From 8941b6e758b08ba59417d7750965d15b56e201e5 Mon Sep 17 00:00:00 2001
From: Lili Andersson-Li <64467552+LilyAnderssonLee@users.noreply.github.com>
Date: Fri, 12 Apr 2024 13:33:04 +0200
Subject: [PATCH 1/4] manully define stub run branch is master

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

diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml
index 22dafd2e..505546f0 100644
--- a/.github/workflows/download_pipeline.yml
+++ b/.github/workflows/download_pipeline.yml
@@ -76,7 +76,7 @@ jobs:
         env:
           NXF_SINGULARITY_CACHEDIR: ./
           NXF_SINGULARITY_HOME_MOUNT: true
-        run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results
+        run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< master) -stub -profile test,singularity --outdir ./results
 
       - name: Run the downloaded pipeline (stub run not supported)
         id: run_pipeline

From 2db93e48f021134c3d9a7734e180f27e3ca49681 Mon Sep 17 00:00:00 2001
From: Lili Andersson-Li <64467552+LilyAnderssonLee@users.noreply.github.com>
Date: Fri, 12 Apr 2024 13:38:29 +0200
Subject: [PATCH 2/4] update changelog and remove disk clean in
 download_pipeline.yml

---
 .github/workflows/download_pipeline.yml | 3 ---
 CHANGELOG.md                            | 1 +
 2 files changed, 1 insertion(+), 3 deletions(-)

diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml
index 505546f0..cac24c15 100644
--- a/.github/workflows/download_pipeline.yml
+++ b/.github/workflows/download_pipeline.yml
@@ -32,9 +32,6 @@ jobs:
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v2
 
-      - name: Disk space cleanup
-        uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
-
       - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
         with:
           python-version: "3.12"
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 778c764c..22b18b49 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -11,6 +11,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#461](https://github.com/nf-core/taxprofiler/pull/461) Turned on 'strict' Nextflow evaluation runs (added by @jfy133)
 - [#461](https://github.com/nf-core/taxprofiler/pull/461) Optimised database compression so each compressed input database is untarred once, and shared amongst each run with different parameters (added by @jfy133)
 - [#461](https://github.com/nf-core/taxprofiler/pull/461) Added new parameter to optionally save uncompressed databases (added by @jfy133)
+- [#471](https://github.com/nf-core/taxprofiler/pull/471) Update `download_pipeline.yml` because the pipeline does not support stub runs on dev (fixed by @LilyAnderssonLee)
 
 ### `Fixed`
 

From 39a66a3b66896f31509f4faa137852b8b891195a Mon Sep 17 00:00:00 2001
From: Lili Andersson-Li <64467552+LilyAnderssonLee@users.noreply.github.com>
Date: Fri, 12 Apr 2024 15:09:13 +0200
Subject: [PATCH 3/4] Update download_pipeline.yml

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

diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml
index cac24c15..1eb590c9 100644
--- a/.github/workflows/download_pipeline.yml
+++ b/.github/workflows/download_pipeline.yml
@@ -73,7 +73,7 @@ jobs:
         env:
           NXF_SINGULARITY_CACHEDIR: ./
           NXF_SINGULARITY_HOME_MOUNT: true
-        run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< master) -stub -profile test,singularity --outdir ./results
+        run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< dev) -stub -profile test,singularity --outdir ./results
 
       - name: Run the downloaded pipeline (stub run not supported)
         id: run_pipeline

From 8fe3968378a6f421faed6695e87e417d9fa23855 Mon Sep 17 00:00:00 2001
From: LilyAnderssonLee <lilili2011me@gmail.com>
Date: Tue, 16 Apr 2024 09:26:12 +0200
Subject: [PATCH 4/4] remove stub run in download pipeline

---
 .github/workflows/download_pipeline.yml | 14 ++------------
 CHANGELOG.md                            |  4 ++--
 2 files changed, 4 insertions(+), 14 deletions(-)

diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml
index 1eb590c9..2bcf451a 100644
--- a/.github/workflows/download_pipeline.yml
+++ b/.github/workflows/download_pipeline.yml
@@ -67,18 +67,8 @@ jobs:
       - name: Inspect download
         run: tree ./${{ env.REPOTITLE_LOWERCASE }}
 
-      - name: Run the downloaded pipeline (stub)
-        id: stub_run_pipeline
-        continue-on-error: true
+      - name: Run the downloaded pipeline
         env:
           NXF_SINGULARITY_CACHEDIR: ./
           NXF_SINGULARITY_HOME_MOUNT: true
-        run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< dev) -stub -profile test,singularity --outdir ./results
-
-      - name: Run the downloaded pipeline (stub run not supported)
-        id: run_pipeline
-        if: ${{ job.steps.stub_run_pipeline.status == failure() }}
-        env:
-          NXF_SINGULARITY_CACHEDIR: ./
-          NXF_SINGULARITY_HOME_MOUNT: true
-        run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results
+        run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test_nothing,singularity --outdir ./results
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 22b18b49..16cf4825 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,7 +3,7 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## v1.1.6 - Augmented Akita Patch [2024-04-12]
+## v1.1.6 - Augmented Akita Patch [2024-04-16]
 
 ### `Added`
 
@@ -11,7 +11,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#461](https://github.com/nf-core/taxprofiler/pull/461) Turned on 'strict' Nextflow evaluation runs (added by @jfy133)
 - [#461](https://github.com/nf-core/taxprofiler/pull/461) Optimised database compression so each compressed input database is untarred once, and shared amongst each run with different parameters (added by @jfy133)
 - [#461](https://github.com/nf-core/taxprofiler/pull/461) Added new parameter to optionally save uncompressed databases (added by @jfy133)
-- [#471](https://github.com/nf-core/taxprofiler/pull/471) Update `download_pipeline.yml` because the pipeline does not support stub runs on dev (fixed by @LilyAnderssonLee)
+- [#471](https://github.com/nf-core/taxprofiler/pull/471) Remove `-stub` run in the `download_pipeline.yml` because the pipeline does not support stub runs on dev (fixed by @LilyAnderssonLee)
 
 ### `Fixed`