From dbad13e6bd9c561d63438ba013558e2f50818371 Mon Sep 17 00:00:00 2001
From: Edmund Miller <git@edmundmiller.dev>
Date: Tue, 18 Jun 2024 14:46:45 -0500
Subject: [PATCH 01/17] ci(#2193): Add condalock file generation

https://github.com/seqeralabs/wave-cli?tab=readme-ov-file#build-a-container-by-using-a-conda-lock-file
---
 .github/workflows/wave.yml | 73 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 73 insertions(+)
 create mode 100644 .github/workflows/wave.yml

diff --git a/.github/workflows/wave.yml b/.github/workflows/wave.yml
new file mode 100644
index 00000000000..d0142d38d7e
--- /dev/null
+++ b/.github/workflows/wave.yml
@@ -0,0 +1,73 @@
+# TODO Change to Wave
+name: Generate conda-lock
+# When environment.yml is changed
+on:
+  pull_request:
+    paths:
+      - "**/environment.yml"
+
+env:
+  WAVE_VER: "1.4.1"
+
+jobs:
+  gen-matrix:
+    name: generate-matrix
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4
+
+      - name: Calculate file differences
+        id: diff
+        uses: tj-actions/changed-files@v44
+        with:
+          json: true
+          quotepath: false
+          # TODO Add Dockerfiles
+          files: |
+            modules/**/environment.yml
+      - name: Debug
+        run: echo ${{ steps.diff.outputs.all_changed_files }}
+      - id: set-matrix
+        run: echo "matrix={\"profile\":[\"docker\", \"singularity\"],\"files\":${{ steps.diff.outputs.all_changed_files }} }" >> "$GITHUB_OUTPUT"
+
+    outputs:
+      matrix: ${{ steps.set-matrix.outputs.matrix }}
+
+  build:
+    if: "${{ fromJson(needs.gen-matrix.outputs.matrix) }}"
+    needs: gen-matrix
+    name: build
+    runs-on: ubuntu-latest
+    timeout-minutes: 60
+    strategy:
+      fail-fast: false
+      matrix: "${{ fromJson(needs.gen-matrix.outputs.matrix) }}"
+    steps:
+      - uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4
+
+      - uses: weiji14/conda-lock-refresh@main
+        with:
+          file: "${{ matrix.files }}"
+          # TODO platform: ["linux-64", "osx-arm64"]
+
+      - name: Commit condalock files to PR
+        run: |
+          if [[ $(git ls-files --modified --others) ]]; then
+            git config --global user.name 'actions-bot'
+            git config --global user.email '58130806+actions-bot@users.noreply.github.com'
+            git add --all
+            git commit --message "[condalock-command] autogenerated conda-lock files"
+            git push
+          fi
+        shell: bash -l {0}
+
+      - name: Get the lock file path
+        uses: actions/github-script@v7
+        id: lockfile-name
+        with:
+          result-encoding: string
+          script: |
+            return '${{ matrix.files }}'.replace('/environment.yml', '/conda-lock.yml');
+
+        # TODO Build containers with Wave

From 6ea762d4726c953de1fa8a336ee0e6dfcbd0cef6 Mon Sep 17 00:00:00 2001
From: Edmund Miller <git@edmundmiller.dev>
Date: Tue, 18 Jun 2024 14:52:03 -0500
Subject: [PATCH 02/17] ci: Add write permissions

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

diff --git a/.github/workflows/wave.yml b/.github/workflows/wave.yml
index d0142d38d7e..c8e9946ad79 100644
--- a/.github/workflows/wave.yml
+++ b/.github/workflows/wave.yml
@@ -38,6 +38,8 @@ jobs:
     if: "${{ fromJson(needs.gen-matrix.outputs.matrix) }}"
     needs: gen-matrix
     name: build
+    permissions:
+      contents: write
     runs-on: ubuntu-latest
     timeout-minutes: 60
     strategy:

From b740f85808e39e378dc1f86b316ea6e70391bf6b Mon Sep 17 00:00:00 2001
From: Edmund Miller <git@edmundmiller.dev>
Date: Tue, 18 Jun 2024 14:56:43 -0500
Subject: [PATCH 03/17] ci: Add gh pr checkout

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

diff --git a/.github/workflows/wave.yml b/.github/workflows/wave.yml
index c8e9946ad79..0e5eda54e3d 100644
--- a/.github/workflows/wave.yml
+++ b/.github/workflows/wave.yml
@@ -53,6 +53,13 @@ jobs:
           file: "${{ matrix.files }}"
           # TODO platform: ["linux-64", "osx-arm64"]
 
+      # Action runs on the issue comment, so we don't get the PR by default
+      # Use the gh cli to check out the PR
+      - name: Checkout Pull Request
+        run: gh pr checkout ${{ github.event.issue.number }}
+        env:
+          GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
+
       - name: Commit condalock files to PR
         run: |
           if [[ $(git ls-files --modified --others) ]]; then

From 95ba6ccd0740af5b1053ee76fe70b0692164ad4a Mon Sep 17 00:00:00 2001
From: Edmund Miller <git@edmundmiller.dev>
Date: Tue, 18 Jun 2024 15:02:12 -0500
Subject: [PATCH 04/17] ci: Try a pre-canned action

---
 .github/workflows/wave.yml | 22 +++++-----------------
 1 file changed, 5 insertions(+), 17 deletions(-)

diff --git a/.github/workflows/wave.yml b/.github/workflows/wave.yml
index 0e5eda54e3d..1403152291e 100644
--- a/.github/workflows/wave.yml
+++ b/.github/workflows/wave.yml
@@ -53,23 +53,11 @@ jobs:
           file: "${{ matrix.files }}"
           # TODO platform: ["linux-64", "osx-arm64"]
 
-      # Action runs on the issue comment, so we don't get the PR by default
-      # Use the gh cli to check out the PR
-      - name: Checkout Pull Request
-        run: gh pr checkout ${{ github.event.issue.number }}
-        env:
-          GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
-
-      - name: Commit condalock files to PR
-        run: |
-          if [[ $(git ls-files --modified --others) ]]; then
-            git config --global user.name 'actions-bot'
-            git config --global user.email '58130806+actions-bot@users.noreply.github.com'
-            git add --all
-            git commit --message "[condalock-command] autogenerated conda-lock files"
-            git push
-          fi
-        shell: bash -l {0}
+      - name: Commit and push changes
+        uses: devops-infra/action-commit-push@master
+        with:
+          github_token: ${{ secrets.nf_core_bot_auth_token }}
+          commit_message: "[automated] autogenerated conda-lock files"
 
       - name: Get the lock file path
         uses: actions/github-script@v7

From 07a250eca50d047ed6708e918687bf9542faf07a Mon Sep 17 00:00:00 2001
From: Edmund Miller <git@edmundmiller.dev>
Date: Tue, 18 Jun 2024 15:16:57 -0500
Subject: [PATCH 05/17] ci: Cut out conda-lock-refresh

Couldn't get it to commit
---
 .github/workflows/wave.yml | 26 +++++++++++++++++++++++---
 1 file changed, 23 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/wave.yml b/.github/workflows/wave.yml
index 1403152291e..56c2a048598 100644
--- a/.github/workflows/wave.yml
+++ b/.github/workflows/wave.yml
@@ -48,10 +48,30 @@ jobs:
     steps:
       - uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4
 
-      - uses: weiji14/conda-lock-refresh@main
+      - uses: mamba-org/setup-micromamba@v1
         with:
-          file: "${{ matrix.files }}"
-          # TODO platform: ["linux-64", "osx-arm64"]
+          environment-name: conda-lock-env
+          create-args: >-
+            python=3.11
+            conda-lock
+            mamba
+
+      # Print debugging information
+      # - name: Print debug info
+      #   run: |
+      #     conda-lock --version
+      #     mamba --version
+      #     echo Locking ${{ inputs.file }} file for ${{ inputs.platform }} platform.
+      #   shell: bash -l {0}
+
+      # Run conda-lock
+      - name: Run conda-lock
+        run: |
+          rm --force conda-lock.yml
+          conda-lock lock $MAMBA --file "${{ matrix.files }}" --kind lock --platform linux-64
+        env:
+          MAMBA: "--mamba"
+        shell: bash -l {0}
 
       - name: Commit and push changes
         uses: devops-infra/action-commit-push@master

From b3ef764a1697bd9345eefc2948265e9a08572fba Mon Sep 17 00:00:00 2001
From: Edmund Miller <git@edmundmiller.dev>
Date: Tue, 18 Jun 2024 15:19:42 -0500
Subject: [PATCH 06/17] ci: Use plain GITHUB_TOKEN secret

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

diff --git a/.github/workflows/wave.yml b/.github/workflows/wave.yml
index 56c2a048598..bb66a9cdbfb 100644
--- a/.github/workflows/wave.yml
+++ b/.github/workflows/wave.yml
@@ -76,7 +76,7 @@ jobs:
       - name: Commit and push changes
         uses: devops-infra/action-commit-push@master
         with:
-          github_token: ${{ secrets.nf_core_bot_auth_token }}
+          github_token: "${{ secrets.GITHUB_TOKEN }}"
           commit_message: "[automated] autogenerated conda-lock files"
 
       - name: Get the lock file path

From 98cbce3c3db78913392439296d70281891eccf9b Mon Sep 17 00:00:00 2001
From: Edmund Miller <git@edmundmiller.dev>
Date: Tue, 18 Jun 2024 15:23:52 -0500
Subject: [PATCH 07/17] ci: Skip committing

---
 .github/workflows/wave.yml | 19 ++++++-------------
 1 file changed, 6 insertions(+), 13 deletions(-)

diff --git a/.github/workflows/wave.yml b/.github/workflows/wave.yml
index bb66a9cdbfb..694dc321c91 100644
--- a/.github/workflows/wave.yml
+++ b/.github/workflows/wave.yml
@@ -56,14 +56,6 @@ jobs:
             conda-lock
             mamba
 
-      # Print debugging information
-      # - name: Print debug info
-      #   run: |
-      #     conda-lock --version
-      #     mamba --version
-      #     echo Locking ${{ inputs.file }} file for ${{ inputs.platform }} platform.
-      #   shell: bash -l {0}
-
       # Run conda-lock
       - name: Run conda-lock
         run: |
@@ -73,11 +65,12 @@ jobs:
           MAMBA: "--mamba"
         shell: bash -l {0}
 
-      - name: Commit and push changes
-        uses: devops-infra/action-commit-push@master
-        with:
-          github_token: "${{ secrets.GITHUB_TOKEN }}"
-          commit_message: "[automated] autogenerated conda-lock files"
+      # FIXME Why can nothing push?
+      # - name: Commit and push changes
+      #   uses: devops-infra/action-commit-push@master
+      #   with:
+      #     github_token: "${{ secrets.GITHUB_TOKEN }}"
+      #     commit_message: "[automated] autogenerated conda-lock files"
 
       - name: Get the lock file path
         uses: actions/github-script@v7

From 253a39875841dff5e4fc0498bc19b35cc1c2adc7 Mon Sep 17 00:00:00 2001
From: Edmund Miller <git@edmundmiller.dev>
Date: Thu, 8 Aug 2024 11:43:51 -0500
Subject: [PATCH 08/17] ci: Use Commit step from prettier linting

https://github.com/nf-core/modules/blob/90b1d1bd7f9474e173abd9e4082dedb559c7542a/.github/workflows/fix-linting.yml#L62-L71

Co-authored-by: mashehu <mashehu@users.noreply.github.com>
---
 .github/workflows/wave.yml | 16 +++++++++-------
 1 file changed, 9 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/wave.yml b/.github/workflows/wave.yml
index 694dc321c91..4b9fe8c4b19 100644
--- a/.github/workflows/wave.yml
+++ b/.github/workflows/wave.yml
@@ -56,7 +56,6 @@ jobs:
             conda-lock
             mamba
 
-      # Run conda-lock
       - name: Run conda-lock
         run: |
           rm --force conda-lock.yml
@@ -65,12 +64,15 @@ jobs:
           MAMBA: "--mamba"
         shell: bash -l {0}
 
-      # FIXME Why can nothing push?
-      # - name: Commit and push changes
-      #   uses: devops-infra/action-commit-push@master
-      #   with:
-      #     github_token: "${{ secrets.GITHUB_TOKEN }}"
-      #     commit_message: "[automated] autogenerated conda-lock files"
+      - name: Commit & push changes
+        run: |
+          git config user.email "core@nf-co.re"
+          git config user.name "nf-core-bot"
+          git config push.default upstream
+          git add .
+          git status
+          git commit -m "[automated] autogenerated conda-lock files"
+          git push
 
       - name: Get the lock file path
         uses: actions/github-script@v7

From f085cc15ae6fbe9c8963ae7addbb629331cad3e1 Mon Sep 17 00:00:00 2001
From: Edmund Miller <git@edmundmiller.dev>
Date: Thu, 8 Aug 2024 11:54:28 -0500
Subject: [PATCH 09/17] ci: Try actions/checkout#719

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

diff --git a/.github/workflows/wave.yml b/.github/workflows/wave.yml
index 4b9fe8c4b19..044ff25ddf3 100644
--- a/.github/workflows/wave.yml
+++ b/.github/workflows/wave.yml
@@ -47,6 +47,8 @@ jobs:
       matrix: "${{ fromJson(needs.gen-matrix.outputs.matrix) }}"
     steps:
       - uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4
+        with:
+          ref: ${{ github.event.pull_request.head.ref }}
 
       - uses: mamba-org/setup-micromamba@v1
         with:

From fe828fa5c4eb9c5275231487c78c37a37b2b961e Mon Sep 17 00:00:00 2001
From: Edmund Miller <git@edmundmiller.dev>
Date: Thu, 8 Aug 2024 12:09:06 -0500
Subject: [PATCH 10/17] ci: Clean up commit message

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

diff --git a/.github/workflows/wave.yml b/.github/workflows/wave.yml
index 044ff25ddf3..92c3ce36722 100644
--- a/.github/workflows/wave.yml
+++ b/.github/workflows/wave.yml
@@ -73,7 +73,7 @@ jobs:
           git config push.default upstream
           git add .
           git status
-          git commit -m "[automated] autogenerated conda-lock files"
+          git commit -m "[automated] autogenerated conda-lock file"
           git push
 
       - name: Get the lock file path

From 8433c87a950a4eb4fc30f86be8605472996e802d Mon Sep 17 00:00:00 2001
From: Edmund Miller <git@edmundmiller.dev>
Date: Thu, 8 Aug 2024 12:25:30 -0500
Subject: [PATCH 11/17] ci: Output lock file to the directory

---
 .github/workflows/wave.yml | 20 ++++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/.github/workflows/wave.yml b/.github/workflows/wave.yml
index 92c3ce36722..084f0f77701 100644
--- a/.github/workflows/wave.yml
+++ b/.github/workflows/wave.yml
@@ -58,10 +58,18 @@ jobs:
             conda-lock
             mamba
 
+      - name: Get the lock file path
+        uses: actions/github-script@v7
+        id: lockfile-name
+        with:
+          result-encoding: string
+          script: |
+            return '${{ matrix.files }}'.replace('/environment.yml', '/conda-lock.yml');
+
       - name: Run conda-lock
         run: |
-          rm --force conda-lock.yml
-          conda-lock lock $MAMBA --file "${{ matrix.files }}" --kind lock --platform linux-64
+          rm --force "${{steps.lockfile-name.outputs.result}}"
+          conda-lock lock $MAMBA --file "${{ matrix.files }}" --kind lock --platform linux-64 --lockfile "${{steps.lockfile-name.outputs.result}}"
         env:
           MAMBA: "--mamba"
         shell: bash -l {0}
@@ -76,12 +84,4 @@ jobs:
           git commit -m "[automated] autogenerated conda-lock file"
           git push
 
-      - name: Get the lock file path
-        uses: actions/github-script@v7
-        id: lockfile-name
-        with:
-          result-encoding: string
-          script: |
-            return '${{ matrix.files }}'.replace('/environment.yml', '/conda-lock.yml');
-
         # TODO Build containers with Wave

From a9f4d26a363ad396227fe40c09c877f287080a20 Mon Sep 17 00:00:00 2001
From: Edmund Miller <git@edmundmiller.dev>
Date: Thu, 8 Aug 2024 12:43:31 -0500
Subject: [PATCH 12/17] chore: Update an environment file for testing

---
 modules/nf-core/bowtie2/align/environment.yml | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/modules/nf-core/bowtie2/align/environment.yml b/modules/nf-core/bowtie2/align/environment.yml
index d2796359aeb..68adde8fc36 100644
--- a/modules/nf-core/bowtie2/align/environment.yml
+++ b/modules/nf-core/bowtie2/align/environment.yml
@@ -4,6 +4,9 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::bowtie2=2.5.2
-  - bioconda::samtools=1.18
-  - conda-forge::pigz=2.6
+  # renovate: datasource=conda depName=bioconda/bowtie2
+  - bowtie2=2.5.2
+  # renovate: datasource=conda depName=bioconda/samtools
+  - samtools=1.18
+  # renovate: datasource=conda depName=conda-forge/pigz
+  - pigz=2.6

From 22c4985118c92f90b4f8e5fa5be3871e2cb775a5 Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Thu, 8 Aug 2024 17:58:27 +0000
Subject: [PATCH 13/17] [automated] autogenerated conda-lock file

---
 modules/nf-core/bowtie2/align/conda-lock.yml | 615 +++++++++++++++++++
 1 file changed, 615 insertions(+)
 create mode 100644 modules/nf-core/bowtie2/align/conda-lock.yml

diff --git a/modules/nf-core/bowtie2/align/conda-lock.yml b/modules/nf-core/bowtie2/align/conda-lock.yml
new file mode 100644
index 00000000000..b3725d07f66
--- /dev/null
+++ b/modules/nf-core/bowtie2/align/conda-lock.yml
@@ -0,0 +1,615 @@
+# This lock file was generated by conda-lock (https://github.com/conda/conda-lock). DO NOT EDIT!
+#
+# A "lock file" contains a concrete list of package versions (with checksums) to be installed. Unlike
+# e.g. `conda env create`, the resulting environment will not change as new package versions become
+# available, unless you explicitly update the lock file.
+#
+# Install this environment as "YOURENV" with:
+#     conda-lock install -n YOURENV conda-lock.yml
+# To update a single package to the latest version compatible with the version constraints in the source:
+#     conda-lock lock  --lockfile conda-lock.yml --update PACKAGE
+# To re-solve the entire environment, e.g. after changing a version constraint in the source file:
+#     conda-lock -f environment.yml --lockfile conda-lock.yml
+version: 1
+metadata:
+  content_hash:
+    linux-64: b864a48e350c8ce3992e145bfed6961e07ccf9dc5a7e67b0a03943d2f2d87e94
+  channels:
+  - url: conda-forge
+    used_env_vars: []
+  - url: bioconda
+    used_env_vars: []
+  - url: defaults
+    used_env_vars: []
+  platforms:
+  - linux-64
+  sources:
+  - environment.yml
+package:
+- name: _libgcc_mutex
+  version: '0.1'
+  manager: conda
+  platform: linux-64
+  dependencies: {}
+  url: https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2
+  hash:
+    md5: d7c89558ba9fa0495403155b64376d81
+    sha256: fe51de6107f9edc7aa4f786a70f4a883943bc9d39b3bb7307c04c41410990726
+  category: main
+  optional: false
+- name: _openmp_mutex
+  version: '4.5'
+  manager: conda
+  platform: linux-64
+  dependencies:
+    _libgcc_mutex: '0.1'
+    libgomp: '>=7.5.0'
+  url: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2
+  hash:
+    md5: 73aaf86a425cc6e73fcf236a5a46396d
+    sha256: fbe2c5e56a653bebb982eda4876a9178aedfc2b545f25d0ce9c4c0b508253d22
+  category: main
+  optional: false
+- name: bowtie2
+  version: 2.5.2
+  manager: conda
+  platform: linux-64
+  dependencies:
+    libgcc-ng: '>=12'
+    libstdcxx-ng: '>=12'
+    libzlib: '>=1.2.13,<1.3.0a0'
+    perl: ''
+    python: '>=3.10,<3.11.0a0'
+    python_abi: 3.10.*
+    tbb: '>=2021.10.0'
+    zlib: ''
+    zstd: '>=1.5.5,<1.6.0a0'
+  url: https://conda.anaconda.org/bioconda/linux-64/bowtie2-2.5.2-py310ha0a81b8_0.tar.bz2
+  hash:
+    md5: 81764fc4a9f32df1724741af3f82e93d
+    sha256: 39d1db19a8e6fdbdc4270d53511c3a93a06c69da87f78bc0e61e9d0159a25291
+  category: main
+  optional: false
+- name: bzip2
+  version: 1.0.8
+  manager: conda
+  platform: linux-64
+  dependencies:
+    __glibc: '>=2.17,<3.0.a0'
+    libgcc-ng: '>=12'
+  url: https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda
+  hash:
+    md5: 62ee74e96c5ebb0af99386de58cf9553
+    sha256: 5ced96500d945fb286c9c838e54fa759aa04a7129c59800f0846b4335cee770d
+  category: main
+  optional: false
+- name: c-ares
+  version: 1.32.3
+  manager: conda
+  platform: linux-64
+  dependencies:
+    __glibc: '>=2.17,<3.0.a0'
+    libgcc-ng: '>=12'
+  url: https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.32.3-h4bc722e_0.conda
+  hash:
+    md5: 7624e34ee6baebfc80d67bac76cc9d9d
+    sha256: 3c5a844bb60b0d52d89c3f1bd828c9856417fe33a6102fd8bbd5c13c3351704a
+  category: main
+  optional: false
+- name: ca-certificates
+  version: 2024.7.4
+  manager: conda
+  platform: linux-64
+  dependencies: {}
+  url: https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.7.4-hbcca054_0.conda
+  hash:
+    md5: 23ab7665c5f63cfb9f1f6195256daac6
+    sha256: c1548a3235376f464f9931850b64b02492f379b2f2bb98bc786055329b080446
+  category: main
+  optional: false
+- name: htslib
+  version: '1.20'
+  manager: conda
+  platform: linux-64
+  dependencies:
+    bzip2: '>=1.0.8,<2.0a0'
+    libcurl: '>=8.8.0,<9.0a0'
+    libdeflate: '>=1.20,<1.22.0a0'
+    libgcc-ng: '>=12'
+    libzlib: '>=1.2.13,<2.0a0'
+    openssl: '>=3.3.1,<4.0a0'
+    xz: '>=5.2.6,<6.0a0'
+  url: https://conda.anaconda.org/bioconda/linux-64/htslib-1.20-h5efdd21_2.tar.bz2
+  hash:
+    md5: f0923cdb85b44dc77bdead8018645ea9
+    sha256: 791ef4ff30944a56803344b168ffb400b4a8d1ea52edb1c348541d2a67a838ba
+  category: main
+  optional: false
+- name: icu
+  version: '73.2'
+  manager: conda
+  platform: linux-64
+  dependencies:
+    libgcc-ng: '>=12'
+    libstdcxx-ng: '>=12'
+  url: https://conda.anaconda.org/conda-forge/linux-64/icu-73.2-h59595ed_0.conda
+  hash:
+    md5: cc47e1facc155f91abd89b11e48e72ff
+    sha256: e12fd90ef6601da2875ebc432452590bc82a893041473bc1c13ef29001a73ea8
+  category: main
+  optional: false
+- name: keyutils
+  version: 1.6.1
+  manager: conda
+  platform: linux-64
+  dependencies:
+    libgcc-ng: '>=10.3.0'
+  url: https://conda.anaconda.org/conda-forge/linux-64/keyutils-1.6.1-h166bdaf_0.tar.bz2
+  hash:
+    md5: 30186d27e2c9fa62b45fb1476b7200e3
+    sha256: 150c05a6e538610ca7c43beb3a40d65c90537497a4f6a5f4d15ec0451b6f5ebb
+  category: main
+  optional: false
+- name: krb5
+  version: 1.21.3
+  manager: conda
+  platform: linux-64
+  dependencies:
+    keyutils: '>=1.6.1,<2.0a0'
+    libedit: '>=3.1.20191231,<4.0a0'
+    libgcc-ng: '>=12'
+    libstdcxx-ng: '>=12'
+    openssl: '>=3.3.1,<4.0a0'
+  url: https://conda.anaconda.org/conda-forge/linux-64/krb5-1.21.3-h659f571_0.conda
+  hash:
+    md5: 3f43953b7d3fb3aaa1d0d0723d91e368
+    sha256: 99df692f7a8a5c27cd14b5fb1374ee55e756631b9c3d659ed3ee60830249b238
+  category: main
+  optional: false
+- name: ld_impl_linux-64
+  version: '2.40'
+  manager: conda
+  platform: linux-64
+  dependencies: {}
+  url: https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-hf3520f5_7.conda
+  hash:
+    md5: b80f2f396ca2c28b8c14c437a4ed1e74
+    sha256: 764b6950aceaaad0c67ef925417594dd14cd2e22fff864aeef455ac259263d15
+  category: main
+  optional: false
+- name: libcurl
+  version: 8.8.0
+  manager: conda
+  platform: linux-64
+  dependencies:
+    krb5: '>=1.21.3,<1.22.0a0'
+    libgcc-ng: '>=12'
+    libnghttp2: '>=1.58.0,<2.0a0'
+    libssh2: '>=1.11.0,<2.0a0'
+    libzlib: '>=1.2.13,<2.0a0'
+    openssl: '>=3.3.1,<4.0a0'
+    zstd: '>=1.5.6,<1.6.0a0'
+  url: https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.8.0-hca28451_1.conda
+  hash:
+    md5: b8afb3e3cb3423cc445cf611ab95fdb0
+    sha256: 6b5b64cdcdb643368ebe236de07eedee99b025bb95129bbe317c46e5bdc693f3
+  category: main
+  optional: false
+- name: libdeflate
+  version: '1.21'
+  manager: conda
+  platform: linux-64
+  dependencies:
+    __glibc: '>=2.17,<3.0.a0'
+    libgcc-ng: '>=12'
+  url: https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.21-h4bc722e_0.conda
+  hash:
+    md5: 36ce76665bf67f5aac36be7a0d21b7f3
+    sha256: 728c24ce835700bfdfdf106bf04233fdb040a61ca4ecfd3f41b46fa90cd4f971
+  category: main
+  optional: false
+- name: libedit
+  version: 3.1.20191231
+  manager: conda
+  platform: linux-64
+  dependencies:
+    libgcc-ng: '>=7.5.0'
+    ncurses: '>=6.2,<7.0.0a0'
+  url: https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20191231-he28a2e2_2.tar.bz2
+  hash:
+    md5: 4d331e44109e3f0e19b4cb8f9b82f3e1
+    sha256: a57d37c236d8f7c886e01656f4949d9dcca131d2a0728609c6f7fa338b65f1cf
+  category: main
+  optional: false
+- name: libev
+  version: '4.33'
+  manager: conda
+  platform: linux-64
+  dependencies:
+    libgcc-ng: '>=12'
+  url: https://conda.anaconda.org/conda-forge/linux-64/libev-4.33-hd590300_2.conda
+  hash:
+    md5: 172bf1cd1ff8629f2b1179945ed45055
+    sha256: 1cd6048169fa0395af74ed5d8f1716e22c19a81a8a36f934c110ca3ad4dd27b4
+  category: main
+  optional: false
+- name: libffi
+  version: 3.4.2
+  manager: conda
+  platform: linux-64
+  dependencies:
+    libgcc-ng: '>=9.4.0'
+  url: https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.2-h7f98852_5.tar.bz2
+  hash:
+    md5: d645c6d2ac96843a2bfaccd2d62b3ac3
+    sha256: ab6e9856c21709b7b517e940ae7028ae0737546122f83c2aa5d692860c3b149e
+  category: main
+  optional: false
+- name: libgcc-ng
+  version: 14.1.0
+  manager: conda
+  platform: linux-64
+  dependencies:
+    _libgcc_mutex: '0.1'
+    _openmp_mutex: '>=4.5'
+  url: https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-14.1.0-h77fa898_0.conda
+  hash:
+    md5: ca0fad6a41ddaef54a153b78eccb5037
+    sha256: b8e869ac96591cda2704bf7e77a301025e405227791a0bddf14a3dac65125538
+  category: main
+  optional: false
+- name: libgomp
+  version: 14.1.0
+  manager: conda
+  platform: linux-64
+  dependencies:
+    _libgcc_mutex: '0.1'
+  url: https://conda.anaconda.org/conda-forge/linux-64/libgomp-14.1.0-h77fa898_0.conda
+  hash:
+    md5: ae061a5ed5f05818acdf9adab72c146d
+    sha256: 7699df61a1f6c644b3576a40f54791561f2845983120477a16116b951c9cdb05
+  category: main
+  optional: false
+- name: libhwloc
+  version: 2.11.1
+  manager: conda
+  platform: linux-64
+  dependencies:
+    __glibc: '>=2.17,<3.0.a0'
+    libgcc-ng: '>=12'
+    libstdcxx-ng: '>=12'
+    libxml2: '>=2.12.7,<3.0a0'
+  url: https://conda.anaconda.org/conda-forge/linux-64/libhwloc-2.11.1-default_hecaa2ac_1000.conda
+  hash:
+    md5: f54aeebefb5c5ff84eca4fb05ca8aa3a
+    sha256: 8473a300e10b79557ce0ac81602506b47146aff3df4cc3568147a7dd07f480a2
+  category: main
+  optional: false
+- name: libiconv
+  version: '1.17'
+  manager: conda
+  platform: linux-64
+  dependencies:
+    libgcc-ng: '>=12'
+  url: https://conda.anaconda.org/conda-forge/linux-64/libiconv-1.17-hd590300_2.conda
+  hash:
+    md5: d66573916ffcf376178462f1b61c941e
+    sha256: 8ac2f6a9f186e76539439e50505d98581472fedb347a20e7d1f36429849f05c9
+  category: main
+  optional: false
+- name: libnghttp2
+  version: 1.58.0
+  manager: conda
+  platform: linux-64
+  dependencies:
+    c-ares: '>=1.23.0,<2.0a0'
+    libev: '>=4.33,<5.0a0'
+    libgcc-ng: '>=12'
+    libstdcxx-ng: '>=12'
+    libzlib: '>=1.2.13,<2.0.0a0'
+    openssl: '>=3.2.0,<4.0a0'
+  url: https://conda.anaconda.org/conda-forge/linux-64/libnghttp2-1.58.0-h47da74e_1.conda
+  hash:
+    md5: 700ac6ea6d53d5510591c4344d5c989a
+    sha256: 1910c5306c6aa5bcbd623c3c930c440e9c77a5a019008e1487810e3c1d3716cb
+  category: main
+  optional: false
+- name: libnsl
+  version: 2.0.1
+  manager: conda
+  platform: linux-64
+  dependencies:
+    libgcc-ng: '>=12'
+  url: https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hd590300_0.conda
+  hash:
+    md5: 30fd6e37fe21f86f4bd26d6ee73eeec7
+    sha256: 26d77a3bb4dceeedc2a41bd688564fe71bf2d149fdcf117049970bc02ff1add6
+  category: main
+  optional: false
+- name: libsqlite
+  version: 3.46.0
+  manager: conda
+  platform: linux-64
+  dependencies:
+    libgcc-ng: '>=12'
+    libzlib: '>=1.2.13,<2.0a0'
+  url: https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.46.0-hde9e2c9_0.conda
+  hash:
+    md5: 18aa975d2094c34aef978060ae7da7d8
+    sha256: daee3f68786231dad457d0dfde3f7f1f9a7f2018adabdbb864226775101341a8
+  category: main
+  optional: false
+- name: libssh2
+  version: 1.11.0
+  manager: conda
+  platform: linux-64
+  dependencies:
+    libgcc-ng: '>=12'
+    libzlib: '>=1.2.13,<2.0.0a0'
+    openssl: '>=3.1.1,<4.0a0'
+  url: https://conda.anaconda.org/conda-forge/linux-64/libssh2-1.11.0-h0841786_0.conda
+  hash:
+    md5: 1f5a58e686b13bcfde88b93f547d23fe
+    sha256: 50e47fd9c4f7bf841a11647ae7486f65220cfc988ec422a4475fe8d5a823824d
+  category: main
+  optional: false
+- name: libstdcxx-ng
+  version: 14.1.0
+  manager: conda
+  platform: linux-64
+  dependencies:
+    libgcc-ng: 14.1.0
+  url: https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-14.1.0-hc0a3c3a_0.conda
+  hash:
+    md5: 1cb187a157136398ddbaae90713e2498
+    sha256: 88c42b388202ffe16adaa337e36cf5022c63cf09b0405cf06fc6aeacccbe6146
+  category: main
+  optional: false
+- name: libuuid
+  version: 2.38.1
+  manager: conda
+  platform: linux-64
+  dependencies:
+    libgcc-ng: '>=12'
+  url: https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda
+  hash:
+    md5: 40b61aab5c7ba9ff276c41cfffe6b80b
+    sha256: 787eb542f055a2b3de553614b25f09eefb0a0931b0c87dbcce6efdfd92f04f18
+  category: main
+  optional: false
+- name: libxcrypt
+  version: 4.4.36
+  manager: conda
+  platform: linux-64
+  dependencies:
+    libgcc-ng: '>=12'
+  url: https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda
+  hash:
+    md5: 5aa797f8787fe7a17d1b0821485b5adc
+    sha256: 6ae68e0b86423ef188196fff6207ed0c8195dd84273cb5623b85aa08033a410c
+  category: main
+  optional: false
+- name: libxml2
+  version: 2.12.7
+  manager: conda
+  platform: linux-64
+  dependencies:
+    icu: '>=73.2,<74.0a0'
+    libgcc-ng: '>=12'
+    libiconv: '>=1.17,<2.0a0'
+    libzlib: '>=1.2.13,<2.0a0'
+    xz: '>=5.2.6,<6.0a0'
+  url: https://conda.anaconda.org/conda-forge/linux-64/libxml2-2.12.7-hc051c1a_1.conda
+  hash:
+    md5: 340278ded8b0dc3a73f3660bbb0adbc6
+    sha256: 576ea9134176636283ff052897bf7a91ffd8ac35b2c505dfde2890ec52849698
+  category: main
+  optional: false
+- name: libzlib
+  version: 1.2.13
+  manager: conda
+  platform: linux-64
+  dependencies:
+    libgcc-ng: '>=12'
+  url: https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-h4ab18f5_6.conda
+  hash:
+    md5: 27329162c0dc732bcf67a4e0cd488125
+    sha256: 8ced4afed6322172182af503f21725d072a589a6eb918f8a58135c1e00d35980
+  category: main
+  optional: false
+- name: ncurses
+  version: '6.5'
+  manager: conda
+  platform: linux-64
+  dependencies:
+    libgcc-ng: '>=12'
+  url: https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h59595ed_0.conda
+  hash:
+    md5: fcea371545eda051b6deafb24889fc69
+    sha256: 4fc3b384f4072b68853a0013ea83bdfd3d66b0126e2238e1d6e1560747aa7586
+  category: main
+  optional: false
+- name: openssl
+  version: 3.3.1
+  manager: conda
+  platform: linux-64
+  dependencies:
+    __glibc: '>=2.17,<3.0.a0'
+    ca-certificates: ''
+    libgcc-ng: '>=12'
+  url: https://conda.anaconda.org/conda-forge/linux-64/openssl-3.3.1-h4bc722e_2.conda
+  hash:
+    md5: e1b454497f9f7c1147fdde4b53f1b512
+    sha256: b294b3cc706ad1048cdb514f0db3da9f37ae3fcc0c53a7104083dd0918adb200
+  category: main
+  optional: false
+- name: perl
+  version: 5.32.1
+  manager: conda
+  platform: linux-64
+  dependencies:
+    libgcc-ng: '>=12'
+    libxcrypt: '>=4.4.36'
+  url: https://conda.anaconda.org/conda-forge/linux-64/perl-5.32.1-7_hd590300_perl5.conda
+  hash:
+    md5: f2cfec9406850991f4e3d960cc9e3321
+    sha256: 9ec32b6936b0e37bcb0ed34f22ec3116e75b3c0964f9f50ecea5f58734ed6ce9
+  category: main
+  optional: false
+- name: pigz
+  version: '2.6'
+  manager: conda
+  platform: linux-64
+  dependencies:
+    libgcc-ng: '>=12'
+    libzlib: '>=1.2.13,<2.0.0a0'
+    zlib: ''
+  url: https://conda.anaconda.org/conda-forge/linux-64/pigz-2.6-h2797004_1.conda
+  hash:
+    md5: 5f19233669faf26889f27a2d2710e170
+    sha256: 074bfefe3552545257babaaca0d6e00a5f9732118d0824382c6eb5c7befe7c7e
+  category: main
+  optional: false
+- name: python
+  version: 3.10.14
+  manager: conda
+  platform: linux-64
+  dependencies:
+    bzip2: '>=1.0.8,<2.0a0'
+    ld_impl_linux-64: '>=2.36.1'
+    libffi: '>=3.4,<4.0a0'
+    libgcc-ng: '>=12'
+    libnsl: '>=2.0.1,<2.1.0a0'
+    libsqlite: '>=3.45.2,<4.0a0'
+    libuuid: '>=2.38.1,<3.0a0'
+    libxcrypt: '>=4.4.36'
+    libzlib: '>=1.2.13,<2.0.0a0'
+    ncurses: '>=6.4.20240210,<7.0a0'
+    openssl: '>=3.2.1,<4.0a0'
+    readline: '>=8.2,<9.0a0'
+    tk: '>=8.6.13,<8.7.0a0'
+    tzdata: ''
+    xz: '>=5.2.6,<6.0a0'
+  url: https://conda.anaconda.org/conda-forge/linux-64/python-3.10.14-hd12c33a_0_cpython.conda
+  hash:
+    md5: 2b4ba962994e8bd4be9ff5b64b75aff2
+    sha256: 76a5d12e73542678b70a94570f7b0f7763f9a938f77f0e75d9ea615ef22aa84c
+  category: main
+  optional: false
+- name: python_abi
+  version: '3.10'
+  manager: conda
+  platform: linux-64
+  dependencies: {}
+  url: https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.10-4_cp310.conda
+  hash:
+    md5: 26322ec5d7712c3ded99dd656142b8ce
+    sha256: 456bec815bfc2b364763084d08b412fdc4c17eb9ccc66a36cb775fa7ac3cbaec
+  category: main
+  optional: false
+- name: readline
+  version: '8.2'
+  manager: conda
+  platform: linux-64
+  dependencies:
+    libgcc-ng: '>=12'
+    ncurses: '>=6.3,<7.0a0'
+  url: https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8228510_1.conda
+  hash:
+    md5: 47d31b792659ce70f470b5c82fdfb7a4
+    sha256: 5435cf39d039387fbdc977b0a762357ea909a7694d9528ab40f005e9208744d7
+  category: main
+  optional: false
+- name: samtools
+  version: '1.18'
+  manager: conda
+  platform: linux-64
+  dependencies:
+    htslib: '>=1.18,<1.21.0a0'
+    libgcc-ng: '>=12'
+    libzlib: '>=1.2.13,<1.3.0a0'
+    ncurses: '>=6.4,<7.0a0'
+  url: https://conda.anaconda.org/bioconda/linux-64/samtools-1.18-h50ea8bc_1.tar.bz2
+  hash:
+    md5: 7a53b527d66566e2bd8d436766e9c39e
+    sha256: f18a5e13293da2452dcf22c139daeaacebecad7908699764585c03925da1a92d
+  category: main
+  optional: false
+- name: tbb
+  version: 2021.12.0
+  manager: conda
+  platform: linux-64
+  dependencies:
+    __glibc: '>=2.17,<3.0.a0'
+    libgcc-ng: '>=12'
+    libhwloc: '>=2.11.1,<2.11.2.0a0'
+    libstdcxx-ng: '>=12'
+  url: https://conda.anaconda.org/conda-forge/linux-64/tbb-2021.12.0-h434a139_3.conda
+  hash:
+    md5: c667c11d1e488a38220ede8a34441bff
+    sha256: e901e1887205a3f90d6a77e1302ccc5ffe48fd30de16907dfdbdbf1dbef0a177
+  category: main
+  optional: false
+- name: tk
+  version: 8.6.13
+  manager: conda
+  platform: linux-64
+  dependencies:
+    libgcc-ng: '>=12'
+    libzlib: '>=1.2.13,<2.0.0a0'
+  url: https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_h4845f30_101.conda
+  hash:
+    md5: d453b98d9c83e71da0741bb0ff4d76bc
+    sha256: e0569c9caa68bf476bead1bed3d79650bb080b532c64a4af7d8ca286c08dea4e
+  category: main
+  optional: false
+- name: tzdata
+  version: 2024a
+  manager: conda
+  platform: linux-64
+  dependencies: {}
+  url: https://conda.anaconda.org/conda-forge/noarch/tzdata-2024a-h0c530f3_0.conda
+  hash:
+    md5: 161081fc7cec0bfda0d86d7cb595f8d8
+    sha256: 7b2b69c54ec62a243eb6fba2391b5e443421608c3ae5dbff938ad33ca8db5122
+  category: main
+  optional: false
+- name: xz
+  version: 5.2.6
+  manager: conda
+  platform: linux-64
+  dependencies:
+    libgcc-ng: '>=12'
+  url: https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2
+  hash:
+    md5: 2161070d867d1b1204ea749c8eec4ef0
+    sha256: 03a6d28ded42af8a347345f82f3eebdd6807a08526d47899a42d62d319609162
+  category: main
+  optional: false
+- name: zlib
+  version: 1.2.13
+  manager: conda
+  platform: linux-64
+  dependencies:
+    libgcc-ng: '>=12'
+    libzlib: 1.2.13
+  url: https://conda.anaconda.org/conda-forge/linux-64/zlib-1.2.13-h4ab18f5_6.conda
+  hash:
+    md5: 559d338a4234c2ad6e676f460a093e67
+    sha256: 534824ea44939f3e59ca8ebb95e3ece6f50f9d2a0e69999fbc692311252ed6ac
+  category: main
+  optional: false
+- name: zstd
+  version: 1.5.6
+  manager: conda
+  platform: linux-64
+  dependencies:
+    libgcc-ng: '>=12'
+    libstdcxx-ng: '>=12'
+    libzlib: '>=1.2.13,<2.0.0a0'
+  url: https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.6-ha6fb4c9_0.conda
+  hash:
+    md5: 4d056880988120e29d75bfff282e0f45
+    sha256: c558b9cc01d9c1444031bd1ce4b9cff86f9085765f17627a6cd85fc623c8a02b
+  category: main
+  optional: false

From 3afecb6b0b746493427a159af3e7ac6894eed942 Mon Sep 17 00:00:00 2001
From: Edmund Miller <git@edmundmiller.dev>
Date: Thu, 8 Aug 2024 13:08:58 -0500
Subject: [PATCH 14/17] ci: Clean up the matrix to avoid a race condition

---
 .github/workflows/wave.yml | 12 +++---------
 1 file changed, 3 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/wave.yml b/.github/workflows/wave.yml
index 084f0f77701..9039cdcf647 100644
--- a/.github/workflows/wave.yml
+++ b/.github/workflows/wave.yml
@@ -1,4 +1,3 @@
-# TODO Change to Wave
 name: Generate conda-lock
 # When environment.yml is changed
 on:
@@ -6,9 +5,6 @@ on:
     paths:
       - "**/environment.yml"
 
-env:
-  WAVE_VER: "1.4.1"
-
 jobs:
   gen-matrix:
     name: generate-matrix
@@ -23,25 +19,23 @@ jobs:
         with:
           json: true
           quotepath: false
-          # TODO Add Dockerfiles
           files: |
             modules/**/environment.yml
       - name: Debug
         run: echo ${{ steps.diff.outputs.all_changed_files }}
       - id: set-matrix
-        run: echo "matrix={\"profile\":[\"docker\", \"singularity\"],\"files\":${{ steps.diff.outputs.all_changed_files }} }" >> "$GITHUB_OUTPUT"
+        run: echo "matrix={\"files\":${{ steps.diff.outputs.all_changed_files }} }" >> "$GITHUB_OUTPUT"
 
     outputs:
       matrix: ${{ steps.set-matrix.outputs.matrix }}
 
-  build:
+  lock:
     if: "${{ fromJson(needs.gen-matrix.outputs.matrix) }}"
     needs: gen-matrix
-    name: build
+    name: Generate conda-lock file
     permissions:
       contents: write
     runs-on: ubuntu-latest
-    timeout-minutes: 60
     strategy:
       fail-fast: false
       matrix: "${{ fromJson(needs.gen-matrix.outputs.matrix) }}"

From c6b7ae66421deefaed8456f68c04590bd970072f Mon Sep 17 00:00:00 2001
From: Edmund Miller <git@edmundmiller.dev>
Date: Thu, 8 Aug 2024 13:33:11 -0500
Subject: [PATCH 15/17] style: Ignore conda-lock for prettier

---
 .prettierignore | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.prettierignore b/.prettierignore
index 41fc3479697..cb3f3e47fb4 100644
--- a/.prettierignore
+++ b/.prettierignore
@@ -15,3 +15,4 @@ __pycache__
 *.pyo
 *.pyc
 .github/renovate.json5
+**/conda-lock.yml

From 251b8cabf365bbf538349130259f6cb4fa07bd85 Mon Sep 17 00:00:00 2001
From: Edmund Miller <git@edmundmiller.dev>
Date: Thu, 8 Aug 2024 13:44:07 -0500
Subject: [PATCH 16/17] ci: Allow no conda-lock updates

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

diff --git a/.github/workflows/wave.yml b/.github/workflows/wave.yml
index 9039cdcf647..849e59ee2b2 100644
--- a/.github/workflows/wave.yml
+++ b/.github/workflows/wave.yml
@@ -69,6 +69,7 @@ jobs:
         shell: bash -l {0}
 
       - name: Commit & push changes
+        id: commit-and-push
         run: |
           git config user.email "core@nf-co.re"
           git config user.name "nf-core-bot"
@@ -78,4 +79,9 @@ jobs:
           git commit -m "[automated] autogenerated conda-lock file"
           git push
 
+      - name: If no conda-lock update
+        if: steps.commit-and-push.outcome == 'failure'
+        run: |
+          echo "No conda-lock update"
+
         # TODO Build containers with Wave

From de2fdf78092816e986068db18bed83ce493854e6 Mon Sep 17 00:00:00 2001
From: Edmund Miller <git@edmundmiller.dev>
Date: Fri, 9 Aug 2024 13:15:21 -0500
Subject: [PATCH 17/17] build: Try a conda-lock file

---
 modules/nf-core/bowtie2/align/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/bowtie2/align/main.nf b/modules/nf-core/bowtie2/align/main.nf
index 809525ad36c..9f5480c5175 100644
--- a/modules/nf-core/bowtie2/align/main.nf
+++ b/modules/nf-core/bowtie2/align/main.nf
@@ -2,7 +2,7 @@ process BOWTIE2_ALIGN {
     tag "$meta.id"
     label 'process_high'
 
-    conda "${moduleDir}/environment.yml"
+    conda "${moduleDir}/conda-lock.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:f70b31a2db15c023d641c32f433fb02cd04df5a6-0' :
         'biocontainers/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:f70b31a2db15c023d641c32f433fb02cd04df5a6-0' }"