From fd193f0e7117a9ea0a9cefc73b08874664ac4643 Mon Sep 17 00:00:00 2001
From: Sebastian Uhrig <suhrig@altoslabs.com>
Date: Wed, 29 Mar 2023 17:11:52 +0200
Subject: [PATCH 01/17] number groups after removing irrelevant components from
 sample name

---
 bin/deseq2_qc.r | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bin/deseq2_qc.r b/bin/deseq2_qc.r
index fa2e2c78a..d99bc7c2b 100755
--- a/bin/deseq2_qc.r
+++ b/bin/deseq2_qc.r
@@ -77,10 +77,10 @@ decompose       <- n_components!=1 && all(sapply(name_components, length)==n_com
 coldata         <- data.frame(samples.vec, sample=samples.vec, row.names=1)
 if (decompose) {
     groupings        <- as.data.frame(lapply(1:n_components, function(i) sapply(name_components, "[[", i)))
-    names(groupings) <- paste0("Group", 1:n_components)
     n_distinct       <- sapply(groupings, function(grp) length(unique(grp)))
     groupings        <- groupings[n_distinct!=1 & n_distinct!=length(samples.vec)]
     if (ncol(groupings)!=0) {
+        names(groupings) <- paste0("Group", 1:ncol(groupings))
         coldata <- cbind(coldata, groupings)
     } else {
         decompose <- FALSE

From cd48584185044a011449114eb6e4ee9306463097 Mon Sep 17 00:00:00 2001
From: Sebastian Uhrig <suhrig@altoslabs.com>
Date: Wed, 29 Mar 2023 18:21:04 +0200
Subject: [PATCH 02/17] update CHANGELOG.md

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 42f7496ea..9528e55d5 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -37,6 +37,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [[#961](https://github.com/nf-core/rnaseq/issues/961)] - Add warnings to STDOUT for all skipped and failed strandedness check samples
 - [[#975](https://github.com/nf-core/rnaseq/issues/975)] - `SALMON_INDEX` runs when using `--aligner star_rsem` even if samples have explicit strandedness
 - Remove HISAT2 from automated AWS full-sized tests
+- [[#988](https://github.com/nf-core/rnaseq/issues/988)] - `DESEQ2_QC_STAR_SALMON` fails when sample names have many components
 
 ### Parameters
 

From 930ab4d5b9d09a94f639d75f2701290f30759d6b Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Thu, 30 Mar 2023 15:00:34 +0100
Subject: [PATCH 03/17] Remove wait option from Tower Actions

---
 .github/workflows/cloud_tests_full.yml  | 3 ---
 .github/workflows/cloud_tests_small.yml | 3 ---
 2 files changed, 6 deletions(-)

diff --git a/.github/workflows/cloud_tests_full.yml b/.github/workflows/cloud_tests_full.yml
index 92d784131..d0c3d6e3e 100644
--- a/.github/workflows/cloud_tests_full.yml
+++ b/.github/workflows/cloud_tests_full.yml
@@ -36,7 +36,6 @@ jobs:
                 "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
                 "outdir": "${{ secrets.TOWER_BUCKET_AWS }}/rnaseq/results-${{ github.sha }}/aligner_${{ matrix.aligner }}"
             }
-          wait: false
       - uses: actions/upload-artifact@v3
         with:
           name: Tower debug log file
@@ -61,7 +60,6 @@ jobs:
                 "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
                 "outdir": "${{ secrets.TOWER_BUCKET_GCP }}/rnaseq/results-${{ github.sha }}/aligner_${{ matrix.aligner }}"
             }
-          wait: false
       - uses: actions/upload-artifact@v3
         with:
           name: Tower debug log file
@@ -87,7 +85,6 @@ jobs:
                 "outdir": "${{ secrets.TOWER_BUCKET_AZURE }}/rnaseq/results-${{ github.sha }}/aligner_${{ matrix.aligner }}",
                 "igenomes_base": "${{ secrets.TOWER_IGENOMES_BASE_AZURE }}"
             }
-          wait: false
       - uses: actions/upload-artifact@v3
         with:
           name: Tower debug log file
diff --git a/.github/workflows/cloud_tests_small.yml b/.github/workflows/cloud_tests_small.yml
index 318601912..6f2e6d8a9 100644
--- a/.github/workflows/cloud_tests_small.yml
+++ b/.github/workflows/cloud_tests_small.yml
@@ -30,7 +30,6 @@ jobs:
             {
                 "outdir": "${{ secrets.TOWER_BUCKET_AWS }}/rnaseq/results-test-${{ github.sha }}"
             }
-          wait: false
       - uses: actions/upload-artifact@v3
         with:
           name: Tower debug log file
@@ -51,7 +50,6 @@ jobs:
             {
                 "outdir": "${{ secrets.TOWER_BUCKET_GCP }}/rnaseq/results-test-${{ github.sha }}"
             }
-          wait: false
       - uses: actions/upload-artifact@v3
         with:
           name: Tower debug log file
@@ -72,7 +70,6 @@ jobs:
             {
                 "outdir": "${{ secrets.TOWER_BUCKET_AZURE }}/rnaseq/results-test-${{ github.sha }}"
             }
-          wait: false
       - uses: actions/upload-artifact@v3
         with:
           name: Tower debug log file

From 851e2c57e47f028c0f0a3f1c096739f9c955d67c Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Thu, 30 Mar 2023 15:04:30 +0100
Subject: [PATCH 04/17] Update CHANGELOG

---
 CHANGELOG.md | 16 +++++++++++++++-
 1 file changed, 15 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 2ecef3a5c..c4034f5eb 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,6 +3,21 @@
 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).
 
+## [[3.11.1](https://github.com/nf-core/rnaseq/releases/tag/3.11.1)] - 2023-03-30
+
+### Credits
+
+Special thanks to the following for their code contributions to the release:
+
+- [Rob Syme](https://github.com/robsyme)
+- [suhrig](https://github.com/suhrig)
+
+### Enhancements & fixes
+
+- [[#988](https://github.com/nf-core/rnaseq/issues/988)] - `DESEQ2_QC_STAR_SALMON` fails when sample names have many components
+- Remove `wait: false` option from Tower Actions which is the default
+- Fix release trigger for full-sized multi-cloud tests
+
 ## [[3.11.0](https://github.com/nf-core/rnaseq/releases/tag/3.11.0)] - 2023-03-30
 
 ### Credits
@@ -37,7 +52,6 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [[#961](https://github.com/nf-core/rnaseq/issues/961)] - Add warnings to STDOUT for all skipped and failed strandedness check samples
 - [[#975](https://github.com/nf-core/rnaseq/issues/975)] - `SALMON_INDEX` runs when using `--aligner star_rsem` even if samples have explicit strandedness
 - Remove HISAT2 from automated AWS full-sized tests
-- [[#988](https://github.com/nf-core/rnaseq/issues/988)] - `DESEQ2_QC_STAR_SALMON` fails when sample names have many components
 
 ### Parameters
 

From f801b1eda588b5247a027806562dc880f872a981 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Thu, 30 Mar 2023 15:05:08 +0100
Subject: [PATCH 05/17] Bump pipeline version to 3.11.1

---
 nextflow.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nextflow.config b/nextflow.config
index c5ca21943..a5b94fd04 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -261,7 +261,7 @@ manifest {
     description     = """RNA sequencing analysis pipeline for gene/isoform quantification and extensive quality control."""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=22.10.1'
-    version         = '3.11.0'
+    version         = '3.11.1'
     doi             = 'https://doi.org/10.5281/zenodo.1400710'
 }
 

From 302254cdfe97f5132a5c8cc2a06b1836f317ee2a Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Thu, 30 Mar 2023 15:18:56 +0100
Subject: [PATCH 06/17] Update umitools modules to use different labels

---
 modules.json                             | 6 +++---
 modules/nf-core/umitools/dedup/main.nf   | 2 +-
 modules/nf-core/umitools/extract/main.nf | 1 +
 3 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/modules.json b/modules.json
index 018c1ecae..a209ca3d2 100644
--- a/modules.json
+++ b/modules.json
@@ -211,13 +211,13 @@
                     },
                     "umitools/dedup": {
                         "branch": "master",
-                        "git_sha": "6d9c7e43404e20a97d2f6f88548456afe78282e6",
+                        "git_sha": "ffe2f5865f608848e440a52b73c304ea79aaf818",
                         "installed_by": ["bam_dedup_stats_samtools_umitools"]
                     },
                     "umitools/extract": {
                         "branch": "master",
-                        "git_sha": "6d9c7e43404e20a97d2f6f88548456afe78282e6",
-                        "installed_by": ["fastq_fastqc_umitools_trimgalore", "fastq_fastqc_umitools_fastp"]
+                        "git_sha": "ffe2f5865f608848e440a52b73c304ea79aaf818",
+                        "installed_by": ["fastq_fastqc_umitools_fastp", "fastq_fastqc_umitools_trimgalore"]
                     },
                     "untar": {
                         "branch": "master",
diff --git a/modules/nf-core/umitools/dedup/main.nf b/modules/nf-core/umitools/dedup/main.nf
index 68fc9b9e7..aa6fdd24e 100644
--- a/modules/nf-core/umitools/dedup/main.nf
+++ b/modules/nf-core/umitools/dedup/main.nf
@@ -1,6 +1,6 @@
 process UMITOOLS_DEDUP {
     tag "$meta.id"
-    label "process_single"
+    label "process_medium"
 
     conda "bioconda::umi_tools=1.1.4"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
diff --git a/modules/nf-core/umitools/extract/main.nf b/modules/nf-core/umitools/extract/main.nf
index ba2826e1f..64fdd367f 100644
--- a/modules/nf-core/umitools/extract/main.nf
+++ b/modules/nf-core/umitools/extract/main.nf
@@ -1,6 +1,7 @@
 process UMITOOLS_EXTRACT {
     tag "$meta.id"
     label "process_single"
+    label "process_long"
 
     conda "bioconda::umi_tools=1.1.4"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

From 5c2456aabbf44be3c29b4abbf1a8e68480d96a00 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Thu, 30 Mar 2023 16:40:09 +0100
Subject: [PATCH 07/17] Test [ci fast]

---
 .github/workflows/ci.yml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index fc63a1509..19fd3004a 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -65,7 +65,7 @@ jobs:
 
   star_salmon:
     name: Test STAR Salmon with workflow parameters
-    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq') }}
+    if: ${{ (github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq')) && !contains(github.event.head_commit.message, '[ci fast]') }}
     runs-on: ubuntu-latest
     strategy:
       matrix:
@@ -122,7 +122,7 @@ jobs:
 
   star_rsem:
     name: Test STAR RSEM with workflow parameters
-    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq') }}
+    if: ${{ (github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq')) && !contains(github.event.head_commit.message, '[ci fast]') }}
     runs-on: ubuntu-latest
     strategy:
       matrix:
@@ -168,7 +168,7 @@ jobs:
 
   hisat2:
     name: Test HISAT2 with workflow parameters
-    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq') }}
+    if: ${{ (github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq')) && !contains(github.event.head_commit.message, '[ci fast]') }}
     runs-on: ubuntu-latest
     strategy:
       matrix:
@@ -214,7 +214,7 @@ jobs:
 
   salmon:
     name: Test Salmon with workflow parameters
-    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq') }}
+    if: ${{ (github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq')) && !contains(github.event.head_commit.message, '[ci fast]') }}
     runs-on: ubuntu-latest
     strategy:
       matrix:

From 490f319d52c9d07eb2f8c4aeef9f708d1cf9ca92 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Thu, 30 Mar 2023 16:55:19 +0100
Subject: [PATCH 08/17] Update CHANGELOG [ci fast]

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index c4034f5eb..2ae20d8b9 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -17,6 +17,7 @@ Special thanks to the following for their code contributions to the release:
 - [[#988](https://github.com/nf-core/rnaseq/issues/988)] - `DESEQ2_QC_STAR_SALMON` fails when sample names have many components
 - Remove `wait: false` option from Tower Actions which is the default
 - Fix release trigger for full-sized multi-cloud tests
+- Adding `[ci fast]` to commit message now skips all tests except for standard `-profile test` pipeline run
 
 ## [[3.11.0](https://github.com/nf-core/rnaseq/releases/tag/3.11.0)] - 2023-03-30
 

From 00f578086c4f900c48695a6fe0e18f9d282ef2fc Mon Sep 17 00:00:00 2001
From: Adam Talbot <adam.talbot@seqera.io>
Date: Wed, 29 Mar 2023 15:39:03 +0100
Subject: [PATCH 09/17] Create hash of github.workspace ID and use that as
 cache key

---
 .github/workflows/ci.yml | 30 +++++++++++++++---------------
 1 file changed, 15 insertions(+), 15 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index fc63a1509..dd08f3c22 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -52,8 +52,8 @@ jobs:
 
       - name: Replace remote paths in samplesheets
         run: |
-          for f in ${{ github.workspace }}/test-datasets/samplesheet/v3.10/*.csv; do
-            sed -i "s=https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/=${{ github.workspace }}/test-datasets/=g" $f
+          for f in ./test-datasets/samplesheet/v3.10/*.csv; do
+            sed -i "s=https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/=./test-datasets/=g" $f
             echo "========== $f ============"
             cat $f
             echo "========================================"
@@ -61,7 +61,7 @@ jobs:
 
       - name: Run pipeline with test data
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets/
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results --test_data_base ./test-datasets/
 
   star_salmon:
     name: Test STAR Salmon with workflow parameters
@@ -104,8 +104,8 @@ jobs:
 
       - name: Replace remote paths in samplesheets
         run: |
-          for f in ${{ github.workspace }}/test-datasets/samplesheet/v3.10/*.csv; do
-            sed -i "s=https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/=${{ github.workspace }}/test-datasets/=g" $f
+          for f in ./test-datasets/samplesheet/v3.10/*.csv; do
+            sed -i "s=https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/=./test-datasets/=g" $f
             echo "========== $f ============"
             cat $f
             echo "========================================"
@@ -118,7 +118,7 @@ jobs:
 
       - name: Run pipeline with STAR and various parameters
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner star_salmon ${{ matrix.parameters }} --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets/
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner star_salmon ${{ matrix.parameters }} --outdir ./results --test_data_base ./test-datasets/
 
   star_rsem:
     name: Test STAR RSEM with workflow parameters
@@ -150,8 +150,8 @@ jobs:
 
       - name: Replace remote paths in samplesheets
         run: |
-          for f in ${{ github.workspace }}/test-datasets/samplesheet/v3.10/*.csv; do
-            sed -i "s=https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/=${{ github.workspace }}/test-datasets/=g" $f
+          for f in ./test-datasets/samplesheet/v3.10/*.csv; do
+            sed -i "s=https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/=./test-datasets/=g" $f
             echo "========== $f ============"
             cat $f
             echo "========================================"
@@ -164,7 +164,7 @@ jobs:
 
       - name: Run pipeline with RSEM STAR and various parameters
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner star_rsem ${{ matrix.parameters }} --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets/
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner star_rsem ${{ matrix.parameters }} --outdir ./results --test_data_base ./test-datasets/
 
   hisat2:
     name: Test HISAT2 with workflow parameters
@@ -196,8 +196,8 @@ jobs:
 
       - name: Replace remote paths in samplesheets
         run: |
-          for f in ${{ github.workspace }}/test-datasets/samplesheet/v3.10/*.csv; do
-            sed -i "s=https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/=${{ github.workspace }}/test-datasets/=g" $f
+          for f in ./test-datasets/samplesheet/v3.10/*.csv; do
+            sed -i "s=https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/=./test-datasets/=g" $f
             echo "========== $f ============"
             cat $f
             echo "========================================"
@@ -210,7 +210,7 @@ jobs:
 
       - name: Run pipeline with HISAT2 and various parameters
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner hisat2 ${{ matrix.parameters }} --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets/
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner hisat2 ${{ matrix.parameters }} --outdir ./results --test_data_base ./test-datasets/
 
   salmon:
     name: Test Salmon with workflow parameters
@@ -242,8 +242,8 @@ jobs:
 
       - name: Replace remote paths in samplesheets
         run: |
-          for f in ${{ github.workspace }}/test-datasets/samplesheet/v3.10/*.csv; do
-            sed -i "s=https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/=${{ github.workspace }}/test-datasets/=g" $f
+          for f in ./test-datasets/samplesheet/v3.10/*.csv; do
+            sed -i "s=https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/=./test-datasets/=g" $f
             echo "========== $f ============"
             cat $f
             echo "========================================"
@@ -256,4 +256,4 @@ jobs:
 
       - name: Run pipeline with Salmon and various parameters
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --pseudo_aligner salmon ${{ matrix.parameters }} --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets/
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --pseudo_aligner salmon ${{ matrix.parameters }} --outdir ./results --test_data_base ./test-datasets/

From 1ac037e9e8fa6d4a1d7a701e00810e58dd90decf Mon Sep 17 00:00:00 2001
From: Adam Talbot <adam.talbot@seqera.io>
Date: Thu, 30 Mar 2023 17:03:20 +0100
Subject: [PATCH 10/17] fixup

---
 .github/workflows/ci.yml | 66 ++++++++++++++++++++++++++++------------
 1 file changed, 46 insertions(+), 20 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index dd08f3c22..1a932c551 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -35,12 +35,17 @@ jobs:
         with:
           version: "${{ matrix.NXF_VER }}"
 
+      - name: Hash Github Workspace
+        id: hash_workspace
+        run: |
+          echo "digest=$(echo RNA_3.10.1_${{ github.workspace }} | md5sum | cut -c 1-25)" >> $GITHUB_OUTPUT
+          
       - name: Cache test data
         id: cache-testdata
         uses: actions/cache@v3
         with:
           path: test-datasets/
-          key: rnaseq3_10-test-data
+          key: ${{ steps.hash_workspace.outputs.digest }}
 
       - name: Check out test data
         if: steps.cache-testdata.outputs.cache-hit != 'true'
@@ -52,8 +57,8 @@ jobs:
 
       - name: Replace remote paths in samplesheets
         run: |
-          for f in ./test-datasets/samplesheet/v3.10/*.csv; do
-            sed -i "s=https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/=./test-datasets/=g" $f
+          for f in ${{ github.workspace }}/test-datasets/samplesheet/v3.10/*.csv; do
+            sed -i "s=https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/=${{ github.workspace }}/test-datasets/=g" $f
             echo "========== $f ============"
             cat $f
             echo "========================================"
@@ -61,7 +66,7 @@ jobs:
 
       - name: Run pipeline with test data
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results --test_data_base ./test-datasets/
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets/
 
   star_salmon:
     name: Test STAR Salmon with workflow parameters
@@ -87,12 +92,17 @@ jobs:
       - name: Check out pipeline code
         uses: actions/checkout@v2
 
+      - name: Hash Github Workspace
+        id: hash_workspace
+        run: |
+          echo "digest=$(echo RNA_3.10.1_${{ github.workspace }} | md5sum | cut -c 1-25)" >> $GITHUB_OUTPUT
+          
       - name: Cache test data
         id: cache-testdata
         uses: actions/cache@v3
         with:
           path: test-datasets/
-          key: rnaseq3_10-test-data
+          key: ${{ steps.hash_workspace.outputs.digest }}
 
       - name: Check out test data
         if: steps.cache-testdata.outputs.cache-hit != 'true'
@@ -104,8 +114,8 @@ jobs:
 
       - name: Replace remote paths in samplesheets
         run: |
-          for f in ./test-datasets/samplesheet/v3.10/*.csv; do
-            sed -i "s=https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/=./test-datasets/=g" $f
+          for f in ${{ github.workspace }}/test-datasets/samplesheet/v3.10/*.csv; do
+            sed -i "s=https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/=${{ github.workspace }}/test-datasets/=g" $f
             echo "========== $f ============"
             cat $f
             echo "========================================"
@@ -118,7 +128,7 @@ jobs:
 
       - name: Run pipeline with STAR and various parameters
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner star_salmon ${{ matrix.parameters }} --outdir ./results --test_data_base ./test-datasets/
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner star_salmon ${{ matrix.parameters }} --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets/
 
   star_rsem:
     name: Test STAR RSEM with workflow parameters
@@ -133,12 +143,17 @@ jobs:
       - name: Check out pipeline code
         uses: actions/checkout@v2
 
+      - name: Hash Github Workspace
+        id: hash_workspace
+        run: |
+          echo "digest=$(echo RNA_3.10.1_${{ github.workspace }} | md5sum | cut -c 1-25)" >> $GITHUB_OUTPUT
+          
       - name: Cache test data
         id: cache-testdata
         uses: actions/cache@v3
         with:
           path: test-datasets/
-          key: rnaseq3_10-test-data
+          key: rnaseq-${{ steps.hash_workspace.outputs.digest }}
 
       - name: Check out test data
         if: steps.cache-testdata.outputs.cache-hit != 'true'
@@ -150,8 +165,8 @@ jobs:
 
       - name: Replace remote paths in samplesheets
         run: |
-          for f in ./test-datasets/samplesheet/v3.10/*.csv; do
-            sed -i "s=https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/=./test-datasets/=g" $f
+          for f in ${{ github.workspace }}/test-datasets/samplesheet/v3.10/*.csv; do
+            sed -i "s=https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/=${{ github.workspace }}/test-datasets/=g" $f
             echo "========== $f ============"
             cat $f
             echo "========================================"
@@ -164,7 +179,7 @@ jobs:
 
       - name: Run pipeline with RSEM STAR and various parameters
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner star_rsem ${{ matrix.parameters }} --outdir ./results --test_data_base ./test-datasets/
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner star_rsem ${{ matrix.parameters }} --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets/
 
   hisat2:
     name: Test HISAT2 with workflow parameters
@@ -179,12 +194,17 @@ jobs:
       - name: Check out pipeline code
         uses: actions/checkout@v2
 
+      - name: Hash Github Workspace
+        id: hash_workspace
+        run: |
+          echo "digest=$(echo RNA_3.10.1_${{ github.workspace }} | md5sum | cut -c 1-25)" >> $GITHUB_OUTPUT
+          
       - name: Cache test data
         id: cache-testdata
         uses: actions/cache@v3
         with:
           path: test-datasets/
-          key: rnaseq3_10-test-data
+          key: rnaseq-${{ steps.hash_workspace.outputs.digest }}
 
       - name: Check out test data
         if: steps.cache-testdata.outputs.cache-hit != 'true'
@@ -196,8 +216,8 @@ jobs:
 
       - name: Replace remote paths in samplesheets
         run: |
-          for f in ./test-datasets/samplesheet/v3.10/*.csv; do
-            sed -i "s=https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/=./test-datasets/=g" $f
+          for f in ${{ github.workspace }}/test-datasets/samplesheet/v3.10/*.csv; do
+            sed -i "s=https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/=${{ github.workspace }}/test-datasets/=g" $f
             echo "========== $f ============"
             cat $f
             echo "========================================"
@@ -210,7 +230,7 @@ jobs:
 
       - name: Run pipeline with HISAT2 and various parameters
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner hisat2 ${{ matrix.parameters }} --outdir ./results --test_data_base ./test-datasets/
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner hisat2 ${{ matrix.parameters }} --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets/
 
   salmon:
     name: Test Salmon with workflow parameters
@@ -225,12 +245,18 @@ jobs:
       - name: Check out pipeline code
         uses: actions/checkout@v2
 
+      - name: Hash Github Workspace
+        id: hash_workspace
+        run: |
+          echo "digest=$(echo RNA_3.10.1_${{ github.workspace }} | md5sum | cut -c 1-25)" >> $GITHUB_OUTPUT
+          
+
       - name: Cache test data
         id: cache-testdata
         uses: actions/cache@v3
         with:
           path: test-datasets/
-          key: rnaseq3_10-test-data
+          key: ${{ steps.hash_workspace.outputs.digest }}
 
       - name: Check out test data
         if: steps.cache-testdata.outputs.cache-hit != 'true'
@@ -242,8 +268,8 @@ jobs:
 
       - name: Replace remote paths in samplesheets
         run: |
-          for f in ./test-datasets/samplesheet/v3.10/*.csv; do
-            sed -i "s=https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/=./test-datasets/=g" $f
+          for f in ${{ github.workspace }}/test-datasets/samplesheet/v3.10/*.csv; do
+            sed -i "s=https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/=${{ github.workspace }}/test-datasets/=g" $f
             echo "========== $f ============"
             cat $f
             echo "========================================"
@@ -256,4 +282,4 @@ jobs:
 
       - name: Run pipeline with Salmon and various parameters
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --pseudo_aligner salmon ${{ matrix.parameters }} --outdir ./results --test_data_base ./test-datasets/
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --pseudo_aligner salmon ${{ matrix.parameters }} --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets/

From 1f228a2f209fbf81c01884af94e28dfd8dd83f3c Mon Sep 17 00:00:00 2001
From: Adam Talbot <adam.talbot@seqera.io>
Date: Thu, 30 Mar 2023 17:04:10 +0100
Subject: [PATCH 11/17] changelog

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 42f7496ea..a98da1e30 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -37,6 +37,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [[#961](https://github.com/nf-core/rnaseq/issues/961)] - Add warnings to STDOUT for all skipped and failed strandedness check samples
 - [[#975](https://github.com/nf-core/rnaseq/issues/975)] - `SALMON_INDEX` runs when using `--aligner star_rsem` even if samples have explicit strandedness
 - Remove HISAT2 from automated AWS full-sized tests
+- Fix issue with incorrect cacheing of test datasets during CI/CD
 
 ### Parameters
 

From 1964135eb783a25eaf913e96f8a226d5f5c8c085 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Thu, 30 Mar 2023 17:06:13 +0100
Subject: [PATCH 12/17] Fix Actions to trigger full-sized tests on release

---
 .github/workflows/cloud_tests_full.yml | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/cloud_tests_full.yml b/.github/workflows/cloud_tests_full.yml
index d0c3d6e3e..3c4b23106 100644
--- a/.github/workflows/cloud_tests_full.yml
+++ b/.github/workflows/cloud_tests_full.yml
@@ -17,7 +17,7 @@ on:
           - gcp
 jobs:
   run-full-tests-on-aws:
-    if: ${{ github.event.inputs.platform == 'all' || github.event.inputs.platform == 'aws' }}
+    if: ${{ github.event.inputs.platform == 'all' || github.event.inputs.platform == 'aws' || !github.event.inputs }}
     runs-on: ubuntu-latest
     strategy:
       matrix:
@@ -34,6 +34,7 @@ jobs:
           parameters: |
             {
                 "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
+                "aligner": "${{ matrix.aligner }}",
                 "outdir": "${{ secrets.TOWER_BUCKET_AWS }}/rnaseq/results-${{ github.sha }}/aligner_${{ matrix.aligner }}"
             }
       - uses: actions/upload-artifact@v3
@@ -41,7 +42,7 @@ jobs:
           name: Tower debug log file
           path: tower_action_*.log
   run-full-tests-on-gcp:
-    if: ${{ github.event.inputs.platform == 'all' || github.event.inputs.platform == 'gcp' }}
+    if: ${{ github.event.inputs.platform == 'all' || github.event.inputs.platform == 'gcp' || !github.event.inputs }}
     runs-on: ubuntu-latest
     strategy:
       matrix:
@@ -58,6 +59,7 @@ jobs:
           parameters: |
             {
                 "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
+                "aligner": "${{ matrix.aligner }}",
                 "outdir": "${{ secrets.TOWER_BUCKET_GCP }}/rnaseq/results-${{ github.sha }}/aligner_${{ matrix.aligner }}"
             }
       - uses: actions/upload-artifact@v3
@@ -65,7 +67,7 @@ jobs:
           name: Tower debug log file
           path: tower_action_*.log
   run-full-tests-on-azure:
-    if: ${{ github.event.inputs.platform == 'all' || github.event.inputs.platform == 'azure' }}
+    if: ${{ github.event.inputs.platform == 'all' || github.event.inputs.platform == 'azure' || !github.event.inputs }}
     runs-on: ubuntu-latest
     strategy:
       matrix:
@@ -82,6 +84,7 @@ jobs:
           parameters: |
             {
                 "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
+                "aligner": "${{ matrix.aligner }}",
                 "outdir": "${{ secrets.TOWER_BUCKET_AZURE }}/rnaseq/results-${{ github.sha }}/aligner_${{ matrix.aligner }}",
                 "igenomes_base": "${{ secrets.TOWER_IGENOMES_BASE_AZURE }}"
             }

From c3cc602244cea3ee92c75961b7d1aa3d276f1f8f Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Thu, 30 Mar 2023 17:06:38 +0100
Subject: [PATCH 13/17] Add Adam to CHANGELOG [ci skip]

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 2ae20d8b9..06be5ef99 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -9,6 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 Special thanks to the following for their code contributions to the release:
 
+- [Adam Talbot](https://github.com/adamrtalbot)
 - [Rob Syme](https://github.com/robsyme)
 - [suhrig](https://github.com/suhrig)
 

From 18e910b05f5d6f5f99db9f232b05370d8455e119 Mon Sep 17 00:00:00 2001
From: Adam Talbot <adam.talbot@seqera.io>
Date: Thu, 30 Mar 2023 17:14:58 +0100
Subject: [PATCH 14/17] [ci skip] Changelog

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 2ace6f5cf..920fa29af 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -38,7 +38,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [[#975](https://github.com/nf-core/rnaseq/issues/975)] - `SALMON_INDEX` runs when using `--aligner star_rsem` even if samples have explicit strandedness
 - Remove HISAT2 from automated AWS full-sized tests
 - [[#988](https://github.com/nf-core/rnaseq/issues/988)] - `DESEQ2_QC_STAR_SALMON` fails when sample names have many components
-- Fix issue with incorrect cacheing of test datasets during CI/CD
+- [[#987](https://github.com/nf-core/rnaseq/pull/987)] - Fix issue with incorrect cacheing of test datasets during CI/CD
 
 ### Parameters
 

From d010be381541d9fc67ab227e9464af510d5306f2 Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Thu, 30 Mar 2023 16:18:09 +0000
Subject: [PATCH 15/17] [automated] Fix linting with Prettier

---
 .github/workflows/ci.yml | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 1a932c551..21771e649 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -39,7 +39,7 @@ jobs:
         id: hash_workspace
         run: |
           echo "digest=$(echo RNA_3.10.1_${{ github.workspace }} | md5sum | cut -c 1-25)" >> $GITHUB_OUTPUT
-          
+
       - name: Cache test data
         id: cache-testdata
         uses: actions/cache@v3
@@ -96,7 +96,7 @@ jobs:
         id: hash_workspace
         run: |
           echo "digest=$(echo RNA_3.10.1_${{ github.workspace }} | md5sum | cut -c 1-25)" >> $GITHUB_OUTPUT
-          
+
       - name: Cache test data
         id: cache-testdata
         uses: actions/cache@v3
@@ -147,7 +147,7 @@ jobs:
         id: hash_workspace
         run: |
           echo "digest=$(echo RNA_3.10.1_${{ github.workspace }} | md5sum | cut -c 1-25)" >> $GITHUB_OUTPUT
-          
+
       - name: Cache test data
         id: cache-testdata
         uses: actions/cache@v3
@@ -198,7 +198,7 @@ jobs:
         id: hash_workspace
         run: |
           echo "digest=$(echo RNA_3.10.1_${{ github.workspace }} | md5sum | cut -c 1-25)" >> $GITHUB_OUTPUT
-          
+
       - name: Cache test data
         id: cache-testdata
         uses: actions/cache@v3
@@ -249,7 +249,6 @@ jobs:
         id: hash_workspace
         run: |
           echo "digest=$(echo RNA_3.10.1_${{ github.workspace }} | md5sum | cut -c 1-25)" >> $GITHUB_OUTPUT
-          
 
       - name: Cache test data
         id: cache-testdata

From 1333a7adf75d9c863b0643ec9d97ef4aa9ccd428 Mon Sep 17 00:00:00 2001
From: Adam Talbot <adam.talbot@seqera.io>
Date: Thu, 30 Mar 2023 17:21:45 +0100
Subject: [PATCH 16/17] fixup

---
 .github/workflows/ci.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 21771e649..393c9bd24 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -153,7 +153,7 @@ jobs:
         uses: actions/cache@v3
         with:
           path: test-datasets/
-          key: rnaseq-${{ steps.hash_workspace.outputs.digest }}
+          key: ${{ steps.hash_workspace.outputs.digest }}
 
       - name: Check out test data
         if: steps.cache-testdata.outputs.cache-hit != 'true'
@@ -204,7 +204,7 @@ jobs:
         uses: actions/cache@v3
         with:
           path: test-datasets/
-          key: rnaseq-${{ steps.hash_workspace.outputs.digest }}
+          key: ${{ steps.hash_workspace.outputs.digest }}
 
       - name: Check out test data
         if: steps.cache-testdata.outputs.cache-hit != 'true'

From fcb218926c78766c47bffee384262075c513d4b8 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Fri, 31 Mar 2023 14:38:45 +0100
Subject: [PATCH 17/17] Update date in CHANGELOG

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index b7b5011f6..2d5191059 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).
 
-## [[3.11.1](https://github.com/nf-core/rnaseq/releases/tag/3.11.1)] - 2023-03-30
+## [[3.11.1](https://github.com/nf-core/rnaseq/releases/tag/3.11.1)] - 2023-03-31
 
 ### Credits