From a731ae4bf2d17e5ae8e1c66017ce59393efea724 Mon Sep 17 00:00:00 2001
From: Louis Le Nezet <louislenezet@gmail.com>
Date: Tue, 4 Aug 2026 16:36:47 +0200
Subject: [PATCH 01/15] Update to topic

---
 modules/nf-core/phyloflash/main.nf            | 37 ++++++-------------
 modules/nf-core/phyloflash/meta.yml           | 37 +++++++++++++------
 modules/nf-core/phyloflash/tests/main.nf.test |  5 +--
 .../phyloflash/tests/main.nf.test.snap        | 34 +++++------------
 4 files changed, 47 insertions(+), 66 deletions(-)

diff --git a/modules/nf-core/phyloflash/main.nf b/modules/nf-core/phyloflash/main.nf
index add68966cf3b..7e86e740245e 100644
--- a/modules/nf-core/phyloflash/main.nf
+++ b/modules/nf-core/phyloflash/main.nf
@@ -14,7 +14,7 @@ process PHYLOFLASH {
 
     output:
     tuple val(meta), path("${meta.id}*/*"), emit: results
-    path "versions.yml"                   , emit: versions
+    tuple val("${task.process}"), val('phyloflash'), eval("phyloFlash.pl -version 2>&1 | sed 's/^.*phyloFlash v//'"), topic: versions, emit: versions_phyloflash
 
     when:
     task.ext.when == null || task.ext.when
@@ -25,38 +25,28 @@ process PHYLOFLASH {
     if (meta.single_end) {
         """
         phyloFlash.pl \\
-            $args \\
+            ${args} \\
             -read1 ${reads[0]} \\
-            -lib $prefix \\
+            -lib ${prefix} \\
             -interleaved \\
             -dbhome . \\
-            -CPUs $task.cpus
+            -CPUs ${task.cpus}
 
-        mkdir $prefix
-        mv ${prefix}.* $prefix
-
-        cat <<-END_VERSIONS > versions.yml
-        "${task.process}":
-            phyloflash: \$(echo \$(phyloFlash.pl -version 2>&1) | sed "s/^.*phyloFlash v//")
-        END_VERSIONS
+        mkdir ${prefix}
+        mv ${prefix}.* ${prefix}
         """
     } else {
         """
         phyloFlash.pl \\
-            $args \\
+            ${args} \\
             -read1 ${reads[0]} \\
             -read2 ${reads[1]} \\
-            -lib $prefix \\
+            -lib ${prefix} \\
             -dbhome . \\
-            -CPUs $task.cpus
-
-        mkdir $prefix
-        mv ${prefix}.* $prefix
+            -CPUs ${task.cpus}
 
-        cat <<-END_VERSIONS > versions.yml
-        "${task.process}":
-            phyloflash: \$(echo \$(phyloFlash.pl -version 2>&1) | sed "s/^.*phyloFlash v//")
-        END_VERSIONS
+        mkdir ${prefix}
+        mv ${prefix}.* ${prefix}
         """
     }
 
@@ -66,10 +56,5 @@ process PHYLOFLASH {
     mkdir ${prefix}
     touch ${prefix}/${prefix}.SSU.collection.fasta
     touch ${prefix}/${prefix}.phyloFlash
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        phyloflash: \$(echo \$(phyloFlash.pl -version 2>&1) | sed "s/^.*phyloFlash v//")
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/phyloflash/meta.yml b/modules/nf-core/phyloflash/meta.yml
index 46b4cb106374..0a3d370ef383 100644
--- a/modules/nf-core/phyloflash/meta.yml
+++ b/modules/nf-core/phyloflash/meta.yml
@@ -1,19 +1,18 @@
 name: phyloflash
-description: phyloFlash is a pipeline to rapidly reconstruct the SSU rRNAs and explore
-  phylogenetic composition of an illumina (meta)genomic dataset.
+description: phyloFlash is a pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset.
 keywords:
   - metagenomics
   - illumina datasets
   - phylogenetic composition
 tools:
   - phyloflash:
-      description: phyloFlash is a pipeline to rapidly reconstruct the SSU rRNAs and
-        explore phylogenetic composition of an illumina (meta)genomic dataset.
+      description: phyloFlash is a pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset.
       homepage: https://hrgv.github.io/phyloFlash/
       documentation: https://hrgv.github.io/phyloFlash/usage.html
       tool_dev_url: https://github.com/HRGV/phyloFlash
       doi: "10.1128/mSystems.00920-20"
-      licence: ["GPL v3"]
+      licence:
+        - "GPL v3"
       identifier: biotools:phyloflash
 input:
   - - meta:
@@ -44,13 +43,29 @@ output:
           type: directory
           description: Folder containing the results of phyloFlash analysis
           pattern: "${prefix}*"
+  versions_phyloflash:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - phyloflash:
+          type: string
+          description: The name of the tool
+      - phyloFlash.pl -version 2>&1 | sed 's/^.*phyloFlash v//':
+          type: eval
+          description: The expression to obtain the version of the tool
+
+topics:
   versions:
-    - versions.yml:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
-        ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - phyloflash:
+          type: string
+          description: The name of the tool
+      - phyloFlash.pl -version 2>&1 | sed 's/^.*phyloFlash v//':
+          type: eval
+          description: The expression to obtain the version of the tool
+
 authors:
   - "@abhi18av"
 maintainers:
diff --git a/modules/nf-core/phyloflash/tests/main.nf.test b/modules/nf-core/phyloflash/tests/main.nf.test
index 4434aa3ffdc4..0fd5b120fe76 100644
--- a/modules/nf-core/phyloflash/tests/main.nf.test
+++ b/modules/nf-core/phyloflash/tests/main.nf.test
@@ -30,10 +30,7 @@ nextflow_process {
         then {
             assert process.success
             assertAll(
-                { assert snapshot(
-                    process.out,
-                    path(process.out.versions[0]).yaml
-                    ).match() }
+                { assert snapshot(sanitizeOutput(process.out)).match() }
             )
         }
     }
diff --git a/modules/nf-core/phyloflash/tests/main.nf.test.snap b/modules/nf-core/phyloflash/tests/main.nf.test.snap
index f38feaee041c..81979b3a1802 100644
--- a/modules/nf-core/phyloflash/tests/main.nf.test.snap
+++ b/modules/nf-core/phyloflash/tests/main.nf.test.snap
@@ -2,7 +2,7 @@
     "test_phyloflash_single_end -- stub": {
         "content": [
             {
-                "0": [
+                "results": [
                     [
                         {
                             "id": "test",
@@ -14,35 +14,19 @@
                         ]
                     ]
                 ],
-                "1": [
-                    "versions.yml:md5,4880b2dc7060ad23366127e99619a2af"
-                ],
-                "results": [
+                "versions_phyloflash": [
                     [
-                        {
-                            "id": "test",
-                            "single_end": true
-                        },
-                        [
-                            "test.SSU.collection.fasta:md5,d41d8cd98f00b204e9800998ecf8427e",
-                            "test.phyloFlash:md5,d41d8cd98f00b204e9800998ecf8427e"
-                        ]
+                        "PHYLOFLASH",
+                        "phyloflash",
+                        "3.4.2"
                     ]
-                ],
-                "versions": [
-                    "versions.yml:md5,4880b2dc7060ad23366127e99619a2af"
                 ]
-            },
-            {
-                "PHYLOFLASH": {
-                    "phyloflash": "3.4.2"
-                }
             }
         ],
+        "timestamp": "2026-08-04T16:21:31.167874643",
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.6"
-        },
-        "timestamp": "2025-05-14T12:18:39.919595406"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.6"
+        }
     }
 }
\ No newline at end of file

From 7bf32fa702c2529ee9522d0d02482330ace7ea7d Mon Sep 17 00:00:00 2001
From: Louis Le Nezet <louislenezet@gmail.com>
Date: Wed, 5 Aug 2026 17:32:11 +0200
Subject: [PATCH 02/15] Update env

---
 modules/nf-core/phyloflash/environment.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/modules/nf-core/phyloflash/environment.yml b/modules/nf-core/phyloflash/environment.yml
index baacf587e4b3..ec9d8f36388f 100644
--- a/modules/nf-core/phyloflash/environment.yml
+++ b/modules/nf-core/phyloflash/environment.yml
@@ -5,3 +5,4 @@ channels:
   - bioconda
 dependencies:
   - bioconda::phyloflash=3.4.2
+  - bioconda::spades=3.15.5=h5fb382e_3

From 37f4ec1bea23ac5c4f919b364bc05227c8000eb8 Mon Sep 17 00:00:00 2001
From: Louis Le Nezet <louislenezet@gmail.com>
Date: Wed, 5 Aug 2026 18:08:34 +0200
Subject: [PATCH 03/15] Update env

---
 modules/nf-core/phyloflash/environment.yml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/modules/nf-core/phyloflash/environment.yml b/modules/nf-core/phyloflash/environment.yml
index ec9d8f36388f..613d72b67346 100644
--- a/modules/nf-core/phyloflash/environment.yml
+++ b/modules/nf-core/phyloflash/environment.yml
@@ -4,5 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::phyloflash=3.4.2
-  - bioconda::spades=3.15.5=h5fb382e_3
+  - bioconda::phyloflash=3.4.2=hdfd78af_1

From a769fb1ce27c707af626bbf68d6cbb1808a5a3cd Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Louis=20Le=20N=C3=A9zet?=
 <58640615+LouisLeNezet@users.noreply.github.com>
Date: Wed, 5 Aug 2026 18:19:28 +0200
Subject: [PATCH 04/15] Update environment.yml

---
 modules/nf-core/phyloflash/environment.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/modules/nf-core/phyloflash/environment.yml b/modules/nf-core/phyloflash/environment.yml
index 613d72b67346..3163b0ea6325 100644
--- a/modules/nf-core/phyloflash/environment.yml
+++ b/modules/nf-core/phyloflash/environment.yml
@@ -5,3 +5,4 @@ channels:
   - bioconda
 dependencies:
   - bioconda::phyloflash=3.4.2=hdfd78af_1
+  - bioconda::spades-3.15.5-h95f258a_1

From e1cb7c40b5bf1d6d38673138180e664ffdc7966d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Louis=20Le=20N=C3=A9zet?=
 <58640615+LouisLeNezet@users.noreply.github.com>
Date: Wed, 5 Aug 2026 18:19:51 +0200
Subject: [PATCH 05/15] Update environment.yml

---
 modules/nf-core/phyloflash/environment.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/phyloflash/environment.yml b/modules/nf-core/phyloflash/environment.yml
index 3163b0ea6325..d69e455a2d69 100644
--- a/modules/nf-core/phyloflash/environment.yml
+++ b/modules/nf-core/phyloflash/environment.yml
@@ -5,4 +5,4 @@ channels:
   - bioconda
 dependencies:
   - bioconda::phyloflash=3.4.2=hdfd78af_1
-  - bioconda::spades-3.15.5-h95f258a_1
+  - bioconda::spades=3.15.5=h95f258a_3

From 4435bd394623142ff41ab25b4512d16ce264db15 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Louis=20Le=20N=C3=A9zet?=
 <58640615+LouisLeNezet@users.noreply.github.com>
Date: Wed, 5 Aug 2026 18:28:12 +0200
Subject: [PATCH 06/15] Apply suggestion from @LouisLeNezet

---
 modules/nf-core/phyloflash/environment.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/phyloflash/environment.yml b/modules/nf-core/phyloflash/environment.yml
index d69e455a2d69..479472e2530c 100644
--- a/modules/nf-core/phyloflash/environment.yml
+++ b/modules/nf-core/phyloflash/environment.yml
@@ -5,4 +5,4 @@ channels:
   - bioconda
 dependencies:
   - bioconda::phyloflash=3.4.2=hdfd78af_1
-  - bioconda::spades=3.15.5=h95f258a_3
+  - bioconda::spades=3.15.5=h5fb382e_3

From dc99e386d20e4f4e59519fe52f05e5e24caf253a Mon Sep 17 00:00:00 2001
From: Louis Le Nezet <louislenezet@gmail.com>
Date: Wed, 5 Aug 2026 18:56:27 +0200
Subject: [PATCH 07/15] Update env

---
 modules/nf-core/phyloflash/environment.yml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/phyloflash/environment.yml b/modules/nf-core/phyloflash/environment.yml
index 479472e2530c..8e40ccb54f4b 100644
--- a/modules/nf-core/phyloflash/environment.yml
+++ b/modules/nf-core/phyloflash/environment.yml
@@ -4,5 +4,6 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::phyloflash=3.4.2=hdfd78af_1
-  - bioconda::spades=3.15.5=h5fb382e_3
+  - bioconda::phyloflash=3.4.2
+  - bioconda::spades=3.15.5
+  - conda-forge::zlib=1.2.13

From b9b07915ac4e9a11db3cd9e0a34e157f9cd24348 Mon Sep 17 00:00:00 2001
From: Louis Le Nezet <louislenezet@gmail.com>
Date: Thu, 6 Aug 2026 10:32:43 +0200
Subject: [PATCH 08/15] Update env

---
 .github/actions/nf-test-action/action.yml  | 10 +++++++++-
 modules/nf-core/phyloflash/environment.yml |  2 --
 modules/nf-core/phyloflash/main.nf         |  4 ++--
 3 files changed, 11 insertions(+), 5 deletions(-)

diff --git a/.github/actions/nf-test-action/action.yml b/.github/actions/nf-test-action/action.yml
index 50649124cc81..51099b3d541e 100644
--- a/.github/actions/nf-test-action/action.yml
+++ b/.github/actions/nf-test-action/action.yml
@@ -58,10 +58,18 @@ runs:
       if: ${{contains(inputs.profile, 'conda')}}
       uses: conda-incubator/setup-miniconda@8ee1f361103df19b6f8c8655fd3967a8ecb162d5 # v4
       with:
-        auto-update-conda: true
+        auto-update-conda: false
         conda-solver: libmamba
         conda-remove-defaults: true
 
+    - name: Debug conda
+      shell: bash
+      run: |
+        conda --version
+        mamba --version || true
+        conda info
+        conda config --show
+
     # Set up secrets
     - name: Set up Nextflow secrets
       if: env.SENTIEON_ENCRYPTION_KEY != '' && env.SENTIEON_LICENSE_MESSAGE != ''
diff --git a/modules/nf-core/phyloflash/environment.yml b/modules/nf-core/phyloflash/environment.yml
index 8e40ccb54f4b..baacf587e4b3 100644
--- a/modules/nf-core/phyloflash/environment.yml
+++ b/modules/nf-core/phyloflash/environment.yml
@@ -5,5 +5,3 @@ channels:
   - bioconda
 dependencies:
   - bioconda::phyloflash=3.4.2
-  - bioconda::spades=3.15.5
-  - conda-forge::zlib=1.2.13
diff --git a/modules/nf-core/phyloflash/main.nf b/modules/nf-core/phyloflash/main.nf
index 7e86e740245e..3e47ed1a3fb9 100644
--- a/modules/nf-core/phyloflash/main.nf
+++ b/modules/nf-core/phyloflash/main.nf
@@ -4,8 +4,8 @@ process PHYLOFLASH {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/phyloflash:3.4.2--hdfd78af_1' :
-        'quay.io/biocontainers/phyloflash:3.4.2--hdfd78af_1' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/d9/d993344c3f636cb0cca9519b11fcf30faafb13fca2fd33090104e5f52d8fd643/data' :
+        'community.wave.seqera.io/library/phyloflash:3.4.2--87628969a9477d43' }"
 
     input:
     tuple val(meta), path(reads)

From 278130bc1550fc157952a02bde161f0f6e2a3aee Mon Sep 17 00:00:00 2001
From: Louis Le Nezet <louislenezet@gmail.com>
Date: Thu, 6 Aug 2026 11:23:50 +0200
Subject: [PATCH 09/15] Add debugging step

---
 .github/actions/nf-test-action/action.yml | 33 +++++++++++++++++++++++
 1 file changed, 33 insertions(+)

diff --git a/.github/actions/nf-test-action/action.yml b/.github/actions/nf-test-action/action.yml
index 51099b3d541e..7f8d391db3d9 100644
--- a/.github/actions/nf-test-action/action.yml
+++ b/.github/actions/nf-test-action/action.yml
@@ -78,6 +78,22 @@ runs:
         python -m pip install cryptography
         nextflow secrets set SENTIEON_AUTH_DATA $(python3 modules/nf-core/sentieon/license_message.py encrypt --key "$SENTIEON_ENCRYPTION_KEY" --message "$SENTIEON_LICENSE_MESSAGE")
 
+    - name: Debug shell environment
+      if: ${{ contains(inputs.profile, 'conda') }}
+      shell: bash
+      run: |
+        echo "=== Shell options ==="
+        set -o
+        echo
+        echo "=== SHELLOPTS ==="
+        echo "$SHELLOPTS"
+        echo
+        echo "=== BASHOPTS ==="
+        echo "$BASHOPTS"
+        echo
+        echo "=== Conda ==="
+        conda info
+
       # TODO Skip failing conda tests and document their failures
       # https://github.com/nf-core/modules/issues/7017
     - name: Run nf-test
@@ -103,6 +119,23 @@ runs:
           # Save the absolute path of the test.tap file to the output
           echo "tap_file_path=$(realpath test.tap)" >> $GITHUB_OUTPUT
 
+    - name: Inspect failed conda environment
+      if: failure()
+      shell: bash
+      run: |
+        ENV_DIR=$(find . -type d -name "env-*" | head -n1)
+
+        echo "Environment: $ENV_DIR"
+
+        if [ -n "$ENV_DIR" ]; then
+          SCRIPT="$ENV_DIR/etc/conda/deactivate.d/deactivate-gxx_linux-64.sh"
+
+          if [ -f "$SCRIPT" ]; then
+            echo "===== $SCRIPT ====="
+            nl -ba "$SCRIPT" | sed -n '55,80p'
+          fi
+        fi
+
     - name: Generate test summary
       if: ${{ failure() && steps.run-nf-test.conclusion == 'failure' }}
       shell: bash

From aef81e84d08457814da421262d803e3d4e50eba8 Mon Sep 17 00:00:00 2001
From: Louis Le Nezet <louislenezet@gmail.com>
Date: Thu, 6 Aug 2026 11:37:53 +0200
Subject: [PATCH 10/15] Add debugging step

---
 .github/actions/nf-test-action/action.yml | 30 +++--------------------
 1 file changed, 4 insertions(+), 26 deletions(-)

diff --git a/.github/actions/nf-test-action/action.yml b/.github/actions/nf-test-action/action.yml
index 7f8d391db3d9..212fd5a5e6bb 100644
--- a/.github/actions/nf-test-action/action.yml
+++ b/.github/actions/nf-test-action/action.yml
@@ -58,18 +58,10 @@ runs:
       if: ${{contains(inputs.profile, 'conda')}}
       uses: conda-incubator/setup-miniconda@8ee1f361103df19b6f8c8655fd3967a8ecb162d5 # v4
       with:
-        auto-update-conda: false
+        auto-update-conda: true
         conda-solver: libmamba
         conda-remove-defaults: true
 
-    - name: Debug conda
-      shell: bash
-      run: |
-        conda --version
-        mamba --version || true
-        conda info
-        conda config --show
-
     # Set up secrets
     - name: Set up Nextflow secrets
       if: env.SENTIEON_ENCRYPTION_KEY != '' && env.SENTIEON_LICENSE_MESSAGE != ''
@@ -78,31 +70,17 @@ runs:
         python -m pip install cryptography
         nextflow secrets set SENTIEON_AUTH_DATA $(python3 modules/nf-core/sentieon/license_message.py encrypt --key "$SENTIEON_ENCRYPTION_KEY" --message "$SENTIEON_LICENSE_MESSAGE")
 
-    - name: Debug shell environment
-      if: ${{ contains(inputs.profile, 'conda') }}
-      shell: bash
-      run: |
-        echo "=== Shell options ==="
-        set -o
-        echo
-        echo "=== SHELLOPTS ==="
-        echo "$SHELLOPTS"
-        echo
-        echo "=== BASHOPTS ==="
-        echo "$BASHOPTS"
-        echo
-        echo "=== Conda ==="
-        conda info
-
       # TODO Skip failing conda tests and document their failures
       # https://github.com/nf-core/modules/issues/7017
     - name: Run nf-test
       id: run-nf-test
-      shell: bash
+      shell: bash {0}
       env:
         SENTIEON_LICSRVR_IP: ${{ env.SENTIEON_LICSRVR_IP }}
         SENTIEON_AUTH_MECH: "GitHub Actions - token"
       run: |
+        set -e
+        set +u
         NFT_WORKDIR=~
         TAGS=$([ -n "${{ inputs.tags }}" ] && echo "--tag ${{ inputs.tags }}" || echo "")
 

From 397d5282e4aed4781f693bd284a603c435d2bb08 Mon Sep 17 00:00:00 2001
From: Louis Le Nezet <louislenezet@gmail.com>
Date: Thu, 6 Aug 2026 12:01:00 +0200
Subject: [PATCH 11/15] Add debugging step

---
 .github/actions/nf-test-action/action.yml | 33 +++++++++++------------
 1 file changed, 15 insertions(+), 18 deletions(-)

diff --git a/.github/actions/nf-test-action/action.yml b/.github/actions/nf-test-action/action.yml
index 212fd5a5e6bb..678f046f3f17 100644
--- a/.github/actions/nf-test-action/action.yml
+++ b/.github/actions/nf-test-action/action.yml
@@ -58,7 +58,7 @@ runs:
       if: ${{contains(inputs.profile, 'conda')}}
       uses: conda-incubator/setup-miniconda@8ee1f361103df19b6f8c8655fd3967a8ecb162d5 # v4
       with:
-        auto-update-conda: true
+        miniconda-version: "py312_24.11.1-0"
         conda-solver: libmamba
         conda-remove-defaults: true
 
@@ -70,6 +70,13 @@ runs:
         python -m pip install cryptography
         nextflow secrets set SENTIEON_AUTH_DATA $(python3 modules/nf-core/sentieon/license_message.py encrypt --key "$SENTIEON_ENCRYPTION_KEY" --message "$SENTIEON_LICENSE_MESSAGE")
 
+    - name: Configure conda to avoid broken compiler activation
+      if: ${{ contains(inputs.profile, 'conda') }}
+      shell: bash
+      run: |
+        conda config --set auto_activate_base false
+        conda config --set safety_checks warn
+
       # TODO Skip failing conda tests and document their failures
       # https://github.com/nf-core/modules/issues/7017
     - name: Run nf-test
@@ -84,6 +91,13 @@ runs:
         NFT_WORKDIR=~
         TAGS=$([ -n "${{ inputs.tags }}" ] && echo "--tag ${{ inputs.tags }}" || echo "")
 
+        export BASHOPTS=
+        export SHELLOPTS=
+
+        echo "SHELLOPTS=$SHELLOPTS"
+        set -o | grep nounset
+        env | grep BASH
+
         nf-test test \
           --profile=${{ inputs.profile }} \
           --tap=test.tap \
@@ -97,23 +111,6 @@ runs:
           # Save the absolute path of the test.tap file to the output
           echo "tap_file_path=$(realpath test.tap)" >> $GITHUB_OUTPUT
 
-    - name: Inspect failed conda environment
-      if: failure()
-      shell: bash
-      run: |
-        ENV_DIR=$(find . -type d -name "env-*" | head -n1)
-
-        echo "Environment: $ENV_DIR"
-
-        if [ -n "$ENV_DIR" ]; then
-          SCRIPT="$ENV_DIR/etc/conda/deactivate.d/deactivate-gxx_linux-64.sh"
-
-          if [ -f "$SCRIPT" ]; then
-            echo "===== $SCRIPT ====="
-            nl -ba "$SCRIPT" | sed -n '55,80p'
-          fi
-        fi
-
     - name: Generate test summary
       if: ${{ failure() && steps.run-nf-test.conclusion == 'failure' }}
       shell: bash

From bab411c2f2866c21a20fe6dc7ce53ee010be8306 Mon Sep 17 00:00:00 2001
From: Louis Le Nezet <louislenezet@gmail.com>
Date: Thu, 6 Aug 2026 12:05:23 +0200
Subject: [PATCH 12/15] Add debugging step

---
 .github/actions/nf-test-action/action.yml | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/.github/actions/nf-test-action/action.yml b/.github/actions/nf-test-action/action.yml
index 678f046f3f17..b42deaef4ce9 100644
--- a/.github/actions/nf-test-action/action.yml
+++ b/.github/actions/nf-test-action/action.yml
@@ -91,9 +91,6 @@ runs:
         NFT_WORKDIR=~
         TAGS=$([ -n "${{ inputs.tags }}" ] && echo "--tag ${{ inputs.tags }}" || echo "")
 
-        export BASHOPTS=
-        export SHELLOPTS=
-
         echo "SHELLOPTS=$SHELLOPTS"
         set -o | grep nounset
         env | grep BASH

From 7d1cf3f9c4b212c38a3933204c4ade800372d339 Mon Sep 17 00:00:00 2001
From: Louis Le Nezet <louislenezet@gmail.com>
Date: Thu, 6 Aug 2026 12:11:23 +0200
Subject: [PATCH 13/15] Add debugging step

---
 .github/actions/nf-test-action/action.yml | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/.github/actions/nf-test-action/action.yml b/.github/actions/nf-test-action/action.yml
index b42deaef4ce9..099bcc707eef 100644
--- a/.github/actions/nf-test-action/action.yml
+++ b/.github/actions/nf-test-action/action.yml
@@ -91,10 +91,6 @@ runs:
         NFT_WORKDIR=~
         TAGS=$([ -n "${{ inputs.tags }}" ] && echo "--tag ${{ inputs.tags }}" || echo "")
 
-        echo "SHELLOPTS=$SHELLOPTS"
-        set -o | grep nounset
-        env | grep BASH
-
         nf-test test \
           --profile=${{ inputs.profile }} \
           --tap=test.tap \

From ddca22ce774d44b033403f9ddffc1b082a7097c5 Mon Sep 17 00:00:00 2001
From: Louis Le Nezet <louislenezet@gmail.com>
Date: Thu, 6 Aug 2026 12:17:06 +0200
Subject: [PATCH 14/15] Remove debugging step

---
 .github/actions/nf-test-action/action.yml | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/.github/actions/nf-test-action/action.yml b/.github/actions/nf-test-action/action.yml
index 099bcc707eef..1d5a8a1d5dd0 100644
--- a/.github/actions/nf-test-action/action.yml
+++ b/.github/actions/nf-test-action/action.yml
@@ -81,13 +81,11 @@ runs:
       # https://github.com/nf-core/modules/issues/7017
     - name: Run nf-test
       id: run-nf-test
-      shell: bash {0}
+      shell: bash
       env:
         SENTIEON_LICSRVR_IP: ${{ env.SENTIEON_LICSRVR_IP }}
         SENTIEON_AUTH_MECH: "GitHub Actions - token"
       run: |
-        set -e
-        set +u
         NFT_WORKDIR=~
         TAGS=$([ -n "${{ inputs.tags }}" ] && echo "--tag ${{ inputs.tags }}" || echo "")
 

From 36b21d8c416ba8655a699a6ddb248cff3156f968 Mon Sep 17 00:00:00 2001
From: Louis Le Nezet <louislenezet@gmail.com>
Date: Thu, 6 Aug 2026 12:20:43 +0200
Subject: [PATCH 15/15] Remove debugging step

---
 .github/actions/nf-test-action/action.yml | 7 -------
 1 file changed, 7 deletions(-)

diff --git a/.github/actions/nf-test-action/action.yml b/.github/actions/nf-test-action/action.yml
index 1d5a8a1d5dd0..7a297b1c0bb7 100644
--- a/.github/actions/nf-test-action/action.yml
+++ b/.github/actions/nf-test-action/action.yml
@@ -70,13 +70,6 @@ runs:
         python -m pip install cryptography
         nextflow secrets set SENTIEON_AUTH_DATA $(python3 modules/nf-core/sentieon/license_message.py encrypt --key "$SENTIEON_ENCRYPTION_KEY" --message "$SENTIEON_LICENSE_MESSAGE")
 
-    - name: Configure conda to avoid broken compiler activation
-      if: ${{ contains(inputs.profile, 'conda') }}
-      shell: bash
-      run: |
-        conda config --set auto_activate_base false
-        conda config --set safety_checks warn
-
       # TODO Skip failing conda tests and document their failures
       # https://github.com/nf-core/modules/issues/7017
     - name: Run nf-test