx <eascarrunz.dev@mailfence.com>
Date: Thu, 17 Apr 2025 11:24:25 +0200
Subject: [PATCH 03/18] make push trigger exclusive to the main branch

---
 .github/workflows/main.yml | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 0b3d7d5..a348be8 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -1,5 +1,10 @@
 name: CI
-on: [push, pull_request, workflow_dispatch]
+on: 
+  push:
+    branches:
+      - "main"
+  pull_request:
+  workflow_dispatch:
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}

From 0047b7619d6068671365ea0be1f3dc409741623e Mon Sep 17 00:00:00 2001
From: earx <eascarrunz.dev@mailfence.com>
Date: Thu, 17 Apr 2025 11:26:37 +0200
Subject: [PATCH 04/18] fix path

---
 nextflow.config | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/nextflow.config b/nextflow.config
index b438f20..35bfc51 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -55,7 +55,7 @@ profiles {
         params.aligner        = "STAR" 
         params.reads          = "${baseDir}/data/chr21/chr21_small_R1.fastq.gz "
         params.genome         = "${baseDir}/data/chr21/chr21_small.fasta.gz"
-        params.annotation     = "${baseDir}/data/chr21/chr21_small_filtered.gff3"
+        params.annotation     = "${baseDir}/data/chr21/chr21_small_filtered.gff3.gz"
         params.library_type   = "ISR" 
         params.read_type      = "short_single"
     }
@@ -64,7 +64,7 @@ profiles {
         params.aligner        = "STAR" 
         params.reads          = "${baseDir}/data/chr21/"
         params.genome         = "${baseDir}/data/chr21/chr21_small.fasta.gz" 
-        params.annotation     = "${baseDir}/data/chr21/chr21_small_filtered.gff3"
+        params.annotation     = "${baseDir}/data/chr21/chr21_small_filtered.gff3.gz"
         params.library_type   = "ISR" 
         params.read_type      = "short_paired"
     }

From c54701e59b48d551ddbeafd7c2b9ccd39ae62949 Mon Sep 17 00:00:00 2001
From: earx <eascarrunz.dev@mailfence.com>
Date: Thu, 17 Apr 2025 11:42:24 +0200
Subject: [PATCH 05/18] rename building script and add message in github_action
 build mode

---
 .github/workflows/main.yml      | 2 +-
 build_all.sh => build_images.sh | 1 +
 2 files changed, 2 insertions(+), 1 deletion(-)
 rename build_all.sh => build_images.sh (95%)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index a348be8..1542d6f 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -73,7 +73,7 @@ jobs:
             ${{ runner.os }}-buildx-
 
       - name: Build images
-        run: bash build_all.sh github_action
+        run: bash build_images.sh github_action
 
       # Run test(s)
       - name: test short single
diff --git a/build_all.sh b/build_images.sh
similarity index 95%
rename from build_all.sh
rename to build_images.sh
index ed8da65..8c9c4ee 100755
--- a/build_all.sh
+++ b/build_images.sh
@@ -26,6 +26,7 @@ do
 
     # Check "github_action" mode to enable cache
     if [[ ${build_mode} == 'github_action' ]]; then
+        echo ℹ️ Building in github_action mode.
         docker buildx build --cache-from type=local,src=/tmp/.buildx-cache --cache-to type=local,dest=/tmp/.buildx-cache ${docker_arch_option} -t ${imgname} .
     else
         docker build ${docker_arch_option} -t ${imgname} .

From ad5626d48d4d779c544b1f9658ee5c49feb992a3 Mon Sep 17 00:00:00 2001
From: earx <eascarrunz.dev@mailfence.com>
Date: Thu, 17 Apr 2025 11:44:25 +0200
Subject: [PATCH 06/18] fancier info message

---
 build_images.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build_images.sh b/build_images.sh
index 8c9c4ee..1a95d37 100755
--- a/build_images.sh
+++ b/build_images.sh
@@ -26,7 +26,7 @@ do
 
     # Check "github_action" mode to enable cache
     if [[ ${build_mode} == 'github_action' ]]; then
-        echo ℹ️ Building in github_action mode.
+        echo ℹ️ == Building in github_action mode ==ℹ️
         docker buildx build --cache-from type=local,src=/tmp/.buildx-cache --cache-to type=local,dest=/tmp/.buildx-cache ${docker_arch_option} -t ${imgname} .
     else
         docker build ${docker_arch_option} -t ${imgname} .

From 36d619b813ca119c97f18c1047d6ac7a3bcb461b Mon Sep 17 00:00:00 2001
From: earx <eascarrunz.dev@mailfence.com>
Date: Thu, 17 Apr 2025 11:57:48 +0200
Subject: [PATCH 07/18] add load option to the build command

---
 build_images.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build_images.sh b/build_images.sh
index 1a95d37..1197608 100755
--- a/build_images.sh
+++ b/build_images.sh
@@ -27,7 +27,7 @@ do
     # Check "github_action" mode to enable cache
     if [[ ${build_mode} == 'github_action' ]]; then
         echo ℹ️ == Building in github_action mode ==ℹ️
-        docker buildx build --cache-from type=local,src=/tmp/.buildx-cache --cache-to type=local,dest=/tmp/.buildx-cache ${docker_arch_option} -t ${imgname} .
+        docker buildx build --cache-from type=local,src=/tmp/.buildx-cache --cache-to type=local,dest=/tmp/.buildx-cache --load ${docker_arch_option} -t ${imgname} .
     else
         docker build ${docker_arch_option} -t ${imgname} .
     fi

From cb54628c7f02ab2702d79c8e11f4bd337c801913 Mon Sep 17 00:00:00 2001
From: earx <eascarrunz.dev@mailfence.com>
Date: Thu, 17 Apr 2025 12:06:29 +0200
Subject: [PATCH 08/18] use hisat2 in test profiles to speed up CI

---
 nextflow.config | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/nextflow.config b/nextflow.config
index 35bfc51..3293d72 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -52,7 +52,7 @@ profiles {
     }
     test {
         params.aline_profiles = "${baseDir}/config/ressources/base_aline.config" 
-        params.aligner        = "STAR" 
+        params.aligner        = "hisat2" 
         params.reads          = "${baseDir}/data/chr21/chr21_small_R1.fastq.gz "
         params.genome         = "${baseDir}/data/chr21/chr21_small.fasta.gz"
         params.annotation     = "${baseDir}/data/chr21/chr21_small_filtered.gff3.gz"
@@ -61,7 +61,7 @@ profiles {
     }
     test2 {
         params.aline_profiles = "${baseDir}/config/ressources/base_aline.config" 
-        params.aligner        = "STAR" 
+        params.aligner        = "hisat2" 
         params.reads          = "${baseDir}/data/chr21/"
         params.genome         = "${baseDir}/data/chr21/chr21_small.fasta.gz" 
         params.annotation     = "${baseDir}/data/chr21/chr21_small_filtered.gff3.gz"

From 3ebef1ec1d5c47bf5b3ba83d372bf76815824619 Mon Sep 17 00:00:00 2001
From: earx <eascarrunz.dev@mailfence.com>
Date: Thu, 17 Apr 2025 14:55:09 +0200
Subject: [PATCH 09/18] cache images to tarfile and rebuild based on hash of
 dockerfiles

---
 .github/workflows/main.yml | 27 +++++++++++++++++++++------
 build_images.sh            | 22 ++++++++++++++++------
 2 files changed, 37 insertions(+), 12 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 1542d6f..880a7d5 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -61,18 +61,33 @@ jobs:
       - uses: actions/checkout@v4
 
       # Build/cache containers
-      - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v3
+      # - name: Set up Docker Buildx
+        # uses: docker/setup-buildx-action@v3
 
-      - name: Cache Docker layers
+      - name: Cache Dockerfiles
         uses: actions/cache@v4
+        id: cache-dockerfiles
         with:
-          path: /tmp/.buildx-cache
-          key: ${{ runner.os }}-buildx-${{ github.sha }}
+          path: |
+            docker/*/Dockerfile
+          key: ${{ runner.os }}-dockerfiles-${{ hashFiles('docker/*/Dockerfile') }}
           restore-keys: |
-            ${{ runner.os }}-buildx-
+            ${{ runner.os }}-dockerfiles-
+
+      - name: Load cached Docker images
+        id: load-cache
+        run: |
+          if [ -f docker-images.tar ]; then
+            echo "Loading cached Docker images..."
+            docker load -i docker-images.tar || true
+            echo "build=false" >> $GITHUB_ENV
+          else
+            echo "No Docker cache found"
+            echo "build=true" >> $GITHUB_ENV
+          fi
 
       - name: Build images
+        if: env.build == 'true' || steps.cache-dockerfiles.outputs.cache-hit != 'true'
         run: bash build_images.sh github_action
 
       # Run test(s)
diff --git a/build_images.sh b/build_images.sh
index 1197608..72140f0 100755
--- a/build_images.sh
+++ b/build_images.sh
@@ -9,10 +9,15 @@ docker_arch_option=""
 
 # save original working directory
 wd=$(pwd)
+
+# list of image names
+image_list=()
+
 for dir in docker/*
 do 
     cd ${dir}
     imgname=$(echo $dir | rev | cut -d/ -f1 | rev)
+    image_list+=($imgname)
 
     echo ██████████████████▓▒░   Building ${imgname}   ░▒▓██████████████████
     
@@ -25,13 +30,18 @@ do
     fi
 
     # Check "github_action" mode to enable cache
-    if [[ ${build_mode} == 'github_action' ]]; then
-        echo ℹ️ == Building in github_action mode ==ℹ️
-        docker buildx build --cache-from type=local,src=/tmp/.buildx-cache --cache-to type=local,dest=/tmp/.buildx-cache --load ${docker_arch_option} -t ${imgname} .
-    else
-        docker build ${docker_arch_option} -t ${imgname} .
-    fi
+    docker build ${docker_arch_option} -t ${imgname} .
+    # if [[ ${build_mode} == 'github_action' ]]; then
+    #     echo ℹ️ == Building in github_action mode ==ℹ️
+    #     docker buildx build --cache-from type=local,src=/tmp/.buildx-cache --cache-to type=local,dest=/tmp/.buildx-cache --load ${docker_arch_option} -t ${imgname} .
+    # else
+    # fi
     
     # back to the original working directory
     cd $wd
 done
+
+if [[ ${build_mode} == 'github_action' ]]; then
+    echo "Saving docker images to cache..."
+    docker save ${image_list} -o docker-images.tar
+fi

From e61848b86e2b0e0cc3b0d4812f921b376dde1f24 Mon Sep 17 00:00:00 2001
From: earx <eascarrunz.dev@mailfence.com>
Date: Thu, 17 Apr 2025 15:58:51 +0200
Subject: [PATCH 10/18] add docker image archive to the cache

---
 .github/workflows/main.yml | 3 ++-
 build_images.sh            | 1 +
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 880a7d5..6fbc5c8 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -64,12 +64,13 @@ jobs:
       # - name: Set up Docker Buildx
         # uses: docker/setup-buildx-action@v3
 
-      - name: Cache Dockerfiles
+      - name: Cache Dockerfiles and TAR
         uses: actions/cache@v4
         id: cache-dockerfiles
         with:
           path: |
             docker/*/Dockerfile
+            docker-images.tar
           key: ${{ runner.os }}-dockerfiles-${{ hashFiles('docker/*/Dockerfile') }}
           restore-keys: |
             ${{ runner.os }}-dockerfiles-
diff --git a/build_images.sh b/build_images.sh
index 72140f0..71143ea 100755
--- a/build_images.sh
+++ b/build_images.sh
@@ -44,4 +44,5 @@ done
 if [[ ${build_mode} == 'github_action' ]]; then
     echo "Saving docker images to cache..."
     docker save ${image_list} -o docker-images.tar
+    pwd
 fi

From f2d3eb0eedaa158d2c97ddefc706c9cf242579c8 Mon Sep 17 00:00:00 2001
From: earx <eascarrunz.dev@mailfence.com>
Date: Thu, 17 Apr 2025 16:06:57 +0200
Subject: [PATCH 11/18] Improve comments

---
 build_images.sh | 13 ++++++-------
 1 file changed, 6 insertions(+), 7 deletions(-)

diff --git a/build_images.sh b/build_images.sh
index 71143ea..f39fabf 100755
--- a/build_images.sh
+++ b/build_images.sh
@@ -1,5 +1,11 @@
 #!/usr/bin/env sh
 
+# Run this script with the argument "github_action" in order to save images in an archive for caching
+# Pass no arguments to run the script in "normal" build mode suitable for a local machine
+
+# Read first argument as the "build mode"
+# The build is used, for instance, for special build commands
+# for Github actions.
 build_mode=$1
 
 # get architecture
@@ -29,13 +35,7 @@ do
         fi
     fi
 
-    # Check "github_action" mode to enable cache
     docker build ${docker_arch_option} -t ${imgname} .
-    # if [[ ${build_mode} == 'github_action' ]]; then
-    #     echo ℹ️ == Building in github_action mode ==ℹ️
-    #     docker buildx build --cache-from type=local,src=/tmp/.buildx-cache --cache-to type=local,dest=/tmp/.buildx-cache --load ${docker_arch_option} -t ${imgname} .
-    # else
-    # fi
     
     # back to the original working directory
     cd $wd
@@ -44,5 +44,4 @@ done
 if [[ ${build_mode} == 'github_action' ]]; then
     echo "Saving docker images to cache..."
     docker save ${image_list} -o docker-images.tar
-    pwd
 fi

From 398cbd53b462f4b98b6d128326467abf6e7fb25d Mon Sep 17 00:00:00 2001
From: earx <eascarrunz.dev@mailfence.com>
Date: Thu, 17 Apr 2025 16:12:16 +0200
Subject: [PATCH 12/18] use full path for archive lookup

---
 .github/workflows/main.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 6fbc5c8..1e8eb43 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -78,7 +78,7 @@ jobs:
       - name: Load cached Docker images
         id: load-cache
         run: |
-          if [ -f docker-images.tar ]; then
+          if [ -f /home/runner/work/rain/rain/docker-images.tar ]; then
             echo "Loading cached Docker images..."
             docker load -i docker-images.tar || true
             echo "build=false" >> $GITHUB_ENV

From deb4cf1d27a3bf0c96167f01fb2b93fd67a5c3c6 Mon Sep 17 00:00:00 2001
From: earx <eascarrunz.dev@mailfence.com>
Date: Thu, 17 Apr 2025 16:23:09 +0200
Subject: [PATCH 13/18] output cache size info

---
 .github/workflows/main.yml | 6 +-----
 build_images.sh            | 1 +
 2 files changed, 2 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 1e8eb43..8f48817 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -60,10 +60,6 @@ jobs:
       # Check-out the repo under $GITHUB_WORKSPACE so that the job can access it
       - uses: actions/checkout@v4
 
-      # Build/cache containers
-      # - name: Set up Docker Buildx
-        # uses: docker/setup-buildx-action@v3
-
       - name: Cache Dockerfiles and TAR
         uses: actions/cache@v4
         id: cache-dockerfiles
@@ -78,7 +74,7 @@ jobs:
       - name: Load cached Docker images
         id: load-cache
         run: |
-          if [ -f /home/runner/work/rain/rain/docker-images.tar ]; then
+          if [ -f docker-images.tar ]; then
             echo "Loading cached Docker images..."
             docker load -i docker-images.tar || true
             echo "build=false" >> $GITHUB_ENV
diff --git a/build_images.sh b/build_images.sh
index f39fabf..0bbf17b 100755
--- a/build_images.sh
+++ b/build_images.sh
@@ -44,4 +44,5 @@ done
 if [[ ${build_mode} == 'github_action' ]]; then
     echo "Saving docker images to cache..."
     docker save ${image_list} -o docker-images.tar
+    echo Archive size: $(stat --printf="%s" docker-images.tar)
 fi

From cab1831b9377a19065d52a7a53cdfe1c8a3d4aca Mon Sep 17 00:00:00 2001
From: earx <eascarrunz.dev@mailfence.com>
Date: Thu, 17 Apr 2025 16:27:42 +0200
Subject: [PATCH 14/18] change hash key

---
 .github/workflows/main.yml | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 8f48817..945ddc6 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -61,13 +61,11 @@ jobs:
       - uses: actions/checkout@v4
 
       - name: Cache Dockerfiles and TAR
-        uses: actions/cache@v4
         id: cache-dockerfiles
+        uses: actions/cache@v4
         with:
-          path: |
-            docker/*/Dockerfile
-            docker-images.tar
-          key: ${{ runner.os }}-dockerfiles-${{ hashFiles('docker/*/Dockerfile') }}
+          path: docker-images.tar
+          key: ${{ runner.os }}-dockerfiles-${{ hashFiles('docker/*') }}
           restore-keys: |
             ${{ runner.os }}-dockerfiles-
 

From 8287db939e2bfab39fddb318439b22d6e10a41e6 Mon Sep 17 00:00:00 2001
From: earx <eascarrunz.dev@mailfence.com>
Date: Thu, 17 Apr 2025 16:36:45 +0200
Subject: [PATCH 15/18] fix key

---
 .github/workflows/main.yml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 945ddc6..7264156 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -66,8 +66,6 @@ jobs:
         with:
           path: docker-images.tar
           key: ${{ runner.os }}-dockerfiles-${{ hashFiles('docker/*') }}
-          restore-keys: |
-            ${{ runner.os }}-dockerfiles-
 
       - name: Load cached Docker images
         id: load-cache

From 79d8ec76eb5ae6e18bb80609b5376a355aae587b Mon Sep 17 00:00:00 2001
From: earx <eascarrunz.dev@mailfence.com>
Date: Thu, 17 Apr 2025 16:54:44 +0200
Subject: [PATCH 16/18] Revert test profile aligner to STAR

---
 nextflow.config | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/nextflow.config b/nextflow.config
index 3293d72..35bfc51 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -52,7 +52,7 @@ profiles {
     }
     test {
         params.aline_profiles = "${baseDir}/config/ressources/base_aline.config" 
-        params.aligner        = "hisat2" 
+        params.aligner        = "STAR" 
         params.reads          = "${baseDir}/data/chr21/chr21_small_R1.fastq.gz "
         params.genome         = "${baseDir}/data/chr21/chr21_small.fasta.gz"
         params.annotation     = "${baseDir}/data/chr21/chr21_small_filtered.gff3.gz"
@@ -61,7 +61,7 @@ profiles {
     }
     test2 {
         params.aline_profiles = "${baseDir}/config/ressources/base_aline.config" 
-        params.aligner        = "hisat2" 
+        params.aligner        = "STAR" 
         params.reads          = "${baseDir}/data/chr21/"
         params.genome         = "${baseDir}/data/chr21/chr21_small.fasta.gz" 
         params.annotation     = "${baseDir}/data/chr21/chr21_small_filtered.gff3.gz"

From 448d2f361a306c4d9f666150dffb0b68a4b165d8 Mon Sep 17 00:00:00 2001
From: earx <eascarrunz.dev@mailfence.com>
Date: Thu, 17 Apr 2025 17:21:16 +0200
Subject: [PATCH 17/18] fix image list

---
 build_images.sh | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/build_images.sh b/build_images.sh
index 0bbf17b..da28da7 100755
--- a/build_images.sh
+++ b/build_images.sh
@@ -17,13 +17,13 @@ docker_arch_option=""
 wd=$(pwd)
 
 # list of image names
-image_list=()
+image_list=( )
 
 for dir in docker/*
 do 
     cd ${dir}
     imgname=$(echo $dir | rev | cut -d/ -f1 | rev)
-    image_list+=($imgname)
+    image_list+=(${imgname})
 
     echo ██████████████████▓▒░   Building ${imgname}   ░▒▓██████████████████
     
@@ -43,6 +43,6 @@ done
 
 if [[ ${build_mode} == 'github_action' ]]; then
     echo "Saving docker images to cache..."
-    docker save ${image_list} -o docker-images.tar
+    docker save ${image_list[@]} -o docker-images.tar
     echo Archive size: $(stat --printf="%s" docker-images.tar)
 fi

From 9c5b4cec4bc84515860f2fb7ce3167bb6fa89038 Mon Sep 17 00:00:00 2001
From: earx <eascarrunz.dev@mailfence.com>
Date: Fri, 18 Apr 2025 09:36:26 +0200
Subject: [PATCH 18/18] fix hash for docker stuff

---
 .github/workflows/main.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 7264156..2654e41 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -65,7 +65,7 @@ jobs:
         uses: actions/cache@v4
         with:
           path: docker-images.tar
-          key: ${{ runner.os }}-dockerfiles-${{ hashFiles('docker/*') }}
+          key: ${{ runner.os }}-dockerfiles-${{ hashFiles('docker/**/*') }}
 
       - name: Load cached Docker images
         id: load-cache