From 2a91bc148525091428d8f978fecc7c102d7976d6 Mon Sep 17 00:00:00 2001
From: Adam Talbot <adam.talbot@seqera.io>
Date: Fri, 28 Jul 2023 09:49:51 +0100
Subject: [PATCH 01/32] Add wait-for-status workflow

---
 .github/workflows/wait-for-status.yml | 13 +++++++++++++
 1 file changed, 13 insertions(+)
 create mode 100644 .github/workflows/wait-for-status.yml

diff --git a/.github/workflows/wait-for-status.yml b/.github/workflows/wait-for-status.yml
new file mode 100644
index 00000000000..59ad31577f8
--- /dev/null
+++ b/.github/workflows/wait-for-status.yml
@@ -0,0 +1,13 @@
+name: summary
+on:
+  pull_request:
+jobs:
+  enforce-all-checks:
+    runs-on: ubuntu-latest
+    permissions:
+      checks: read
+    steps:
+      - name: GitHub Checks
+        uses: poseidon/wait-for-status-checks@v0.1.0
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}

From 888d8206303dad243ec464f365e76e46d03334b5 Mon Sep 17 00:00:00 2001
From: Adam Talbot <adam.talbot@seqera.io>
Date: Fri, 28 Jul 2023 10:16:49 +0100
Subject: [PATCH 02/32] Rename and tidy all GHA workflows for branch protection

---
 .github/workflows/code-linting.yml    |  2 +-
 .github/workflows/fix-linting.yml     |  4 ++++
 .github/workflows/nf-core-linting.yml | 13 +++++++++++++
 .github/workflows/pytest-workflow.yml | 15 +++++++++++++++
 .github/workflows/wait-for-status.yml | 13 -------------
 5 files changed, 33 insertions(+), 14 deletions(-)
 delete mode 100644 .github/workflows/wait-for-status.yml

diff --git a/.github/workflows/code-linting.yml b/.github/workflows/code-linting.yml
index 831453f8ea2..0c4ca69e8d7 100644
--- a/.github/workflows/code-linting.yml
+++ b/.github/workflows/code-linting.yml
@@ -1,4 +1,4 @@
-name: code-lint
+name: code-linting
 on:
   push:
     branches: [master]
diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml
index 8558ceef715..7c2c01cd15b 100644
--- a/.github/workflows/fix-linting.yml
+++ b/.github/workflows/fix-linting.yml
@@ -5,7 +5,11 @@ on:
     types: [created]
 
 jobs:
+<<<<<<< HEAD
   fix-linting:
+=======
+  fix_linting:
+>>>>>>> 568afbcc2 (Rename and tidy all GHA workflows for branch protection)
     # Only run if comment is on a PR with the main repo, and if it contains the magic keywords
     if: >
       contains(github.event.comment.html_url, '/pull/') &&
diff --git a/.github/workflows/nf-core-linting.yml b/.github/workflows/nf-core-linting.yml
index 123decf27e6..ef72c2f3ce1 100644
--- a/.github/workflows/nf-core-linting.yml
+++ b/.github/workflows/nf-core-linting.yml
@@ -1,5 +1,10 @@
+<<<<<<< HEAD
 name: nf-core-lint
 run-name: nf-core-lint
+=======
+name: nf-core linting
+run-name: nf-core linting
+>>>>>>> 568afbcc2 (Rename and tidy all GHA workflows for branch protection)
 # This workflow is triggered on pushes and PRs to the repository.
 # It runs the `nf-core lint` tests to ensure that the module code meets the nf-core guidelines
 on:
@@ -15,7 +20,11 @@ concurrency:
 
 jobs:
   changes:
+<<<<<<< HEAD
     name: check-changes
+=======
+    name: check-for-changes
+>>>>>>> 568afbcc2 (Rename and tidy all GHA workflows for branch protection)
     runs-on: ubuntu-latest
     outputs:
       # Expose matched filters as job 'modules' output variable
@@ -30,7 +39,11 @@ jobs:
 
   lint:
     runs-on: ubuntu-20.04
+<<<<<<< HEAD
     name: lint
+=======
+    name: nf-core-lint
+>>>>>>> 568afbcc2 (Rename and tidy all GHA workflows for branch protection)
     needs: changes
     if: needs.changes.outputs.modules != '[]'
     strategy:
diff --git a/.github/workflows/pytest-workflow.yml b/.github/workflows/pytest-workflow.yml
index dcfe6db7cf0..b77978855a3 100644
--- a/.github/workflows/pytest-workflow.yml
+++ b/.github/workflows/pytest-workflow.yml
@@ -1,5 +1,10 @@
+<<<<<<< HEAD
 name: pytest
 run-name: pytest
+=======
+name: pytest-workflow
+run-name: pytest-workflow
+>>>>>>> 568afbcc2 (Rename and tidy all GHA workflows for branch protection)
 on:
   push:
     branches: [master]
@@ -16,7 +21,11 @@ concurrency:
 
 jobs:
   changes:
+<<<<<<< HEAD
     name: check-changes
+=======
+    name: check-for-changes
+>>>>>>> 568afbcc2 (Rename and tidy all GHA workflows for branch protection)
     runs-on: ubuntu-latest
     outputs:
       # Expose matched filters as job 'modules' output variable
@@ -29,9 +38,15 @@ jobs:
         with:
           filters: "tests/config/pytest_modules.yml"
 
+<<<<<<< HEAD
   pytest:
     runs-on: ubuntu-20.04
     name: pytest
+=======
+  pytest_workflow:
+    runs-on: ubuntu-20.04
+    name: pytest-workflow
+>>>>>>> 568afbcc2 (Rename and tidy all GHA workflows for branch protection)
     needs: changes
     if: needs.changes.outputs.modules != '[]'
     strategy:
diff --git a/.github/workflows/wait-for-status.yml b/.github/workflows/wait-for-status.yml
deleted file mode 100644
index 59ad31577f8..00000000000
--- a/.github/workflows/wait-for-status.yml
+++ /dev/null
@@ -1,13 +0,0 @@
-name: summary
-on:
-  pull_request:
-jobs:
-  enforce-all-checks:
-    runs-on: ubuntu-latest
-    permissions:
-      checks: read
-    steps:
-      - name: GitHub Checks
-        uses: poseidon/wait-for-status-checks@v0.1.0
-        with:
-          token: ${{ secrets.GITHUB_TOKEN }}

From d92ca5ceacd4263a3c8e512cb776c14ab67b1701 Mon Sep 17 00:00:00 2001
From: Adam Talbot <adam.talbot@seqera.io>
Date: Fri, 28 Jul 2023 10:29:39 +0100
Subject: [PATCH 03/32] Changing some stuff to kick off real CI/CD

---
 modules/nf-core/gatk4/haplotypecaller/main.nf | 2 +-
 modules/nf-core/samtools/sort/main.nf         | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/gatk4/haplotypecaller/main.nf b/modules/nf-core/gatk4/haplotypecaller/main.nf
index 478681bd18a..382d6cca9e5 100644
--- a/modules/nf-core/gatk4/haplotypecaller/main.nf
+++ b/modules/nf-core/gatk4/haplotypecaller/main.nf
@@ -5,7 +5,7 @@ process GATK4_HAPLOTYPECALLER {
     conda "bioconda::gatk4=4.4.0.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0':
-        'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }"
+        'quay.io/biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }"
 
     input:
     tuple val(meta), path(input), path(input_index), path(intervals), path(dragstr_model)
diff --git a/modules/nf-core/samtools/sort/main.nf b/modules/nf-core/samtools/sort/main.nf
index 2b7753fd863..ef281c4856d 100644
--- a/modules/nf-core/samtools/sort/main.nf
+++ b/modules/nf-core/samtools/sort/main.nf
@@ -5,7 +5,7 @@ process SAMTOOLS_SORT {
     conda "bioconda::samtools=1.17"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' :
-        'biocontainers/samtools:1.17--h00cdaf9_0' }"
+        'quay.io/biocontainers/samtools:1.17--h00cdaf9_0' }"
 
     input:
     tuple val(meta), path(bam)

From ae773bd8feacc2ca51a05705c81b2535425d930f Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Fri, 28 Jul 2023 12:46:00 +0100
Subject: [PATCH 04/32] Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
---
 .github/workflows/nf-core-linting.yml |  96 ---------
 .github/workflows/pytest-workflow.yml | 267 --------------------------
 2 files changed, 363 deletions(-)
 delete mode 100644 .github/workflows/nf-core-linting.yml
 delete mode 100644 .github/workflows/pytest-workflow.yml

diff --git a/.github/workflows/nf-core-linting.yml b/.github/workflows/nf-core-linting.yml
deleted file mode 100644
index ef72c2f3ce1..00000000000
--- a/.github/workflows/nf-core-linting.yml
+++ /dev/null
@@ -1,96 +0,0 @@
-<<<<<<< HEAD
-name: nf-core-lint
-run-name: nf-core-lint
-=======
-name: nf-core linting
-run-name: nf-core linting
->>>>>>> 568afbcc2 (Rename and tidy all GHA workflows for branch protection)
-# This workflow is triggered on pushes and PRs to the repository.
-# It runs the `nf-core lint` tests to ensure that the module code meets the nf-core guidelines
-on:
-  push:
-    branches: [master]
-  pull_request:
-    branches: [master]
-
-# Cancel if a newer run is started
-concurrency:
-  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
-  cancel-in-progress: true
-
-jobs:
-  changes:
-<<<<<<< HEAD
-    name: check-changes
-=======
-    name: check-for-changes
->>>>>>> 568afbcc2 (Rename and tidy all GHA workflows for branch protection)
-    runs-on: ubuntu-latest
-    outputs:
-      # Expose matched filters as job 'modules' output variable
-      modules: ${{ steps.filter.outputs.changes }}
-    steps:
-      - uses: actions/checkout@v3
-
-      - uses: dorny/paths-filter@v2
-        id: filter
-        with:
-          filters: "tests/config/pytest_modules.yml"
-
-  lint:
-    runs-on: ubuntu-20.04
-<<<<<<< HEAD
-    name: lint
-=======
-    name: nf-core-lint
->>>>>>> 568afbcc2 (Rename and tidy all GHA workflows for branch protection)
-    needs: changes
-    if: needs.changes.outputs.modules != '[]'
-    strategy:
-      fail-fast: false
-      matrix:
-        tags: ["${{ fromJson(needs.changes.outputs.modules) }}"]
-    steps:
-      - uses: actions/checkout@v3
-
-      - name: Set up Python
-        uses: actions/setup-python@v4
-        with:
-          python-version: "3.x"
-
-      - uses: actions/cache@v3
-        with:
-          path: ~/.cache/pip
-          key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
-          restore-keys: |
-            ${{ runner.os }}-pip-
-
-      - name: Set up Python
-        uses: actions/setup-python@v4
-        with:
-          python-version: "3.x"
-
-      - name: Install pip
-        run: python -m pip install --upgrade pip
-
-      - name: Install nf-core tools
-        run: python -m pip install nf-core
-
-      - name: Install Nextflow
-        env:
-          CAPSULE_LOG: none
-        run: |
-          wget -qO- get.nextflow.io | bash
-          sudo mv nextflow /usr/local/bin/
-
-      - name: Lint ${{ matrix.tags }}
-        run: nf-core modules lint ${{ matrix.tags }}
-        # HACK
-        if: startsWith( matrix.tags, 'subworkflow' ) != true
-
-      - uses: actions/cache@v3
-        with:
-          path: /usr/local/bin/nextflow
-          key: ${{ runner.os }}
-          restore-keys: |
-            ${{ runner.os }}
diff --git a/.github/workflows/pytest-workflow.yml b/.github/workflows/pytest-workflow.yml
deleted file mode 100644
index b77978855a3..00000000000
--- a/.github/workflows/pytest-workflow.yml
+++ /dev/null
@@ -1,267 +0,0 @@
-<<<<<<< HEAD
-name: pytest
-run-name: pytest
-=======
-name: pytest-workflow
-run-name: pytest-workflow
->>>>>>> 568afbcc2 (Rename and tidy all GHA workflows for branch protection)
-on:
-  push:
-    branches: [master]
-  pull_request:
-    branches: [master]
-  merge_group:
-    types: [checks_requested]
-    branches: [master]
-
-# Cancel if a newer run is started
-concurrency:
-  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
-  cancel-in-progress: true
-
-jobs:
-  changes:
-<<<<<<< HEAD
-    name: check-changes
-=======
-    name: check-for-changes
->>>>>>> 568afbcc2 (Rename and tidy all GHA workflows for branch protection)
-    runs-on: ubuntu-latest
-    outputs:
-      # Expose matched filters as job 'modules' output variable
-      modules: ${{ steps.filter.outputs.changes }}
-    steps:
-      - uses: actions/checkout@v3
-
-      - uses: dorny/paths-filter@v2
-        id: filter
-        with:
-          filters: "tests/config/pytest_modules.yml"
-
-<<<<<<< HEAD
-  pytest:
-    runs-on: ubuntu-20.04
-    name: pytest
-=======
-  pytest_workflow:
-    runs-on: ubuntu-20.04
-    name: pytest-workflow
->>>>>>> 568afbcc2 (Rename and tidy all GHA workflows for branch protection)
-    needs: changes
-    if: needs.changes.outputs.modules != '[]'
-    strategy:
-      fail-fast: false
-      matrix:
-        tags: ["${{ fromJson(needs.changes.outputs.modules) }}"]
-        profile: ["docker", "singularity", "conda"]
-        exclude:
-          - profile: "conda"
-            tags: annotsv
-          - profile: "conda"
-            tags: cellpose
-          - profile: "conda"
-            tags: mcquant
-          - profile: "conda"
-            tags: bases2fastq
-          - profile: "conda"
-            tags: backsub
-          - profile: "conda"
-            tags: basicpy
-          - profile: "conda"
-            tags: bcl2fastq
-          - profile: "conda"
-            tags: bclconvert
-          - profile: "conda"
-            tags: cellranger/count
-          - profile: "conda"
-            tags: cellranger/mkfastq
-          - profile: "conda"
-            tags: cellranger/mkgtf
-          - profile: "conda"
-            tags: cellranger/mkref
-          - profile: "conda"
-            tags: cellranger/mkvdjref
-          - profile: "conda"
-            tags: cellranger/multi
-          - profile: "conda"
-            tags: cellranger/vdj
-          - profile: "conda"
-            tags: coreograph
-          - profile: "conda"
-            tags: deepcell/mesmer
-          - profile: "conda"
-            tags: deepvariant
-          - profile: "conda"
-            tags: fastk/fastk
-          - profile: "conda"
-            tags: fastk/histex
-          - profile: "conda"
-            tags: fastk/merge
-          - profile: "conda"
-            tags: fcs/fcsadaptor
-          - profile: "conda"
-            tags: fcs/fcsgx
-          - profile: "conda"
-            tags: gatk4/baserecalibratorspark
-          - profile: "conda"
-            tags: gatk4/cnnscorevariants
-          - profile: "conda"
-            tags: gatk4/determinegermlinecontigploidy
-          - profile: "conda"
-            tags: gatk4/germlinecnvcaller
-          - profile: "conda"
-            tags: gatk4/markduplicatesspark
-          - profile: "conda"
-            tags: gatk4/postprocessgermlinecnvcalls
-          - profile: "conda"
-            tags: genescopefk
-          - profile: "conda"
-            tags: ilastik/multicut
-          - profile: "conda"
-            tags: ilastik/pixelclassification
-          - profile: "conda"
-            tags: imputeme/vcftoprs
-          - profile: "conda"
-            tags: merquryfk/katcomp
-          - profile: "conda"
-            tags: merquryfk/katgc
-          - profile: "conda"
-            tags: merquryfk/merquryfk
-          - profile: "conda"
-            tags: merquryfk/ploidyplot
-          - profile: "conda"
-            tags: mitohifi/findmitoreference
-          - profile: "conda"
-            tags: scimap/mcmicro
-          - profile: "conda"
-            tags: sentieon/applyvarcal
-          - profile: "conda"
-            tags: sentieon/bwaindex
-          - profile: "conda"
-            tags: sentieon/bwamem
-          - profile: "conda"
-            tags: sentieon/dedup
-          - profile: "conda"
-            tags: sentieon/gvcftyper
-          - profile: "conda"
-            tags: sentieon/haplotyper
-          - profile: "conda"
-            tags: sentieon/varcal
-          - profile: "conda"
-            tags: spaceranger/count
-          - profile: "conda"
-            tags: spaceranger/mkgtf
-          - profile: "conda"
-            tags: spaceranger/mkref
-          - profile: "conda"
-            tags: universc
-          - profile: "singularity"
-            tags: universc
-          - profile: "singularity"
-            tags: gatk4/determinegermlinecontigploidy
-          - profile: "conda"
-            tags: subworkflows/bcl_demultiplex
-          - profile: "conda"
-            tags: subworkflows/fasta_clean_fcs
-          - profile: "conda"
-            tags: islandpath
-    env:
-      NXF_ANSI_LOG: false
-      SENTIEON_LICENSE_BASE64: ${{ secrets.SENTIEON_LICENSE_BASE64 }}
-    steps:
-      - uses: actions/checkout@v3
-
-      - name: Set up Python
-        uses: actions/setup-python@v4
-        with:
-          python-version: "3.x"
-
-      - uses: actions/cache@v3
-        with:
-          path: ~/.cache/pip
-          key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
-          restore-keys: |
-            ${{ runner.os }}-pip-
-
-      - name: Install Python dependencies
-        run: python -m pip install --upgrade pip pytest-workflow cryptography
-
-      - uses: actions/cache@v3
-        with:
-          path: /usr/local/bin/nextflow
-          key: ${{ runner.os }}
-          restore-keys: |
-            ${{ runner.os }}-nextflow-
-
-      - name: Install Nextflow
-        env:
-          CAPSULE_LOG: none
-        run: |
-          wget -qO- get.nextflow.io | bash
-          sudo mv nextflow /usr/local/bin/
-
-      - name: Set up Singularity
-        if: matrix.profile == 'singularity'
-        uses: eWaterCycle/setup-singularity@v5
-        with:
-          singularity-version: 3.7.1
-
-      - name: Set up miniconda
-        if: matrix.profile == 'conda'
-        uses: conda-incubator/setup-miniconda@v2
-        with:
-          auto-update-conda: true
-          channels: conda-forge,bioconda,defaults
-          python-version: ${{ matrix.python-version }}
-
-      - name: Conda setup
-        if: matrix.profile == 'conda'
-        run: |
-          conda clean -a
-          conda install -n base conda-libmamba-solver
-          conda config --set solver libmamba
-
-      # Set up secrets
-      - name: Set up nextflow secrets
-        if: env.SENTIEON_LICENSE_BASE64 != null
-        run: |
-          nextflow secrets set SENTIEON_LICENSE_BASE64 ${{ secrets.SENTIEON_LICENSE_BASE64 }}
-          nextflow secrets set SENTIEON_AUTH_MECH_BASE64 ${{ secrets.SENTIEON_AUTH_MECH_BASE64 }}
-          SENTIEON_ENCRYPTION_KEY=$(echo -n "${{ secrets.ENCRYPTION_KEY_BASE64 }}" | base64 -d)
-          SENTIEON_LICENSE_MESSAGE=$(echo -n "${{ secrets.LICENSE_MESSAGE_BASE64 }}" | base64 -d)
-          SENTIEON_AUTH_DATA=$(python tests/modules/nf-core/sentieon/license_message.py encrypt --key "$SENTIEON_ENCRYPTION_KEY" --message "$SENTIEON_LICENSE_MESSAGE")
-          SENTIEON_AUTH_DATA_BASE64=$(echo -n "$SENTIEON_AUTH_DATA" | base64 -w 0)
-          nextflow secrets set SENTIEON_AUTH_DATA_BASE64 $SENTIEON_AUTH_DATA_BASE64
-
-      # Test the module
-      - name: Run pytest-workflow
-        # only use one thread for pytest-workflow to avoid race condition on conda cache.
-        run: TMPDIR=~ PROFILE=${{ matrix.profile }} pytest --tag ${{ matrix.tags }} --symlink --kwdof --git-aware --color=yes
-
-      - name: Output log on failure
-        if: failure()
-        run: |
-          sudo apt-get update > /dev/null
-          sudo apt-get install bat > /dev/null
-          batcat --decorations=always --color=always /home/runner/pytest_workflow_*/*/log.{out,err}
-
-      - name: Setting global variables
-        uses: actions/github-script@v6
-        id: parsed
-        with:
-          script: |
-            return '${{ matrix.tags }}'.toLowerCase().replaceAll(/\//g, '-').trim('-').trim('"')
-          result-encoding: string
-
-      - name: Upload logs on failure
-        if: failure()
-        uses: actions/upload-artifact@v2
-        with:
-          name: logs-${{ matrix.profile }}-${{ steps.parsed.outputs.result }}
-          path: |
-            /home/runner/pytest_workflow_*/*/.nextflow.log
-            /home/runner/pytest_workflow_*/*/log.out
-            /home/runner/pytest_workflow_*/*/log.err
-            /home/runner/pytest_workflow_*/*/work
-            !/home/runner/pytest_workflow_*/*/work/conda
-            !/home/runner/pytest_workflow_*/*/work/singularity

From e4cba90226d6272050b7784d87410b2309e3f652 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Fri, 28 Jul 2023 12:50:40 +0100
Subject: [PATCH 05/32] Update .github/workflows/code-linting.yml

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
---
 .github/workflows/code-linting.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/code-linting.yml b/.github/workflows/code-linting.yml
index 0c4ca69e8d7..831453f8ea2 100644
--- a/.github/workflows/code-linting.yml
+++ b/.github/workflows/code-linting.yml
@@ -1,4 +1,4 @@
-name: code-linting
+name: code-lint
 on:
   push:
     branches: [master]

From ce5579dfd8c5e83aa2d00ae8abf069851cdea061 Mon Sep 17 00:00:00 2001
From: Adam Talbot <adam.talbot@seqera.io>
Date: Fri, 28 Jul 2023 10:37:06 +0100
Subject: [PATCH 06/32] Should reduce concurrent burden at the expense of time.
 Code is required to lint before running. This will help us during hackathons
 etc when there is a high burden on the GHA runners, but will be slower in
 general use.

Changes:
 - linting and testing in one GHA file
 - Linting is required to pass before pytest or nf-test runs
 - Check for changes only happens once
---
 .github/workflows/test.yml                    | 506 ++++++++++++++++++
 modules/nf-core/gatk4/haplotypecaller/main.nf |   4 +-
 modules/nf-core/samtools/index/main.nf        |   2 +
 modules/nf-core/samtools/sort/main.nf         |   2 +-
 tests/modules/nf-core/fastqc/main.nf.test     |   2 +
 5 files changed, 514 insertions(+), 2 deletions(-)
 create mode 100644 .github/workflows/test.yml

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
new file mode 100644
index 00000000000..acec4ed352d
--- /dev/null
+++ b/.github/workflows/test.yml
@@ -0,0 +1,506 @@
+name: test
+on:
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+  merge_group:
+    types: [checks_requested]
+    branches: [master]
+
+# Cancel if a newer run is started
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  Prettier:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v3
+
+      - name: Install NodeJS
+        uses: actions/setup-node@v3
+
+      - name: Install Prettier
+        run: npm install -g prettier
+
+      - name: Run Prettier --check
+        run: prettier --check .
+
+  EditorConfig:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: actions/setup-node@v3
+
+      - name: Install editorconfig-checker
+        run: npm install -g editorconfig-checker
+
+      - name: Run ECLint check
+        run: editorconfig-checker -exclude README.md $(git ls-files | grep -v test)
+
+  pytest-changes:
+    name: pytest-changes
+    runs-on: ubuntu-latest
+    needs: [Prettier, EditorConfig]
+    outputs:
+      # Expose matched filters as job 'modules' output variable
+      modules: ${{ steps.filter.outputs.changes }}
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: dorny/paths-filter@v2
+        id: filter
+        with:
+          filters: "tests/config/pytest_modules.yml"
+
+  nf-core-lint:
+    runs-on: ubuntu-20.04
+    name: nf-core-lint
+    needs: pytest-changes
+    if: needs.pytest-changes.outputs.modules != '[]'
+    strategy:
+      fail-fast: false
+      matrix:
+        tags: ["${{ fromJson(needs.pytest-changes.outputs.modules) }}"]
+        exclude:
+          - tags: "nf-test"
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: "3.x"
+
+      - uses: actions/cache@v3
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
+          restore-keys: |
+            ${{ runner.os }}-pip-
+
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: "3.x"
+
+      - name: Install pip
+        run: python -m pip install --upgrade pip
+
+      - name: Install nf-core tools
+        run: python -m pip install nf-core
+
+      - name: Install Nextflow
+        env:
+          CAPSULE_LOG: none
+        run: |
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+
+      - name: Lint ${{ matrix.tags }}
+        run: nf-core modules lint ${{ matrix.tags }}
+        # HACK
+        if: startsWith( matrix.tags, 'subworkflow' ) != true
+
+      - uses: actions/cache@v3
+        with:
+          path: /usr/local/bin/nextflow
+          key: ${{ runner.os }}
+          restore-keys: |
+            ${{ runner.os }}
+
+  pytest:
+    runs-on: ubuntu-20.04
+    name: pytest
+    needs: [changes, Prettier, EditorConfig, nf_core_lint]
+    if: needs.changes.outputs.modules != '[]'
+    strategy:
+      fail-fast: false
+      matrix:
+        tags: ["${{ fromJson(needs.pytest-changes.outputs.modules) }}"]
+        profile: ["docker", "singularity", "conda"]
+        exclude:
+          - tags: "nf-test"
+          - profile: "conda"
+            tags: annotsv
+          - profile: "conda"
+            tags: cellpose
+          - profile: "conda"
+            tags: mcquant
+          - profile: "conda"
+            tags: bases2fastq
+          - profile: "conda"
+            tags: backsub
+          - profile: "conda"
+            tags: basicpy
+          - profile: "conda"
+            tags: bcl2fastq
+          - profile: "conda"
+            tags: bclconvert
+          - profile: "conda"
+            tags: cellranger/count
+          - profile: "conda"
+            tags: cellranger/mkfastq
+          - profile: "conda"
+            tags: cellranger/mkgtf
+          - profile: "conda"
+            tags: cellranger/mkref
+          - profile: "conda"
+            tags: cellranger/mkvdjref
+          - profile: "conda"
+            tags: cellranger/multi
+          - profile: "conda"
+            tags: cellranger/vdj
+          - profile: "conda"
+            tags: coreograph
+          - profile: "conda"
+            tags: deepcell/mesmer
+          - profile: "conda"
+            tags: deepvariant
+          - profile: "conda"
+            tags: fastk/fastk
+          - profile: "conda"
+            tags: fastk/histex
+          - profile: "conda"
+            tags: fastk/merge
+          - profile: "conda"
+            tags: fcs/fcsadaptor
+          - profile: "conda"
+            tags: fcs/fcsgx
+          - profile: "conda"
+            tags: gatk4/baserecalibratorspark
+          - profile: "conda"
+            tags: gatk4/cnnscorevariants
+          - profile: "conda"
+            tags: gatk4/determinegermlinecontigploidy
+          - profile: "conda"
+            tags: gatk4/germlinecnvcaller
+          - profile: "conda"
+            tags: gatk4/markduplicatesspark
+          - profile: "conda"
+            tags: gatk4/postprocessgermlinecnvcalls
+          - profile: "conda"
+            tags: genescopefk
+          - profile: "conda"
+            tags: ilastik/multicut
+          - profile: "conda"
+            tags: ilastik/pixelclassification
+          - profile: "conda"
+            tags: imputeme/vcftoprs
+          - profile: "conda"
+            tags: merquryfk/katcomp
+          - profile: "conda"
+            tags: merquryfk/katgc
+          - profile: "conda"
+            tags: merquryfk/merquryfk
+          - profile: "conda"
+            tags: merquryfk/ploidyplot
+          - profile: "conda"
+            tags: mitohifi/findmitoreference
+          - profile: "conda"
+            tags: scimap/mcmicro
+          - profile: "conda"
+            tags: sentieon/applyvarcal
+          - profile: "conda"
+            tags: sentieon/bwaindex
+          - profile: "conda"
+            tags: sentieon/bwamem
+          - profile: "conda"
+            tags: sentieon/dedup
+          - profile: "conda"
+            tags: sentieon/gvcftyper
+          - profile: "conda"
+            tags: sentieon/haplotyper
+          - profile: "conda"
+            tags: sentieon/varcal
+          - profile: "conda"
+            tags: spaceranger/count
+          - profile: "conda"
+            tags: spaceranger/mkgtf
+          - profile: "conda"
+            tags: spaceranger/mkref
+          - profile: "conda"
+            tags: universc
+          - profile: "singularity"
+            tags: universc
+          - profile: "singularity"
+            tags: gatk4/determinegermlinecontigploidy
+          - profile: "conda"
+            tags: subworkflows/bcl_demultiplex
+          - profile: "conda"
+            tags: subworkflows/fasta_clean_fcs
+          - profile: "conda"
+            tags: islandpath
+    env:
+      NXF_ANSI_LOG: false
+      SENTIEON_LICENSE_BASE64: ${{ secrets.SENTIEON_LICENSE_BASE64 }}
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: "3.x"
+
+      - uses: actions/cache@v3
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
+          restore-keys: |
+            ${{ runner.os }}-pip-
+
+      - name: Install Python dependencies
+        run: python -m pip install --upgrade pip pytest-workflow cryptography
+
+      - uses: actions/cache@v3
+        with:
+          path: /usr/local/bin/nextflow
+          key: ${{ runner.os }}
+          restore-keys: |
+            ${{ runner.os }}-nextflow-
+
+      - name: Install Nextflow
+        env:
+          CAPSULE_LOG: none
+        run: |
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+
+      - name: Set up Singularity
+        if: matrix.profile == 'singularity'
+        uses: eWaterCycle/setup-singularity@v5
+        with:
+          singularity-version: 3.7.1
+
+      - name: Set up miniconda
+        if: matrix.profile == 'conda'
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          auto-update-conda: true
+          channels: conda-forge,bioconda,defaults
+          python-version: ${{ matrix.python-version }}
+
+      - name: Conda setup
+        if: matrix.profile == 'conda'
+        run: |
+          conda clean -a
+          conda install -n base conda-libmamba-solver
+          conda config --set solver libmamba
+
+      # Set up secrets
+      - name: Set up nextflow secrets
+        if: env.SENTIEON_LICENSE_BASE64 != null
+        run: |
+          nextflow secrets set SENTIEON_LICENSE_BASE64 ${{ secrets.SENTIEON_LICENSE_BASE64 }}
+          nextflow secrets set SENTIEON_AUTH_MECH_BASE64 ${{ secrets.SENTIEON_AUTH_MECH_BASE64 }}
+          SENTIEON_ENCRYPTION_KEY=$(echo -n "${{ secrets.ENCRYPTION_KEY_BASE64 }}" | base64 -d)
+          SENTIEON_LICENSE_MESSAGE=$(echo -n "${{ secrets.LICENSE_MESSAGE_BASE64 }}" | base64 -d)
+          SENTIEON_AUTH_DATA=$(python tests/modules/nf-core/sentieon/license_message.py encrypt --key "$SENTIEON_ENCRYPTION_KEY" --message "$SENTIEON_LICENSE_MESSAGE")
+          SENTIEON_AUTH_DATA_BASE64=$(echo -n "$SENTIEON_AUTH_DATA" | base64 -w 0)
+          nextflow secrets set SENTIEON_AUTH_DATA_BASE64 $SENTIEON_AUTH_DATA_BASE64
+
+      # Test the module
+      - name: Run pytest-workflow
+        # only use one thread for pytest-workflow to avoid race condition on conda cache.
+        run: TMPDIR=~ PROFILE=${{ matrix.profile }} pytest --tag ${{ matrix.tags }} --symlink --kwdof --git-aware --color=yes
+
+      - name: Output log on failure
+        if: failure()
+        run: |
+          sudo apt-get update > /dev/null
+          sudo apt-get install bat > /dev/null
+          batcat --decorations=always --color=always /home/runner/pytest_workflow_*/*/log.{out,err}
+
+      - name: Setting global variables
+        uses: actions/github-script@v6
+        id: parsed
+        with:
+          script: |
+            return '${{ matrix.tags }}'.toLowerCase().replaceAll(/\//g, '-').trim('-').trim('"')
+          result-encoding: string
+
+      - name: Upload logs on failure
+        if: failure()
+        uses: actions/upload-artifact@v2
+        with:
+          name: logs-${{ matrix.profile }}-${{ steps.parsed.outputs.result }}
+          path: |
+            /home/runner/pytest_workflow_*/*/.nextflow.log
+            /home/runner/pytest_workflow_*/*/log.out
+            /home/runner/pytest_workflow_*/*/log.err
+            /home/runner/pytest_workflow_*/*/work
+            !/home/runner/pytest_workflow_*/*/work/conda
+            !/home/runner/pytest_workflow_*/*/work/singularity
+
+  nf-test-changes:
+    name: nf-test-changes
+    runs-on: ubuntu-latest
+    needs: [Prettier, EditorConfig]
+    outputs:
+      # Expose matched filters as job 'modules' output variable
+      modules: ${{ steps.filter.outputs.changes }}
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: dorny/paths-filter@v2
+        id: filter
+        with:
+          filters: "tests/config/pytest_modules.yml"
+
+  nf-test:
+    runs-on: ubuntu-20.04
+    name: nf-test
+    needs: [nf-test-changes, Prettier, EditorConfig, nf_core_lint]
+    if: needs.nf-test-changes.outputs.modules != '[]'
+    strategy:
+      fail-fast: false
+      matrix:
+        tags: ["${{ fromJson(needs.nf-test-changes.outputs.modules) }}"]
+        profile: ["docker", "singularity", "conda"]
+        exclude:
+          - tags: "nf-test"
+          - profile: "conda"
+            tags: annotsv
+          - profile: "conda"
+            tags: bases2fastq
+          - profile: "conda"
+            tags: bcl2fastq
+          - profile: "conda"
+            tags: bclconvert
+          - profile: "conda"
+            tags: cellranger/count
+          - profile: "conda"
+            tags: cellranger/mkfastq
+          - profile: "conda"
+            tags: cellranger/mkgtf
+          - profile: "conda"
+            tags: cellranger/mkref
+          - profile: "conda"
+            tags: deepvariant
+          - profile: "conda"
+            tags: ensemblvep/vep
+          - profile: "conda"
+            tags: fastk/fastk
+          - profile: "conda"
+            tags: fastk/histex
+          - profile: "conda"
+            tags: fastk/merge
+          - profile: "conda"
+            tags: fcs/fcsadaptor
+          - profile: "conda"
+            tags: fcs/fcsgx
+          - profile: "conda"
+            tags: gatk4/cnnscorevariants
+          - profile: "conda"
+            tags: gatk4/determinegermlinecontigploidy
+          - profile: "conda"
+            tags: genescopefk
+          - profile: "conda"
+            tags: ilastik/multicut
+          - profile: "conda"
+            tags: ilastik/pixelclassification
+          - profile: "conda"
+            tags: imputeme/vcftoprs
+          - profile: "conda"
+            tags: merquryfk/katcomp
+          - profile: "conda"
+            tags: merquryfk/katgc
+          - profile: "conda"
+            tags: merquryfk/merquryfk
+          - profile: "conda"
+            tags: merquryfk/ploidyplot
+          - profile: "conda"
+            tags: sentieon/bwaindex
+          - profile: "conda"
+            tags: sentieon/bwamem
+          - profile: "conda"
+            tags: universc
+          - profile: "singularity"
+            tags: universc
+          - profile: "conda"
+            tags: subworkflows/vcf_annotate_ensemblvep
+    env:
+      NXF_ANSI_LOG: false
+      SENTIEON_LICENSE_BASE64: ${{ secrets.SENTIEON_LICENSE_BASE64 }}
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: actions/cache@v3
+        with:
+          path: /usr/local/bin/nextflow
+          key: ${{ runner.os }}
+          restore-keys: |
+            ${{ runner.os }}-nextflow-
+
+      - name: Install Nextflow
+        env:
+          CAPSULE_LOG: none
+        run: |
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+
+      - name: Cache nf-test installation
+        id: cache-software
+        uses: actions/cache@v3
+        with:
+          path: |
+            /usr/local/bin/nf-test
+            /home/runner/.nf-test/nf-test.jar
+          key: ${{ runner.os }}-nftest
+
+      - name: Install nf-test
+        if: steps.cache-software.outputs.cache-hit != 'true'
+        run: |
+          wget -qO- https://code.askimed.com/install/nf-test | bash
+          sudo mv nf-test /usr/local/bin/
+
+      - name: Set up Singularity
+        if: matrix.profile == 'singularity'
+        uses: eWaterCycle/setup-singularity@v5
+        with:
+          singularity-version: 3.7.1
+
+      - name: Set up miniconda
+        if: matrix.profile == 'conda'
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          auto-update-conda: true
+          channels: conda-forge,bioconda,defaults
+          python-version: ${{ matrix.python-version }}
+
+      - name: Conda setup
+        if: matrix.profile == 'conda'
+        run: |
+          conda clean -a
+          conda install -n base conda-libmamba-solver
+          conda config --set solver libmamba
+
+      # Set up secrets
+      - name: Set up nextflow secrets
+        if: env.SENTIEON_LICENSE_BASE64 != null
+        run: |
+          nextflow secrets set SENTIEON_LICENSE_BASE64 ${{ secrets.SENTIEON_LICENSE_BASE64 }}
+          nextflow secrets set SENTIEON_AUTH_MECH_BASE64 ${{ secrets.SENTIEON_AUTH_MECH_BASE64 }}
+          SENTIEON_ENCRYPTION_KEY=$(echo -n "${{ secrets.ENCRYPTION_KEY_BASE64 }}" | base64 -d)
+          SENTIEON_LICENSE_MESSAGE=$(echo -n "${{ secrets.LICENSE_MESSAGE_BASE64 }}" | base64 -d)
+          SENTIEON_AUTH_DATA=$(python tests/modules/nf-core/sentieon/license_message.py encrypt --key "$SENTIEON_ENCRYPTION_KEY" --message "$SENTIEON_LICENSE_MESSAGE")
+          SENTIEON_AUTH_DATA_BASE64=$(echo -n "$SENTIEON_AUTH_DATA" | base64 -w 0)
+          nextflow secrets set SENTIEON_AUTH_DATA_BASE64 $SENTIEON_AUTH_DATA_BASE64
+
+      # Test the module
+      - name: Run nf-test
+        run: |
+          nf-test test \
+            --profile=${{ matrix.profile }} \
+            --tag ${{ matrix.tags }} \
+            --tap=test.tap
+
+      - uses: pcolby/tap-summary@v1
+        with:
+          path: >-
+            test.tap
diff --git a/modules/nf-core/gatk4/haplotypecaller/main.nf b/modules/nf-core/gatk4/haplotypecaller/main.nf
index 382d6cca9e5..33bd7de40d5 100644
--- a/modules/nf-core/gatk4/haplotypecaller/main.nf
+++ b/modules/nf-core/gatk4/haplotypecaller/main.nf
@@ -5,7 +5,7 @@ process GATK4_HAPLOTYPECALLER {
     conda "bioconda::gatk4=4.4.0.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0':
-        'quay.io/biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }"
+        'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }"
 
     input:
     tuple val(meta), path(input), path(input_index), path(intervals), path(dragstr_model)
@@ -50,6 +50,8 @@ process GATK4_HAPLOTYPECALLER {
         --tmp-dir . \\
         $args
 
+    # Fake stuff
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
diff --git a/modules/nf-core/samtools/index/main.nf b/modules/nf-core/samtools/index/main.nf
index 0b20aa4bb8a..b2d04be9d8c 100644
--- a/modules/nf-core/samtools/index/main.nf
+++ b/modules/nf-core/samtools/index/main.nf
@@ -28,6 +28,8 @@ process SAMTOOLS_INDEX {
         $args \\
         $input
 
+    # Fake stuff
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
diff --git a/modules/nf-core/samtools/sort/main.nf b/modules/nf-core/samtools/sort/main.nf
index ef281c4856d..2b7753fd863 100644
--- a/modules/nf-core/samtools/sort/main.nf
+++ b/modules/nf-core/samtools/sort/main.nf
@@ -5,7 +5,7 @@ process SAMTOOLS_SORT {
     conda "bioconda::samtools=1.17"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' :
-        'quay.io/biocontainers/samtools:1.17--h00cdaf9_0' }"
+        'biocontainers/samtools:1.17--h00cdaf9_0' }"
 
     input:
     tuple val(meta), path(bam)
diff --git a/tests/modules/nf-core/fastqc/main.nf.test b/tests/modules/nf-core/fastqc/main.nf.test
index 3961de60662..41ba9182bec 100644
--- a/tests/modules/nf-core/fastqc/main.nf.test
+++ b/tests/modules/nf-core/fastqc/main.nf.test
@@ -5,6 +5,8 @@ nextflow_process {
     process "FASTQC"
     tag "fastqc"
 
+    // Fake stuff
+
     test("Single-Read") {
 
         when {

From 0b05e07aec55d76b07e87986de5c046de826760a Mon Sep 17 00:00:00 2001
From: Adam Talbot <adam.talbot@seqera.io>
Date: Fri, 28 Jul 2023 13:04:55 +0100
Subject: [PATCH 07/32] Fix dependencies in GHA

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

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index acec4ed352d..1e3fd796f26 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -116,7 +116,7 @@ jobs:
   pytest:
     runs-on: ubuntu-20.04
     name: pytest
-    needs: [changes, Prettier, EditorConfig, nf_core_lint]
+    needs: [pytest-changes, Prettier, EditorConfig, nf-core-lint]
     if: needs.changes.outputs.modules != '[]'
     strategy:
       fail-fast: false

From a651f01f1ae0d6d6087073e0b91a3077a0cb0de7 Mon Sep 17 00:00:00 2001
From: Adam Talbot <adam.talbot@seqera.io>
Date: Fri, 28 Jul 2023 13:06:33 +0100
Subject: [PATCH 08/32] Remove files again

---
 .github/workflows/code-linting.yml |  43 -------
 .github/workflows/nf-test.yml      | 182 -----------------------------
 2 files changed, 225 deletions(-)
 delete mode 100644 .github/workflows/code-linting.yml
 delete mode 100644 .github/workflows/nf-test.yml

diff --git a/.github/workflows/code-linting.yml b/.github/workflows/code-linting.yml
deleted file mode 100644
index 831453f8ea2..00000000000
--- a/.github/workflows/code-linting.yml
+++ /dev/null
@@ -1,43 +0,0 @@
-name: code-lint
-on:
-  push:
-    branches: [master]
-  pull_request:
-    branches: [master]
-  merge_group:
-    types: [checks_requested]
-    branches: [master]
-
-# Cancel if a newer run is started
-concurrency:
-  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
-  cancel-in-progress: true
-
-jobs:
-  Prettier:
-    runs-on: ubuntu-latest
-    steps:
-      - name: Check out repository
-        uses: actions/checkout@v3
-
-      - name: Install NodeJS
-        uses: actions/setup-node@v2
-
-      - name: Install Prettier
-        run: npm install -g prettier
-
-      - name: Run Prettier --check
-        run: prettier --check .
-
-  EditorConfig:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v3
-
-      - uses: actions/setup-node@v2
-
-      - name: Install editorconfig-checker
-        run: npm install -g editorconfig-checker
-
-      - name: Run ECLint check
-        run: editorconfig-checker -exclude README.md $(git ls-files | grep -v test)
diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml
deleted file mode 100644
index 57df4fef4c2..00000000000
--- a/.github/workflows/nf-test.yml
+++ /dev/null
@@ -1,182 +0,0 @@
-name: nf-test
-run-name: nf-test
-on:
-  push:
-    branches: [master]
-  pull_request:
-    branches: [master]
-  merge_group:
-    types: [checks_requested]
-    branches: [master]
-
-# Cancel if a newer run is started
-concurrency:
-  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
-  cancel-in-progress: true
-
-jobs:
-  changes:
-    name: check-changes
-    runs-on: ubuntu-latest
-    outputs:
-      # Expose matched filters as job 'modules' output variable
-      modules: ${{ steps.filter.outputs.changes }}
-    steps:
-      - uses: actions/checkout@v3
-
-      - uses: dorny/paths-filter@v2
-        id: filter
-        with:
-          filters: "tests/config/nftest_modules.yml"
-
-  nf-test:
-    runs-on: ubuntu-20.04
-    name: nf-test
-    needs: changes
-    if: needs.changes.outputs.modules != '[]'
-    strategy:
-      fail-fast: false
-      matrix:
-        tags: ["${{ fromJson(needs.changes.outputs.modules) }}"]
-        profile: ["docker", "singularity", "conda"]
-        exclude:
-          - profile: "conda"
-            tags: annotsv
-          - profile: "conda"
-            tags: bases2fastq
-          - profile: "conda"
-            tags: bcl2fastq
-          - profile: "conda"
-            tags: bclconvert
-          - profile: "conda"
-            tags: cellranger/count
-          - profile: "conda"
-            tags: cellranger/mkfastq
-          - profile: "conda"
-            tags: cellranger/mkgtf
-          - profile: "conda"
-            tags: cellranger/mkref
-          - profile: "conda"
-            tags: deepvariant
-          - profile: "conda"
-            tags: ensemblvep/vep
-          - profile: "conda"
-            tags: fastk/fastk
-          - profile: "conda"
-            tags: fastk/histex
-          - profile: "conda"
-            tags: fastk/merge
-          - profile: "conda"
-            tags: fcs/fcsadaptor
-          - profile: "conda"
-            tags: fcs/fcsgx
-          - profile: "conda"
-            tags: gatk4/cnnscorevariants
-          - profile: "conda"
-            tags: gatk4/determinegermlinecontigploidy
-          - profile: "conda"
-            tags: genescopefk
-          - profile: "conda"
-            tags: ilastik/multicut
-          - profile: "conda"
-            tags: ilastik/pixelclassification
-          - profile: "conda"
-            tags: imputeme/vcftoprs
-          - profile: "conda"
-            tags: merquryfk/katcomp
-          - profile: "conda"
-            tags: merquryfk/katgc
-          - profile: "conda"
-            tags: merquryfk/merquryfk
-          - profile: "conda"
-            tags: merquryfk/ploidyplot
-          - profile: "conda"
-            tags: sentieon/bwaindex
-          - profile: "conda"
-            tags: sentieon/bwamem
-          - profile: "conda"
-            tags: universc
-          - profile: "singularity"
-            tags: universc
-          - profile: "conda"
-            tags: subworkflows/vcf_annotate_ensemblvep
-    env:
-      NXF_ANSI_LOG: false
-      SENTIEON_LICENSE_BASE64: ${{ secrets.SENTIEON_LICENSE_BASE64 }}
-    steps:
-      - uses: actions/checkout@v3
-
-      - uses: actions/cache@v3
-        with:
-          path: /usr/local/bin/nextflow
-          key: ${{ runner.os }}
-          restore-keys: |
-            ${{ runner.os }}-nextflow-
-
-      - name: Install Nextflow
-        env:
-          CAPSULE_LOG: none
-        run: |
-          wget -qO- get.nextflow.io | bash
-          sudo mv nextflow /usr/local/bin/
-
-      - name: Cache nf-test installation
-        id: cache-software
-        uses: actions/cache@v3
-        with:
-          path: |
-            /usr/local/bin/nf-test
-            /home/runner/.nf-test/nf-test.jar
-          key: ${{ runner.os }}-nftest
-
-      - name: Install nf-test
-        if: steps.cache-software.outputs.cache-hit != 'true'
-        run: |
-          wget -qO- https://code.askimed.com/install/nf-test | bash
-          sudo mv nf-test /usr/local/bin/
-
-      - name: Set up Singularity
-        if: matrix.profile == 'singularity'
-        uses: eWaterCycle/setup-singularity@v5
-        with:
-          singularity-version: 3.7.1
-
-      - name: Set up miniconda
-        if: matrix.profile == 'conda'
-        uses: conda-incubator/setup-miniconda@v2
-        with:
-          auto-update-conda: true
-          channels: conda-forge,bioconda,defaults
-          python-version: ${{ matrix.python-version }}
-
-      - name: Conda setup
-        if: matrix.profile == 'conda'
-        run: |
-          conda clean -a
-          conda install -n base conda-libmamba-solver
-          conda config --set solver libmamba
-
-      # Set up secrets
-      - name: Set up nextflow secrets
-        if: env.SENTIEON_LICENSE_BASE64 != null
-        run: |
-          nextflow secrets set SENTIEON_LICENSE_BASE64 ${{ secrets.SENTIEON_LICENSE_BASE64 }}
-          nextflow secrets set SENTIEON_AUTH_MECH_BASE64 ${{ secrets.SENTIEON_AUTH_MECH_BASE64 }}
-          SENTIEON_ENCRYPTION_KEY=$(echo -n "${{ secrets.ENCRYPTION_KEY_BASE64 }}" | base64 -d)
-          SENTIEON_LICENSE_MESSAGE=$(echo -n "${{ secrets.LICENSE_MESSAGE_BASE64 }}" | base64 -d)
-          SENTIEON_AUTH_DATA=$(python tests/modules/nf-core/sentieon/license_message.py encrypt --key "$SENTIEON_ENCRYPTION_KEY" --message "$SENTIEON_LICENSE_MESSAGE")
-          SENTIEON_AUTH_DATA_BASE64=$(echo -n "$SENTIEON_AUTH_DATA" | base64 -w 0)
-          nextflow secrets set SENTIEON_AUTH_DATA_BASE64 $SENTIEON_AUTH_DATA_BASE64
-
-      # Test the module
-      - name: Run nf-test
-        run: |
-          nf-test test \
-            --profile=${{ matrix.profile }} \
-            --tag ${{ matrix.tags }} \
-            --tap=test.tap
-
-      - uses: pcolby/tap-summary@v1
-        with:
-          path: >-
-            test.tap

From b454fb9c7de1430ada65c01eb086836b884b0897 Mon Sep 17 00:00:00 2001
From: Adam Talbot <adam.talbot@seqera.io>
Date: Fri, 28 Jul 2023 13:08:56 +0100
Subject: [PATCH 09/32] More dependency fixes

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

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 1e3fd796f26..780324d797b 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -354,7 +354,7 @@ jobs:
   nf-test:
     runs-on: ubuntu-20.04
     name: nf-test
-    needs: [nf-test-changes, Prettier, EditorConfig, nf_core_lint]
+    needs: [nf-test-changes, Prettier, EditorConfig, nf-core-lint]
     if: needs.nf-test-changes.outputs.modules != '[]'
     strategy:
       fail-fast: false

From a10564d36e15b952acf3f5879daba4c2c79eebb0 Mon Sep 17 00:00:00 2001
From: Adam Talbot <adam.talbot@seqera.io>
Date: Fri, 28 Jul 2023 13:14:20 +0100
Subject: [PATCH 10/32] Correct nf-test filtering yaml

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

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 780324d797b..ce12a35cfa9 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -349,7 +349,7 @@ jobs:
       - uses: dorny/paths-filter@v2
         id: filter
         with:
-          filters: "tests/config/pytest_modules.yml"
+          filters: "tests/config/nftest_modules.yml"
 
   nf-test:
     runs-on: ubuntu-20.04

From 49fb85d5bb5499071dfbb168ceb8a2f84ce0a87e Mon Sep 17 00:00:00 2001
From: Adam Talbot <adam.talbot@seqera.io>
Date: Fri, 28 Jul 2023 13:25:17 +0100
Subject: [PATCH 11/32] Change to fix-linting for consistency

---
 .github/workflows/fix-linting.yml | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml
index 7c2c01cd15b..8558ceef715 100644
--- a/.github/workflows/fix-linting.yml
+++ b/.github/workflows/fix-linting.yml
@@ -5,11 +5,7 @@ on:
     types: [created]
 
 jobs:
-<<<<<<< HEAD
   fix-linting:
-=======
-  fix_linting:
->>>>>>> 568afbcc2 (Rename and tidy all GHA workflows for branch protection)
     # Only run if comment is on a PR with the main repo, and if it contains the magic keywords
     if: >
       contains(github.event.comment.html_url, '/pull/') &&

From 571e68512f9efe8929ec6e43b1dbd34fed288fea Mon Sep 17 00:00:00 2001
From: Adam Talbot <adam.talbot@seqera.io>
Date: Fri, 28 Jul 2023 14:32:16 +0100
Subject: [PATCH 12/32] Bump setup-python version to v4

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

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index ce12a35cfa9..b8ab46d8828 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -72,7 +72,7 @@ jobs:
       - uses: actions/checkout@v3
 
       - name: Set up Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: "3.x"
 
@@ -84,7 +84,7 @@ jobs:
             ${{ runner.os }}-pip-
 
       - name: Set up Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: "3.x"
 
@@ -242,7 +242,7 @@ jobs:
       - uses: actions/checkout@v3
 
       - name: Set up Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: "3.x"
 

From 79a73a6c58cc7126432aff18b03b1c843bdfa703 Mon Sep 17 00:00:00 2001
From: Adam Talbot <adam.talbot@seqera.io>
Date: Fri, 28 Jul 2023 16:16:43 +0100
Subject: [PATCH 13/32] bump eWaterCycle/setup-singularity to v7

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

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index b8ab46d8828..14d9ecfc37b 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -272,7 +272,7 @@ jobs:
 
       - name: Set up Singularity
         if: matrix.profile == 'singularity'
-        uses: eWaterCycle/setup-singularity@v5
+        uses: eWaterCycle/setup-singularity@v7
         with:
           singularity-version: 3.7.1
 
@@ -461,7 +461,7 @@ jobs:
 
       - name: Set up Singularity
         if: matrix.profile == 'singularity'
-        uses: eWaterCycle/setup-singularity@v5
+        uses: eWaterCycle/setup-singularity@v7
         with:
           singularity-version: 3.7.1
 

From 3a8b0a0897fc7f119b6e075b6d964059abc48a20 Mon Sep 17 00:00:00 2001
From: Adam Talbot <adam.talbot@seqera.io>
Date: Mon, 31 Jul 2023 12:45:45 +0100
Subject: [PATCH 14/32] Add final job to test for pass status of all previous
 jobs

---
 .github/workflows/test.yml | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 14d9ecfc37b..6141e1716b2 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -504,3 +504,15 @@ jobs:
         with:
           path: >-
             test.tap
+
+  confirm-pass:
+    runs-on: ubuntu-latest
+    needs: [Prettier, EditorConfig, nf-core-lint, pytest, nf-test]
+    if: always()
+    steps:
+      - name: All tests ok
+        if: ${{ !(contains(needs.*.result, 'failure')) }}
+        run: exit 0
+      - name: One or more tests failed
+        if: ${{ contains(needs.*.result, 'failure') }}
+        run: exit 1

From 07e940cb63d36a59399419ac82e271c0ce681498 Mon Sep 17 00:00:00 2001
From: Adam Talbot <adam.talbot@seqera.io>
Date: Mon, 31 Jul 2023 12:51:26 +0100
Subject: [PATCH 15/32] Add checking for changes to test requirement

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

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 6141e1716b2..33086e0feda 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -507,7 +507,7 @@ jobs:
 
   confirm-pass:
     runs-on: ubuntu-latest
-    needs: [Prettier, EditorConfig, nf-core-lint, pytest, nf-test]
+    needs: [Prettier, EditorConfig, pytest-changes, nf-core-lint, pytest, nf-test-changes, nf-test]
     if: always()
     steps:
       - name: All tests ok

From f4909746f9edd411b4f271e16daf54476e4f5dc6 Mon Sep 17 00:00:00 2001
From: Adam Talbot <adam.talbot@seqera.io>
Date: Mon, 31 Jul 2023 14:17:16 +0100
Subject: [PATCH 16/32] Revert module changes

---
 modules/nf-core/gatk4/haplotypecaller/main.nf | 2 --
 modules/nf-core/samtools/index/main.nf        | 2 --
 tests/modules/nf-core/fastqc/main.nf.test     | 2 --
 3 files changed, 6 deletions(-)

diff --git a/modules/nf-core/gatk4/haplotypecaller/main.nf b/modules/nf-core/gatk4/haplotypecaller/main.nf
index 33bd7de40d5..478681bd18a 100644
--- a/modules/nf-core/gatk4/haplotypecaller/main.nf
+++ b/modules/nf-core/gatk4/haplotypecaller/main.nf
@@ -50,8 +50,6 @@ process GATK4_HAPLOTYPECALLER {
         --tmp-dir . \\
         $args
 
-    # Fake stuff
-
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
diff --git a/modules/nf-core/samtools/index/main.nf b/modules/nf-core/samtools/index/main.nf
index b2d04be9d8c..0b20aa4bb8a 100644
--- a/modules/nf-core/samtools/index/main.nf
+++ b/modules/nf-core/samtools/index/main.nf
@@ -28,8 +28,6 @@ process SAMTOOLS_INDEX {
         $args \\
         $input
 
-    # Fake stuff
-
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
diff --git a/tests/modules/nf-core/fastqc/main.nf.test b/tests/modules/nf-core/fastqc/main.nf.test
index 41ba9182bec..3961de60662 100644
--- a/tests/modules/nf-core/fastqc/main.nf.test
+++ b/tests/modules/nf-core/fastqc/main.nf.test
@@ -5,8 +5,6 @@ nextflow_process {
     process "FASTQC"
     tag "fastqc"
 
-    // Fake stuff
-
     test("Single-Read") {
 
         when {

From f050865cd6260c2e6278bdeaef2cb62f14a91a7e Mon Sep 17 00:00:00 2001
From: Adam Talbot <adam.talbot@seqera.io>
Date: Mon, 31 Jul 2023 14:17:40 +0100
Subject: [PATCH 17/32] Add fake change to FASTQC

---
 modules/nf-core/fastqc/main.nf | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf
index 249f90644d2..f7f4b8f7d63 100644
--- a/modules/nf-core/fastqc/main.nf
+++ b/modules/nf-core/fastqc/main.nf
@@ -35,6 +35,8 @@ process FASTQC {
         --threads $task.cpus \\
         $renamed_files
 
+    # Fake stuff
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" )

From 27385dfaf0c90d94f9d0c75f58398e5ae3f2daed Mon Sep 17 00:00:00 2001
From: Adam Talbot <adam.talbot@seqera.io>
Date: Mon, 31 Jul 2023 14:45:37 +0100
Subject: [PATCH 18/32] Test in parallel

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

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 33086e0feda..12709690b3b 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -45,7 +45,6 @@ jobs:
   pytest-changes:
     name: pytest-changes
     runs-on: ubuntu-latest
-    needs: [Prettier, EditorConfig]
     outputs:
       # Expose matched filters as job 'modules' output variable
       modules: ${{ steps.filter.outputs.changes }}
@@ -60,7 +59,7 @@ jobs:
   nf-core-lint:
     runs-on: ubuntu-20.04
     name: nf-core-lint
-    needs: pytest-changes
+    needs: [pytest-changes]
     if: needs.pytest-changes.outputs.modules != '[]'
     strategy:
       fail-fast: false
@@ -116,7 +115,7 @@ jobs:
   pytest:
     runs-on: ubuntu-20.04
     name: pytest
-    needs: [pytest-changes, Prettier, EditorConfig, nf-core-lint]
+    needs: [pytest-changes]
     if: needs.changes.outputs.modules != '[]'
     strategy:
       fail-fast: false
@@ -339,7 +338,6 @@ jobs:
   nf-test-changes:
     name: nf-test-changes
     runs-on: ubuntu-latest
-    needs: [Prettier, EditorConfig]
     outputs:
       # Expose matched filters as job 'modules' output variable
       modules: ${{ steps.filter.outputs.changes }}
@@ -354,7 +352,7 @@ jobs:
   nf-test:
     runs-on: ubuntu-20.04
     name: nf-test
-    needs: [nf-test-changes, Prettier, EditorConfig, nf-core-lint]
+    needs: [nf-test-changes]
     if: needs.nf-test-changes.outputs.modules != '[]'
     strategy:
       fail-fast: false

From d3c9b76084722818b40e637ae424d0fbc46a50f8 Mon Sep 17 00:00:00 2001
From: Adam Talbot <adam.talbot@seqera.io>
Date: Mon, 31 Jul 2023 17:27:29 +0100
Subject: [PATCH 19/32] Revert "Add fake change to FASTQC"

This reverts commit f050865cd6260c2e6278bdeaef2cb62f14a91a7e.
---
 modules/nf-core/fastqc/main.nf | 2 --
 1 file changed, 2 deletions(-)

diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf
index f7f4b8f7d63..249f90644d2 100644
--- a/modules/nf-core/fastqc/main.nf
+++ b/modules/nf-core/fastqc/main.nf
@@ -35,8 +35,6 @@ process FASTQC {
         --threads $task.cpus \\
         $renamed_files
 
-    # Fake stuff
-
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" )

From 269c63f509afb022ec716136689156dc2daec7c4 Mon Sep 17 00:00:00 2001
From: Adam Talbot <adam.talbot@seqera.io>
Date: Mon, 31 Jul 2023 17:40:01 +0100
Subject: [PATCH 20/32] Change logic to allow skipped processes

---
 .github/workflows/test.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 12709690b3b..4e294322cff 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -509,7 +509,8 @@ jobs:
     if: always()
     steps:
       - name: All tests ok
-        if: ${{ !(contains(needs.*.result, 'failure')) }}
+        if: |
+          always() && ${{ !contains(needs.*.result, 'failure') }}
         run: exit 0
       - name: One or more tests failed
         if: ${{ contains(needs.*.result, 'failure') }}

From da0a03d50e5a34ff02fabd3921a800843c72d709 Mon Sep 17 00:00:00 2001
From: Adam Talbot <adam.talbot@seqera.io>
Date: Mon, 31 Jul 2023 17:44:20 +0100
Subject: [PATCH 21/32] Format changes

---
 .github/workflows/test.yml | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 4e294322cff..fd44137525d 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -509,9 +509,8 @@ jobs:
     if: always()
     steps:
       - name: All tests ok
-        if: |
-          always() && ${{ !contains(needs.*.result, 'failure') }}
+        if: always() && !contains(needs.*.result, 'failure')
         run: exit 0
       - name: One or more tests failed
-        if: ${{ contains(needs.*.result, 'failure') }}
+        if: contains(needs.*.result, 'failure')
         run: exit 1

From 83fec8c3864265c4f6aa50b7258c78393b767358 Mon Sep 17 00:00:00 2001
From: Adam Talbot <adam.talbot@seqera.io>
Date: Mon, 31 Jul 2023 17:49:38 +0100
Subject: [PATCH 22/32] Change logic again

---
 .github/workflows/test.yml | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index fd44137525d..ec3e53b10f3 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -509,8 +509,11 @@ jobs:
     if: always()
     steps:
       - name: All tests ok
-        if: always() && !contains(needs.*.result, 'failure')
+        if: |
+          always() &&
+          !contains(needs.*.result, 'failure') &&
+          !contains(needs.*.result, 'cancelled')
         run: exit 0
       - name: One or more tests failed
-        if: contains(needs.*.result, 'failure')
+        if: ${{ contains(needs.*.result, 'failure') }}
         run: exit 1

From 4b2c0f7cbc160f661e8800985a79645cf7a25857 Mon Sep 17 00:00:00 2001
From: Adam Talbot <adam.talbot@seqera.io>
Date: Mon, 31 Jul 2023 17:52:14 +0100
Subject: [PATCH 23/32] Change logic again

---
 .github/workflows/test.yml | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index ec3e53b10f3..df0815fd0e4 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -509,10 +509,7 @@ jobs:
     if: always()
     steps:
       - name: All tests ok
-        if: |
-          always() &&
-          !contains(needs.*.result, 'failure') &&
-          !contains(needs.*.result, 'cancelled')
+        if: ${{ success() || failure() || ( always() && ! cancelled() ) }}
         run: exit 0
       - name: One or more tests failed
         if: ${{ contains(needs.*.result, 'failure') }}

From 01ef2f4a21d8706ddc9c3f08f5e1bd7c9c41c8cb Mon Sep 17 00:00:00 2001
From: Adam Talbot <adam.talbot@seqera.io>
Date: Mon, 31 Jul 2023 17:58:48 +0100
Subject: [PATCH 24/32] Change logic again

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

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index df0815fd0e4..628dcde25e3 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -512,5 +512,5 @@ jobs:
         if: ${{ success() || failure() || ( always() && ! cancelled() ) }}
         run: exit 0
       - name: One or more tests failed
-        if: ${{ contains(needs.*.result, 'failure') }}
+        if: contains(needs.*.result, 'failure')
         run: exit 1

From 62d170236c898f3b29307dc829b914c0631cb92b Mon Sep 17 00:00:00 2001
From: Adam Talbot <adam.talbot@seqera.io>
Date: Mon, 31 Jul 2023 18:02:38 +0100
Subject: [PATCH 25/32] Add debug step to help work it out

---
 .github/workflows/test.yml | 13 +++++++++++--
 1 file changed, 11 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 628dcde25e3..be3805f6976 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -509,8 +509,17 @@ jobs:
     if: always()
     steps:
       - name: All tests ok
-        if: ${{ success() || failure() || ( always() && ! cancelled() ) }}
+        if: ${{ success() || !contains(needs.*.result, 'failure') }}
         run: exit 0
       - name: One or more tests failed
-        if: contains(needs.*.result, 'failure')
+        if: ${{ contains(needs.*.result, 'failure') }}
         run: exit 1
+
+      - name: debug-print
+        if: always()
+        run: |
+          echo "toJSON(needs) = ${{ toJSON(needs) }}"
+          echo "toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}"
+          echo "!contains(needs.*.result, 'skipped') = ${{ !contains(needs.*.result, 'skipped') }}"
+          echo "!contains(needs.*.result, 'failure') = ${{ !contains(needs.*.result, 'failure') }}"
+          echo "!contains(needs.*.result, 'success') = ${{ !contains(needs.*.result, 'sucess') }}"

From b2003b0a5f325c440013cd22f6a99c8f93b5f21b Mon Sep 17 00:00:00 2001
From: Adam Talbot <adam.talbot@seqera.io>
Date: Mon, 31 Jul 2023 18:07:37 +0100
Subject: [PATCH 26/32] Caught pytest-changes bug

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

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index be3805f6976..85092e7f455 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -116,7 +116,7 @@ jobs:
     runs-on: ubuntu-20.04
     name: pytest
     needs: [pytest-changes]
-    if: needs.changes.outputs.modules != '[]'
+    if: needs.pytest-changes.outputs.modules != '[]'
     strategy:
       fail-fast: false
       matrix:
@@ -521,5 +521,5 @@ jobs:
           echo "toJSON(needs) = ${{ toJSON(needs) }}"
           echo "toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}"
           echo "!contains(needs.*.result, 'skipped') = ${{ !contains(needs.*.result, 'skipped') }}"
-          echo "!contains(needs.*.result, 'failure') = ${{ !contains(needs.*.result, 'failure') }}"
-          echo "!contains(needs.*.result, 'success') = ${{ !contains(needs.*.result, 'sucess') }}"
+          echo "contains(needs.*.result, 'failure') = ${{ contains(needs.*.result, 'failure') }}"
+          echo "!contains(needs.*.result, 'success') = ${{ !contains(needs.*.result, 'success') }}"

From 197ffeb0efdba72ab6c14c6d05dba583874790dd Mon Sep 17 00:00:00 2001
From: Adam Talbot <adam.talbot@seqera.io>
Date: Mon, 31 Jul 2023 18:09:25 +0100
Subject: [PATCH 27/32] Reintroduce change to FASTQC module

---
 modules/nf-core/fastqc/main.nf | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf
index 249f90644d2..95e3fbdff86 100644
--- a/modules/nf-core/fastqc/main.nf
+++ b/modules/nf-core/fastqc/main.nf
@@ -35,6 +35,8 @@ process FASTQC {
         --threads $task.cpus \\
         $renamed_files
 
+    # Dummy change
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" )

From d75f94b137f826cf3af573152c53f9aab73d9927 Mon Sep 17 00:00:00 2001
From: Adam Talbot <adam.talbot@seqera.io>
Date: Mon, 31 Jul 2023 18:32:42 +0100
Subject: [PATCH 28/32] Remove debug statements

---
 .github/workflows/test.yml | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 85092e7f455..12a4549ff31 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -520,6 +520,3 @@ jobs:
         run: |
           echo "toJSON(needs) = ${{ toJSON(needs) }}"
           echo "toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}"
-          echo "!contains(needs.*.result, 'skipped') = ${{ !contains(needs.*.result, 'skipped') }}"
-          echo "contains(needs.*.result, 'failure') = ${{ contains(needs.*.result, 'failure') }}"
-          echo "!contains(needs.*.result, 'success') = ${{ !contains(needs.*.result, 'success') }}"

From a153d5303e8d53bb3298c181d0ab459471cacb52 Mon Sep 17 00:00:00 2001
From: Adam Talbot <adam.talbot@seqera.io>
Date: Mon, 31 Jul 2023 18:33:03 +0100
Subject: [PATCH 29/32] Revert "Reintroduce change to FASTQC module"

This reverts commit 197ffeb0efdba72ab6c14c6d05dba583874790dd.
---
 modules/nf-core/fastqc/main.nf | 2 --
 1 file changed, 2 deletions(-)

diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf
index 95e3fbdff86..249f90644d2 100644
--- a/modules/nf-core/fastqc/main.nf
+++ b/modules/nf-core/fastqc/main.nf
@@ -35,8 +35,6 @@ process FASTQC {
         --threads $task.cpus \\
         $renamed_files
 
-    # Dummy change
-
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" )

From c28fef48f041da12116d008463394c97080c2568 Mon Sep 17 00:00:00 2001
From: Adam Talbot <adam.talbot@seqera.io>
Date: Mon, 31 Jul 2023 18:34:59 +0100
Subject: [PATCH 30/32] Mess up FASTQC deliberately to test failures

---
 modules/nf-core/fastqc/main.nf | 13 -------------
 1 file changed, 13 deletions(-)

diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf
index 249f90644d2..e9d5bd5535f 100644
--- a/modules/nf-core/fastqc/main.nf
+++ b/modules/nf-core/fastqc/main.nf
@@ -26,19 +26,6 @@ process FASTQC {
     def rename_to = old_new_pairs*.join(' ').join(' ')
     def renamed_files = old_new_pairs.collect{ old_name, new_name -> new_name }.join(' ')
     """
-    printf "%s %s\\n" $rename_to | while read old_name new_name; do
-        [ -f "\${new_name}" ] || ln -s \$old_name \$new_name
-    done
-
-    fastqc \\
-        $args \\
-        --threads $task.cpus \\
-        $renamed_files
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" )
-    END_VERSIONS
     """
 
     stub:

From 4f7c9ac0368ad680859cde3ee122208a21918a6f Mon Sep 17 00:00:00 2001
From: Adam Talbot <adam.talbot@seqera.io>
Date: Mon, 31 Jul 2023 18:50:42 +0100
Subject: [PATCH 31/32] Revert "Mess up FASTQC deliberately to test failures"

This reverts commit c28fef48f041da12116d008463394c97080c2568.
---
 modules/nf-core/fastqc/main.nf | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf
index e9d5bd5535f..249f90644d2 100644
--- a/modules/nf-core/fastqc/main.nf
+++ b/modules/nf-core/fastqc/main.nf
@@ -26,6 +26,19 @@ process FASTQC {
     def rename_to = old_new_pairs*.join(' ').join(' ')
     def renamed_files = old_new_pairs.collect{ old_name, new_name -> new_name }.join(' ')
     """
+    printf "%s %s\\n" $rename_to | while read old_name new_name; do
+        [ -f "\${new_name}" ] || ln -s \$old_name \$new_name
+    done
+
+    fastqc \\
+        $args \\
+        --threads $task.cpus \\
+        $renamed_files
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" )
+    END_VERSIONS
     """
 
     stub:

From 60ca551d16920c03d8649104cadc7a7ce595bb49 Mon Sep 17 00:00:00 2001
From: Adam Talbot <adam.talbot@seqera.io>
Date: Wed, 2 Aug 2023 10:03:46 +0100
Subject: [PATCH 32/32] Changed to all lower case

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

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 12a4549ff31..f992ded1f68 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -14,7 +14,7 @@ concurrency:
   cancel-in-progress: true
 
 jobs:
-  Prettier:
+  prettier:
     runs-on: ubuntu-latest
     steps:
       - name: Check out repository
@@ -29,7 +29,7 @@ jobs:
       - name: Run Prettier --check
         run: prettier --check .
 
-  EditorConfig:
+  editorconfig:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3
@@ -505,7 +505,7 @@ jobs:
 
   confirm-pass:
     runs-on: ubuntu-latest
-    needs: [Prettier, EditorConfig, pytest-changes, nf-core-lint, pytest, nf-test-changes, nf-test]
+    needs: [prettier, editorconfig, pytest-changes, nf-core-lint, pytest, nf-test-changes, nf-test]
     if: always()
     steps:
       - name: All tests ok