From 83533409da603c1dca959296c63bbd510ff48b8a Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Tue, 6 Jun 2023 10:21:30 +0000
Subject: [PATCH 01/36] Update seqeralabs/action-tower-launch to v1.2.4

- Updates the Github action to v1.2.4
- Adds specific revision which no longer defaults to github.sha
- Saves the JSON log created per pipeline as artifact
---
 CHANGELOG.md                                              | 1 +
 .../pipeline-template/.github/workflows/awsfulltest.yml   | 8 ++++++--
 nf_core/pipeline-template/.github/workflows/awstest.yml   | 8 ++++++--
 3 files changed, 13 insertions(+), 4 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 2deeef5f6..a0584f3e3 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -12,6 +12,7 @@
 - Remove `aws_tower` profile ([#2287])(https://github.com/nf-core/tools/pull/2287)
 - Fixed the Slack report to include the pipeline name ([#2291](https://github.com/nf-core/tools/pull/2291))
 - Fix link in the MultiQC report to point to exact version of output docs ([#2298](https://github.com/nf-core/tools/pull/2298))
+- Updates seqeralabs/action-tower-launch to v1.2.4
 
 ### Download
 
diff --git a/nf_core/pipeline-template/.github/workflows/awsfulltest.yml b/nf_core/pipeline-template/.github/workflows/awsfulltest.yml
index 9511ea57b..de2fb535a 100644
--- a/nf_core/pipeline-template/.github/workflows/awsfulltest.yml
+++ b/nf_core/pipeline-template/.github/workflows/awsfulltest.yml
@@ -14,7 +14,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Launch workflow via tower
-        uses: seqeralabs/action-tower-launch@v1
+        uses: seqeralabs/action-tower-launch@v1.2.4
         # TODO nf-core: You can customise AWS full pipeline tests as required
         # Add full size test data (but still relatively small datasets for few samples)
         # on the `test_full.config` test runs with only one set of parameters {%- raw %}
@@ -22,13 +22,17 @@ jobs:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
           compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
+          revision: ${{ github.sha }}
           workdir: s3://${{ secrets.AWS_S3_BUCKET }}{% endraw %}/work/{{ short_name }}/{% raw %}work-${{ github.sha }}{% endraw %}
           parameters: |
             {
               "outdir": "s3://{% raw %}${{ secrets.AWS_S3_BUCKET }}{% endraw %}/{{ short_name }}/{% raw %}results-${{ github.sha }}{% endraw %}"
             }
           profiles: test_full
+
       - uses: actions/upload-artifact@v3
         with:
           name: Tower debug log file
-          path: tower_action_*.log
+          path: |
+            tower_action_*.log
+            tower_action_*.json
diff --git a/nf_core/pipeline-template/.github/workflows/awstest.yml b/nf_core/pipeline-template/.github/workflows/awstest.yml
index 6e1fd8c92..6e5a9a9e4 100644
--- a/nf_core/pipeline-template/.github/workflows/awstest.yml
+++ b/nf_core/pipeline-template/.github/workflows/awstest.yml
@@ -12,18 +12,22 @@ jobs:
     steps:
       # Launch workflow using Tower CLI tool action {%- raw %}
       - name: Launch workflow via tower
-        uses: seqeralabs/action-tower-launch@v1
+        uses: seqeralabs/action-tower-launch@v1.2.4
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
           compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
+          revision: ${{ github.sha }}
           workdir: s3://${{ secrets.AWS_S3_BUCKET }}{% endraw %}/work/{{ short_name }}/{% raw %}work-${{ github.sha }}{% endraw %}
           parameters: |
             {
               "outdir": "s3://{% raw %}${{ secrets.AWS_S3_BUCKET }}{% endraw %}/{{ short_name }}/{% raw %}results-test-${{ github.sha }}{% endraw %}"
             }
           profiles: test
+
       - uses: actions/upload-artifact@v3
         with:
           name: Tower debug log file
-          path: tower_action_*.log
+          path: |
+            tower_action_*.log
+            tower_action_*.json

From 410db78bf8fdddb8302256a5c08a5bbb5da60fe6 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Tue, 6 Jun 2023 15:33:47 +0000
Subject: [PATCH 02/36] Update action to v2.0.0 (breaking change)

---
 CHANGELOG.md                                                | 2 +-
 nf_core/pipeline-template/.github/workflows/awsfulltest.yml | 2 +-
 nf_core/pipeline-template/.github/workflows/awstest.yml     | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index a0584f3e3..8a1fb5ae2 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -12,7 +12,7 @@
 - Remove `aws_tower` profile ([#2287])(https://github.com/nf-core/tools/pull/2287)
 - Fixed the Slack report to include the pipeline name ([#2291](https://github.com/nf-core/tools/pull/2291))
 - Fix link in the MultiQC report to point to exact version of output docs ([#2298](https://github.com/nf-core/tools/pull/2298))
-- Updates seqeralabs/action-tower-launch to v1.2.4
+- Updates seqeralabs/action-tower-launch to v2.0.0 ([#2301](https://github.com/nf-core/tools/pull/2301))
 
 ### Download
 
diff --git a/nf_core/pipeline-template/.github/workflows/awsfulltest.yml b/nf_core/pipeline-template/.github/workflows/awsfulltest.yml
index de2fb535a..ebad00719 100644
--- a/nf_core/pipeline-template/.github/workflows/awsfulltest.yml
+++ b/nf_core/pipeline-template/.github/workflows/awsfulltest.yml
@@ -14,7 +14,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Launch workflow via tower
-        uses: seqeralabs/action-tower-launch@v1.2.4
+        uses: seqeralabs/action-tower-launch@v2.0.0
         # TODO nf-core: You can customise AWS full pipeline tests as required
         # Add full size test data (but still relatively small datasets for few samples)
         # on the `test_full.config` test runs with only one set of parameters {%- raw %}
diff --git a/nf_core/pipeline-template/.github/workflows/awstest.yml b/nf_core/pipeline-template/.github/workflows/awstest.yml
index 6e5a9a9e4..8819b7cca 100644
--- a/nf_core/pipeline-template/.github/workflows/awstest.yml
+++ b/nf_core/pipeline-template/.github/workflows/awstest.yml
@@ -12,7 +12,7 @@ jobs:
     steps:
       # Launch workflow using Tower CLI tool action {%- raw %}
       - name: Launch workflow via tower
-        uses: seqeralabs/action-tower-launch@v1.2.4
+        uses: seqeralabs/action-tower-launch@v2.0.0
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}

From e40580ba71445049caa786fb5b7d4dd639c8713b Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Thu, 8 Jun 2023 08:59:02 +0000
Subject: [PATCH 03/36] Reduce to shortened version of action-tower-launch
 version

---
 nf_core/pipeline-template/.github/workflows/awsfulltest.yml | 2 +-
 nf_core/pipeline-template/.github/workflows/awstest.yml     | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/nf_core/pipeline-template/.github/workflows/awsfulltest.yml b/nf_core/pipeline-template/.github/workflows/awsfulltest.yml
index ebad00719..1d5c53bda 100644
--- a/nf_core/pipeline-template/.github/workflows/awsfulltest.yml
+++ b/nf_core/pipeline-template/.github/workflows/awsfulltest.yml
@@ -14,7 +14,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Launch workflow via tower
-        uses: seqeralabs/action-tower-launch@v2.0.0
+        uses: seqeralabs/action-tower-launch@v2
         # TODO nf-core: You can customise AWS full pipeline tests as required
         # Add full size test data (but still relatively small datasets for few samples)
         # on the `test_full.config` test runs with only one set of parameters {%- raw %}
diff --git a/nf_core/pipeline-template/.github/workflows/awstest.yml b/nf_core/pipeline-template/.github/workflows/awstest.yml
index 8819b7cca..9a0bf4afb 100644
--- a/nf_core/pipeline-template/.github/workflows/awstest.yml
+++ b/nf_core/pipeline-template/.github/workflows/awstest.yml
@@ -12,7 +12,7 @@ jobs:
     steps:
       # Launch workflow using Tower CLI tool action {%- raw %}
       - name: Launch workflow via tower
-        uses: seqeralabs/action-tower-launch@v2.0.0
+        uses: seqeralabs/action-tower-launch@v2
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}

From d5b7bd220e96d030c891a307cbc30117a7bc1eca Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Thu, 8 Jun 2023 11:19:32 +0100
Subject: [PATCH 04/36] Add singularity.registry = 'quay.io' to pipeline
 template

---
 .github/ISSUE_TEMPLATE/bug_report.yml                      | 2 +-
 .github/workflows/create-lint-wf.yml                       | 2 +-
 .github/workflows/create-test-wf.yml                       | 2 +-
 CHANGELOG.md                                               | 2 ++
 nf_core/lint/readme.py                                     | 2 +-
 .../.github/ISSUE_TEMPLATE/bug_report.yml                  | 2 +-
 nf_core/pipeline-template/.github/workflows/ci.yml         | 2 +-
 nf_core/pipeline-template/README.md                        | 2 +-
 nf_core/pipeline-template/nextflow.config                  | 7 ++++---
 9 files changed, 13 insertions(+), 10 deletions(-)

diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml
index 1bd2e27fb..8fdd2bd7e 100644
--- a/.github/ISSUE_TEMPLATE/bug_report.yml
+++ b/.github/ISSUE_TEMPLATE/bug_report.yml
@@ -33,7 +33,7 @@ body:
     attributes:
       label: System information
       description: |
-        * Nextflow version _(eg. 22.10.1)_
+        * Nextflow version _(eg. 23.04.0)_
         * Hardware _(eg. HPC, Desktop, Cloud)_
         * Executor _(eg. slurm, local, awsbatch)_
         * OS _(eg. CentOS Linux, macOS, Linux Mint)_
diff --git a/.github/workflows/create-lint-wf.yml b/.github/workflows/create-lint-wf.yml
index 46152d92a..654d248f7 100644
--- a/.github/workflows/create-lint-wf.yml
+++ b/.github/workflows/create-lint-wf.yml
@@ -23,7 +23,7 @@ jobs:
     strategy:
       matrix:
         NXF_VER:
-          - "22.10.1"
+          - "23.04.0"
           - "latest-everything"
     steps:
       # Get the repo code
diff --git a/.github/workflows/create-test-wf.yml b/.github/workflows/create-test-wf.yml
index 8f3c5fdb4..7cff154a0 100644
--- a/.github/workflows/create-test-wf.yml
+++ b/.github/workflows/create-test-wf.yml
@@ -23,7 +23,7 @@ jobs:
     strategy:
       matrix:
         NXF_VER:
-          - "22.10.1"
+          - "23.04.0"
           - "latest-everything"
     steps:
       - uses: actions/checkout@v3
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 2deeef5f6..9572c9544 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -12,6 +12,8 @@
 - Remove `aws_tower` profile ([#2287])(https://github.com/nf-core/tools/pull/2287)
 - Fixed the Slack report to include the pipeline name ([#2291](https://github.com/nf-core/tools/pull/2291))
 - Fix link in the MultiQC report to point to exact version of output docs ([#2298](https://github.com/nf-core/tools/pull/2298))
+- Add `singularity.registry = 'quay.io'` in pipeline template
+- Bump minimum required NF version in pipeline template from `22.10.1` -> `23.04.0`
 
 ### Download
 
diff --git a/nf_core/lint/readme.py b/nf_core/lint/readme.py
index ae5c54283..55060442b 100644
--- a/nf_core/lint/readme.py
+++ b/nf_core/lint/readme.py
@@ -36,7 +36,7 @@ def readme(self):
 
     if "nextflow_badge" not in ignore_configs:
         # Check that there is a readme badge showing the minimum required version of Nextflow
-        # [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A522.10.1-23aa62.svg)](https://www.nextflow.io/)
+        # [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/)
         # and that it has the correct version
         nf_badge_re = r"\[!\[Nextflow\]\(https://img\.shields\.io/badge/nextflow%20DSL2-!?(?:%E2%89%A5|%3E%3D)([\d\.]+)-23aa62\.svg\)\]\(https://www\.nextflow\.io/\)"
         match = re.search(nf_badge_re, content)
diff --git a/nf_core/pipeline-template/.github/ISSUE_TEMPLATE/bug_report.yml b/nf_core/pipeline-template/.github/ISSUE_TEMPLATE/bug_report.yml
index f93cd55d5..063690f29 100644
--- a/nf_core/pipeline-template/.github/ISSUE_TEMPLATE/bug_report.yml
+++ b/nf_core/pipeline-template/.github/ISSUE_TEMPLATE/bug_report.yml
@@ -42,7 +42,7 @@ body:
     attributes:
       label: System information
       description: |
-        * Nextflow version _(eg. 22.10.1)_
+        * Nextflow version _(eg. 23.04.0)_
         * Hardware _(eg. HPC, Desktop, Cloud)_
         * Executor _(eg. slurm, local, awsbatch)_
         * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud, or Apptainer)_
diff --git a/nf_core/pipeline-template/.github/workflows/ci.yml b/nf_core/pipeline-template/.github/workflows/ci.yml
index bf3dc36bc..521f3e664 100644
--- a/nf_core/pipeline-template/.github/workflows/ci.yml
+++ b/nf_core/pipeline-template/.github/workflows/ci.yml
@@ -24,7 +24,7 @@ jobs:
     strategy:
       matrix:
         NXF_VER:
-          - "22.10.1"
+          - "23.04.0"
           - "latest-everything"
     steps:
       - name: Check out pipeline code
diff --git a/nf_core/pipeline-template/README.md b/nf_core/pipeline-template/README.md
index 5ac65123e..e66746dcd 100644
--- a/nf_core/pipeline-template/README.md
+++ b/nf_core/pipeline-template/README.md
@@ -10,7 +10,7 @@
 {%- if github_badges -%}
 [![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
 
-[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A522.10.1-23aa62.svg)](https://www.nextflow.io/)
+[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/)
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config
index 2650572c9..37137bb02 100644
--- a/nf_core/pipeline-template/nextflow.config
+++ b/nf_core/pipeline-template/nextflow.config
@@ -176,8 +176,9 @@ profiles {
 // Set default registry for Docker and Podman independent of -profile
 // Will not be used unless Docker / Podman are enabled
 // Set to your registry if you have a mirror of containers
-docker.registry = 'quay.io'
-podman.registry = 'quay.io'
+singularity.registry = 'quay.io'
+docker.registry      = 'quay.io'
+podman.registry      = 'quay.io'
 
 {% if igenomes %}
 // Load igenomes.config if required
@@ -226,7 +227,7 @@ manifest {
     homePage        = 'https://github.com/{{ name }}'
     description     = """{{ description }}"""
     mainScript      = 'main.nf'
-    nextflowVersion = '!>=22.10.1'
+    nextflowVersion = '!>=23.04.0'
     version         = '{{ version }}'
     doi             = ''
 }

From 114308419617c38654599d062d4befa2780f8840 Mon Sep 17 00:00:00 2001
From: Adam Talbot <adam.talbot@seqera.io>
Date: Thu, 8 Jun 2023 13:09:46 +0100
Subject: [PATCH 05/36] fix: Parsing of container directive

Changes:
  - Strip additional components off container directive prior to parsing
  - Helps parse additional strings that may be present at the front of
    container directive (e.g. 'container ').
  - Should catch more non-standard container directives (of which there
    are many).
---
 CHANGELOG.md                    | 1 +
 nf_core/modules/lint/main_nf.py | 8 ++++----
 2 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 2deeef5f6..d99229df9 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -12,6 +12,7 @@
 - Remove `aws_tower` profile ([#2287])(https://github.com/nf-core/tools/pull/2287)
 - Fixed the Slack report to include the pipeline name ([#2291](https://github.com/nf-core/tools/pull/2291))
 - Fix link in the MultiQC report to point to exact version of output docs ([#2298](https://github.com/nf-core/tools/pull/2298))
+- Fix parsing of container directive when it is not typical nf-core format.
 
 ### Download
 
diff --git a/nf_core/modules/lint/main_nf.py b/nf_core/modules/lint/main_nf.py
index 31b8adca3..cfbc2c4ad 100644
--- a/nf_core/modules/lint/main_nf.py
+++ b/nf_core/modules/lint/main_nf.py
@@ -240,7 +240,7 @@ def check_process_section(self, lines, fix_version, progress_bar):
     # Deprecated enable_conda
     for i, l in enumerate(lines):
         url = None
-        l = l.strip(" '\"")
+        l = l.strip().removeprefix("container ").strip(" \n'\"")
         if _container_type(l) == "conda":
             bioconda_packages = [b for b in l.split() if "bioconda::" in b]
             match = re.search(r"params\.enable_conda", l)
@@ -263,7 +263,7 @@ def check_process_section(self, lines, fix_version, progress_bar):
         if _container_type(l) == "singularity":
             # e.g. "https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' :" -> v1.2.0_cv1
             # e.g. "https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0' :" -> 0.11.9--0
-            match = re.search(r"(?:/)?(?:biocontainers_)?(?::)?([A-Za-z\d\-_.]+?)(?:\.img)?'", l)
+            match = re.search(r"(?:/)?(?:biocontainers_)?(?::)?([A-Za-z\d\-_.]+?)(?:\.img)?", l)
             if match is not None:
                 singularity_tag = match.group(1)
                 self.passed.append(("singularity_tag", f"Found singularity tag: {singularity_tag}", self.main_nf))
@@ -275,13 +275,13 @@ def check_process_section(self, lines, fix_version, progress_bar):
         if _container_type(l) == "docker":
             # e.g. "quay.io/biocontainers/krona:2.7.1--pl526_5' }" -> 2.7.1--pl526_5
             # e.g. "biocontainers/biocontainers:v1.2.0_cv1' }" -> v1.2.0_cv1
-            match = re.search(r"(?:[/])?(?::)?([A-Za-z\d\-_.]+)'", l)
+            match = re.search(r"(?:[/])?(?::)?([A-Za-z\d\-_.]+)", l)
             if match is not None:
                 docker_tag = match.group(1)
                 self.passed.append(("docker_tag", f"Found docker tag: {docker_tag}", self.main_nf))
             else:
                 self.failed.append(("docker_tag", "Unable to parse docker tag", self.main_nf))
-                docker_tag = NoneD
+                docker_tag = None
             if l.startswith("quay.io/"):
                 l_stripped = re.sub(r"\W+$", "", l)
                 self.failed.append(

From da476f2c76e28371ebe54eb54068369963848f95 Mon Sep 17 00:00:00 2001
From: Adam Talbot <adam.talbot@seqera.io>
Date: Thu, 8 Jun 2023 13:16:11 +0100
Subject: [PATCH 06/36] CHANGELOG

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

diff --git a/CHANGELOG.md b/CHANGELOG.md
index d99229df9..d6599be57 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -12,7 +12,7 @@
 - Remove `aws_tower` profile ([#2287])(https://github.com/nf-core/tools/pull/2287)
 - Fixed the Slack report to include the pipeline name ([#2291](https://github.com/nf-core/tools/pull/2291))
 - Fix link in the MultiQC report to point to exact version of output docs ([#2298](https://github.com/nf-core/tools/pull/2298))
-- Fix parsing of container directive when it is not typical nf-core format.
+- Fix parsing of container directive when it is not typical nf-core format ([#2306](https://github.com/nf-core/tools/pull/2306))
 
 ### Download
 

From c98848a8bb088e1d6c75759fe8444c165f118348 Mon Sep 17 00:00:00 2001
From: Adam Talbot <adam.talbot@seqera.io>
Date: Thu, 8 Jun 2023 13:59:10 +0100
Subject: [PATCH 07/36] Removed 'removeprefix' which is Py > 3.9 only

---
 nf_core/modules/lint/main_nf.py | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/nf_core/modules/lint/main_nf.py b/nf_core/modules/lint/main_nf.py
index cfbc2c4ad..c6ea2ed6c 100644
--- a/nf_core/modules/lint/main_nf.py
+++ b/nf_core/modules/lint/main_nf.py
@@ -240,7 +240,12 @@ def check_process_section(self, lines, fix_version, progress_bar):
     # Deprecated enable_conda
     for i, l in enumerate(lines):
         url = None
-        l = l.strip().removeprefix("container ").strip(" \n'\"")
+        l = l.strip(" \n'\"")
+
+        # Catch preceeding "container "
+        if l.startswith("container"):
+            l = l.replace("container", "").strip(" \n'\"")
+
         if _container_type(l) == "conda":
             bioconda_packages = [b for b in l.split() if "bioconda::" in b]
             match = re.search(r"params\.enable_conda", l)

From 8fe15ea2301c9d391ffcfd46957b3abb392dfe5c Mon Sep 17 00:00:00 2001
From: Adam Talbot <adam.talbot@seqera.io>
Date: Thu, 8 Jun 2023 16:52:52 +0100
Subject: [PATCH 08/36] Use specific Nextflow + nf-amazon version to get check
 if tests pass

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

diff --git a/.github/workflows/create-test-wf.yml b/.github/workflows/create-test-wf.yml
index 8f3c5fdb4..d52fa2230 100644
--- a/.github/workflows/create-test-wf.yml
+++ b/.github/workflows/create-test-wf.yml
@@ -23,8 +23,7 @@ jobs:
     strategy:
       matrix:
         NXF_VER:
-          - "22.10.1"
-          - "latest-everything"
+          - "23.04.1"
     steps:
       - uses: actions/checkout@v3
         name: Check out source-code repository
@@ -47,7 +46,7 @@ jobs:
       - name: Run nf-core/tools
         run: |
           nf-core --log-file log.txt create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface" --plain
-          nextflow run nf-core-testpipeline -profile test,docker --outdir ./results
+          nextflow run nf-core-testpipeline -profile test,docker --outdir ./results -plugins nf-amazon@1.16.2
 
       - name: Upload log file artifact
         if: ${{ always() }}

From d24652af1f7e9dd657bfe0d68b4b637b0c2125b9 Mon Sep 17 00:00:00 2001
From: Adam Talbot <adam.talbot@seqera.io>
Date: Thu, 8 Jun 2023 16:52:52 +0100
Subject: [PATCH 09/36] Use specific Nextflow + nf-amazon version to get check
 if tests pass

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

diff --git a/.github/workflows/create-test-wf.yml b/.github/workflows/create-test-wf.yml
index 8f3c5fdb4..d52fa2230 100644
--- a/.github/workflows/create-test-wf.yml
+++ b/.github/workflows/create-test-wf.yml
@@ -23,8 +23,7 @@ jobs:
     strategy:
       matrix:
         NXF_VER:
-          - "22.10.1"
-          - "latest-everything"
+          - "23.04.1"
     steps:
       - uses: actions/checkout@v3
         name: Check out source-code repository
@@ -47,7 +46,7 @@ jobs:
       - name: Run nf-core/tools
         run: |
           nf-core --log-file log.txt create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface" --plain
-          nextflow run nf-core-testpipeline -profile test,docker --outdir ./results
+          nextflow run nf-core-testpipeline -profile test,docker --outdir ./results -plugins nf-amazon@1.16.2
 
       - name: Upload log file artifact
         if: ${{ always() }}

From b4f86d5bd9c052b6edde8bd2f3604dcd1c95a9f0 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelh@users.noreply.github.com>
Date: Thu, 8 Jun 2023 19:55:50 +0100
Subject: [PATCH 10/36] Update create-test-wf.yml

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

diff --git a/.github/workflows/create-test-wf.yml b/.github/workflows/create-test-wf.yml
index d52fa2230..8f3c5fdb4 100644
--- a/.github/workflows/create-test-wf.yml
+++ b/.github/workflows/create-test-wf.yml
@@ -23,7 +23,8 @@ jobs:
     strategy:
       matrix:
         NXF_VER:
-          - "23.04.1"
+          - "22.10.1"
+          - "latest-everything"
     steps:
       - uses: actions/checkout@v3
         name: Check out source-code repository
@@ -46,7 +47,7 @@ jobs:
       - name: Run nf-core/tools
         run: |
           nf-core --log-file log.txt create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface" --plain
-          nextflow run nf-core-testpipeline -profile test,docker --outdir ./results -plugins nf-amazon@1.16.2
+          nextflow run nf-core-testpipeline -profile test,docker --outdir ./results
 
       - name: Upload log file artifact
         if: ${{ always() }}

From 51882b2559ed06fe7c9321ff7c0601e1ee8240cc Mon Sep 17 00:00:00 2001
From: Adam Talbot <adam.talbot@seqera.io>
Date: Fri, 9 Jun 2023 09:19:05 +0100
Subject: [PATCH 11/36] Revert "Use specific Nextflow + nf-amazon version to
 get check if tests pass"

This reverts commit d24652af1f7e9dd657bfe0d68b4b637b0c2125b9.
---
 .github/workflows/create-test-wf.yml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/create-test-wf.yml b/.github/workflows/create-test-wf.yml
index d52fa2230..8f3c5fdb4 100644
--- a/.github/workflows/create-test-wf.yml
+++ b/.github/workflows/create-test-wf.yml
@@ -23,7 +23,8 @@ jobs:
     strategy:
       matrix:
         NXF_VER:
-          - "23.04.1"
+          - "22.10.1"
+          - "latest-everything"
     steps:
       - uses: actions/checkout@v3
         name: Check out source-code repository
@@ -46,7 +47,7 @@ jobs:
       - name: Run nf-core/tools
         run: |
           nf-core --log-file log.txt create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface" --plain
-          nextflow run nf-core-testpipeline -profile test,docker --outdir ./results -plugins nf-amazon@1.16.2
+          nextflow run nf-core-testpipeline -profile test,docker --outdir ./results
 
       - name: Upload log file artifact
         if: ${{ always() }}

From 446a6e5fab4761c778bcf008a513b56ede5b9dce Mon Sep 17 00:00:00 2001
From: Adam Talbot <adam.talbot@seqera.io>
Date: Fri, 9 Jun 2023 12:11:47 +0100
Subject: [PATCH 12/36] Fix regex for containers

---
 nf_core/modules/lint/main_nf.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/nf_core/modules/lint/main_nf.py b/nf_core/modules/lint/main_nf.py
index c6ea2ed6c..5025fa039 100644
--- a/nf_core/modules/lint/main_nf.py
+++ b/nf_core/modules/lint/main_nf.py
@@ -268,7 +268,7 @@ def check_process_section(self, lines, fix_version, progress_bar):
         if _container_type(l) == "singularity":
             # e.g. "https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' :" -> v1.2.0_cv1
             # e.g. "https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0' :" -> 0.11.9--0
-            match = re.search(r"(?:/)?(?:biocontainers_)?(?::)?([A-Za-z\d\-_.]+?)(?:\.img)?", l)
+            match = re.search(r"(?:/)?(?:biocontainers_)?(?::)?([A-Za-z\d\-_.]+?)(?:\.img)'", l)
             if match is not None:
                 singularity_tag = match.group(1)
                 self.passed.append(("singularity_tag", f"Found singularity tag: {singularity_tag}", self.main_nf))
@@ -280,7 +280,7 @@ def check_process_section(self, lines, fix_version, progress_bar):
         if _container_type(l) == "docker":
             # e.g. "quay.io/biocontainers/krona:2.7.1--pl526_5' }" -> 2.7.1--pl526_5
             # e.g. "biocontainers/biocontainers:v1.2.0_cv1' }" -> v1.2.0_cv1
-            match = re.search(r"(?:[/])?(?::)?([A-Za-z\d\-_.]+)", l)
+            match = re.search(r"(?:[/])?(?::)?([A-Za-z\d\-_.]+)'", l)
             if match is not None:
                 docker_tag = match.group(1)
                 self.passed.append(("docker_tag", f"Found docker tag: {docker_tag}", self.main_nf))

From 32fa7707498e6073211a85947d3f70de406520df Mon Sep 17 00:00:00 2001
From: Adam Talbot <adam.talbot@seqera.io>
Date: Fri, 9 Jun 2023 12:28:05 +0100
Subject: [PATCH 13/36] Fix parsing of tags so they should match in most
 situations

---
 nf_core/modules/lint/main_nf.py | 11 ++++-------
 1 file changed, 4 insertions(+), 7 deletions(-)

diff --git a/nf_core/modules/lint/main_nf.py b/nf_core/modules/lint/main_nf.py
index 5025fa039..08645f56b 100644
--- a/nf_core/modules/lint/main_nf.py
+++ b/nf_core/modules/lint/main_nf.py
@@ -222,9 +222,6 @@ def check_process_section(self, lines, fix_version, progress_bar):
         return
     self.passed.append(("process_exist", "Process definition exists", self.main_nf))
 
-    # Checks that build numbers of bioconda, singularity and docker container are matching
-    singularity_tag = "singularity"
-    docker_tag = "docker"
     bioconda_packages = []
 
     # Process name should be all capital letters
@@ -240,11 +237,11 @@ def check_process_section(self, lines, fix_version, progress_bar):
     # Deprecated enable_conda
     for i, l in enumerate(lines):
         url = None
-        l = l.strip(" \n'\"")
+        l = l.strip(" \n'\"}:")
 
         # Catch preceeding "container "
         if l.startswith("container"):
-            l = l.replace("container", "").strip(" \n'\"")
+            l = l.replace("container", "").strip(": \n'\"}")
 
         if _container_type(l) == "conda":
             bioconda_packages = [b for b in l.split() if "bioconda::" in b]
@@ -268,7 +265,7 @@ def check_process_section(self, lines, fix_version, progress_bar):
         if _container_type(l) == "singularity":
             # e.g. "https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' :" -> v1.2.0_cv1
             # e.g. "https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0' :" -> 0.11.9--0
-            match = re.search(r"(?:/)?(?:biocontainers_)?(?::)?([A-Za-z\d\-_.]+?)(?:\.img)'", l)
+            match = re.search(r":([A-Za-z\d\-_.]+)$", l)
             if match is not None:
                 singularity_tag = match.group(1)
                 self.passed.append(("singularity_tag", f"Found singularity tag: {singularity_tag}", self.main_nf))
@@ -280,7 +277,7 @@ def check_process_section(self, lines, fix_version, progress_bar):
         if _container_type(l) == "docker":
             # e.g. "quay.io/biocontainers/krona:2.7.1--pl526_5' }" -> 2.7.1--pl526_5
             # e.g. "biocontainers/biocontainers:v1.2.0_cv1' }" -> v1.2.0_cv1
-            match = re.search(r"(?:[/])?(?::)?([A-Za-z\d\-_.]+)'", l)
+            match = re.search(r":([A-Za-z\d\-_.]+)$", l)
             if match is not None:
                 docker_tag = match.group(1)
                 self.passed.append(("docker_tag", f"Found docker tag: {docker_tag}", self.main_nf))

From 90dc179cdd00097c9be1fbad4e587329a5f14eae Mon Sep 17 00:00:00 2001
From: Adam Talbot <adam.talbot@seqera.io>
Date: Fri, 9 Jun 2023 12:29:52 +0100
Subject: [PATCH 14/36] Match strip strings for consistency

---
 nf_core/modules/lint/main_nf.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nf_core/modules/lint/main_nf.py b/nf_core/modules/lint/main_nf.py
index 08645f56b..a31318d93 100644
--- a/nf_core/modules/lint/main_nf.py
+++ b/nf_core/modules/lint/main_nf.py
@@ -241,7 +241,7 @@ def check_process_section(self, lines, fix_version, progress_bar):
 
         # Catch preceeding "container "
         if l.startswith("container"):
-            l = l.replace("container", "").strip(": \n'\"}")
+            l = l.replace("container", "").strip(" \n'\"}:")
 
         if _container_type(l) == "conda":
             bioconda_packages = [b for b in l.split() if "bioconda::" in b]

From b6dbc8b8f2e061afde5fb310c21599f47a100610 Mon Sep 17 00:00:00 2001
From: Adam Talbot <adam.talbot@seqera.io>
Date: Fri, 9 Jun 2023 12:37:10 +0100
Subject: [PATCH 15/36] Revert setting docker_tag and singularity_tag

---
 nf_core/modules/lint/main_nf.py | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/nf_core/modules/lint/main_nf.py b/nf_core/modules/lint/main_nf.py
index a31318d93..85e1f9aa9 100644
--- a/nf_core/modules/lint/main_nf.py
+++ b/nf_core/modules/lint/main_nf.py
@@ -222,6 +222,11 @@ def check_process_section(self, lines, fix_version, progress_bar):
         return
     self.passed.append(("process_exist", "Process definition exists", self.main_nf))
 
+    # Checks that build numbers of bioconda, singularity and docker container are matching
+    singularity_tag = "singularity"
+    docker_tag = "docker"
+    bioconda_packages = []
+
     bioconda_packages = []
 
     # Process name should be all capital letters

From 56d1a994b08d3a0be581f089afb454abfc2334f0 Mon Sep 17 00:00:00 2001
From: Adam Talbot <adam.talbot@seqera.io>
Date: Fri, 9 Jun 2023 17:36:51 +0100
Subject: [PATCH 16/36] Fewer false positives for docker container names

---
 nf_core/modules/lint/main_nf.py | 14 ++++++++------
 1 file changed, 8 insertions(+), 6 deletions(-)

diff --git a/nf_core/modules/lint/main_nf.py b/nf_core/modules/lint/main_nf.py
index 85e1f9aa9..6f2d355a7 100644
--- a/nf_core/modules/lint/main_nf.py
+++ b/nf_core/modules/lint/main_nf.py
@@ -223,10 +223,8 @@ def check_process_section(self, lines, fix_version, progress_bar):
     self.passed.append(("process_exist", "Process definition exists", self.main_nf))
 
     # Checks that build numbers of bioconda, singularity and docker container are matching
-    singularity_tag = "singularity"
-    docker_tag = "docker"
-    bioconda_packages = []
-
+    singularity_tag = None
+    docker_tag = None
     bioconda_packages = []
 
     # Process name should be all capital letters
@@ -419,7 +417,11 @@ def check_process_section(self, lines, fix_version, progress_bar):
             else:
                 self.passed.append(("bioconda_latest", f"Conda package is the latest available: `{bp}`", self.main_nf))
 
-    return docker_tag == singularity_tag
+    # Check if a tag exists at all. If not, return None.
+    if singularity_tag is None or docker_tag is None:
+        return None
+    else:
+        return docker_tag == singularity_tag
 
 
 def check_process_labels(self, lines):
@@ -608,5 +610,5 @@ def _container_type(line):
         if url_match:
             return "singularity"
         return None
-    if line.count("/") >= 1 and line.count(":") == 1:
+    if line.count("/") >= 1 and line.count(":") == 1 and line.count(" ") == 0:
         return "docker"

From 1a04dfca1713e86ba503b7bba133b93c36809d55 Mon Sep 17 00:00:00 2001
From: Adam Talbot <adam.talbot@seqera.io>
Date: Fri, 9 Jun 2023 18:10:10 +0100
Subject: [PATCH 17/36] More singularity tag parsing

---
 nf_core/modules/lint/main_nf.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nf_core/modules/lint/main_nf.py b/nf_core/modules/lint/main_nf.py
index 6f2d355a7..bddf99a06 100644
--- a/nf_core/modules/lint/main_nf.py
+++ b/nf_core/modules/lint/main_nf.py
@@ -268,7 +268,7 @@ def check_process_section(self, lines, fix_version, progress_bar):
         if _container_type(l) == "singularity":
             # e.g. "https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' :" -> v1.2.0_cv1
             # e.g. "https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0' :" -> 0.11.9--0
-            match = re.search(r":([A-Za-z\d\-_.]+)$", l)
+            match = re.search(r"(?::)?([A-Za-z\d\-_.]+?)(?:\.img)?(?:\.sif)?$", l)
             if match is not None:
                 singularity_tag = match.group(1)
                 self.passed.append(("singularity_tag", f"Found singularity tag: {singularity_tag}", self.main_nf))

From 87144bfff9386b7c28b37f3687fcff87752ceabb Mon Sep 17 00:00:00 2001
From: Adam Talbot <adam.talbot@seqera.io>
Date: Mon, 12 Jun 2023 09:26:08 +0100
Subject: [PATCH 18/36] Update comment description of check_process_section
 where it extracts the container tag

---
 nf_core/modules/lint/main_nf.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/nf_core/modules/lint/main_nf.py b/nf_core/modules/lint/main_nf.py
index bddf99a06..d86566a6f 100644
--- a/nf_core/modules/lint/main_nf.py
+++ b/nf_core/modules/lint/main_nf.py
@@ -266,8 +266,8 @@ def check_process_section(self, lines, fix_version, progress_bar):
                     )
                 )
         if _container_type(l) == "singularity":
-            # e.g. "https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' :" -> v1.2.0_cv1
-            # e.g. "https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0' :" -> 0.11.9--0
+            # e.g. "https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img -> v1.2.0_cv1
+            # e.g. "https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0 -> 0.11.9--0
             match = re.search(r"(?::)?([A-Za-z\d\-_.]+?)(?:\.img)?(?:\.sif)?$", l)
             if match is not None:
                 singularity_tag = match.group(1)
@@ -278,8 +278,8 @@ def check_process_section(self, lines, fix_version, progress_bar):
             url = urlparse(l.split("'")[0])
 
         if _container_type(l) == "docker":
-            # e.g. "quay.io/biocontainers/krona:2.7.1--pl526_5' }" -> 2.7.1--pl526_5
-            # e.g. "biocontainers/biocontainers:v1.2.0_cv1' }" -> v1.2.0_cv1
+            # e.g. "quay.io/biocontainers/krona:2.7.1--pl526_5 -> 2.7.1--pl526_5
+            # e.g. "biocontainers/biocontainers:v1.2.0_cv1 -> v1.2.0_cv1
             match = re.search(r":([A-Za-z\d\-_.]+)$", l)
             if match is not None:
                 docker_tag = match.group(1)

From 6ef1fa3c5ed205510ca48467cbd56bd0a88d15e3 Mon Sep 17 00:00:00 2001
From: Adam Talbot <adam.talbot@seqera.io>
Date: Mon, 12 Jun 2023 10:06:12 +0100
Subject: [PATCH 19/36] Add period to singularity tag parsing

---
 nf_core/modules/lint/main_nf.py | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/nf_core/modules/lint/main_nf.py b/nf_core/modules/lint/main_nf.py
index d86566a6f..73d1df365 100644
--- a/nf_core/modules/lint/main_nf.py
+++ b/nf_core/modules/lint/main_nf.py
@@ -268,7 +268,8 @@ def check_process_section(self, lines, fix_version, progress_bar):
         if _container_type(l) == "singularity":
             # e.g. "https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img -> v1.2.0_cv1
             # e.g. "https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0 -> 0.11.9--0
-            match = re.search(r"(?::)?([A-Za-z\d\-_.]+?)(?:\.img)?(?:\.sif)?$", l)
+            # Please god let's find a better way to do this than regex
+            match = re.search(r"(?:[:.])?([A-Za-z\d\-_.]+?)(?:\.img)?(?:\.sif)?$", l)
             if match is not None:
                 singularity_tag = match.group(1)
                 self.passed.append(("singularity_tag", f"Found singularity tag: {singularity_tag}", self.main_nf))
@@ -600,7 +601,7 @@ def _container_type(line):
     """Returns the container type of a build."""
     if line.startswith("conda"):
         return "conda"
-    if line.startswith("https://containers") or line.startswith("https://depot"):
+    if line.startswith("https://") or line.startswith("https://depot"):
         # Look for a http download URL.
         # Thanks Stack Overflow for the regex: https://stackoverflow.com/a/3809435/713980
         url_regex = (
@@ -610,5 +611,5 @@ def _container_type(line):
         if url_match:
             return "singularity"
         return None
-    if line.count("/") >= 1 and line.count(":") == 1 and line.count(" ") == 0:
+    if line.count("/") >= 1 and line.count(":") == 1 and line.count(" ") == 0 and "https://" not in line:
         return "docker"

From 5d00842f9c4ffd97c1a846f0ce95324b5b02b702 Mon Sep 17 00:00:00 2001
From: Adam Talbot <adam.talbot@seqera.io>
Date: Fri, 9 Jun 2023 12:09:33 +0100
Subject: [PATCH 20/36] Add ability to select custom registry when linting
 modules

Changes:
 - Adds --registry parameter to nf-core modules lint
 - Will check container definition via this registry
 - Default to quay.io
---
 CHANGELOG.md                     |  1 +
 nf_core/__main__.py              |  6 +++++-
 nf_core/modules/lint/__init__.py | 16 +++++++++-------
 nf_core/modules/lint/main_nf.py  | 24 ++++++++++++++++--------
 tests/modules/lint.py            | 10 ++++++++++
 5 files changed, 41 insertions(+), 16 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index d6599be57..407e04ed4 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -13,6 +13,7 @@
 - Fixed the Slack report to include the pipeline name ([#2291](https://github.com/nf-core/tools/pull/2291))
 - Fix link in the MultiQC report to point to exact version of output docs ([#2298](https://github.com/nf-core/tools/pull/2298))
 - Fix parsing of container directive when it is not typical nf-core format ([#2306](https://github.com/nf-core/tools/pull/2306))
+- Add ability to specify custom registry for linting modules, defaults to quay.io
 
 ### Download
 
diff --git a/nf_core/__main__.py b/nf_core/__main__.py
index 6d6ded471..00fba3631 100644
--- a/nf_core/__main__.py
+++ b/nf_core/__main__.py
@@ -807,6 +807,9 @@ def create_test_yml(ctx, tool, run_tests, output, force, no_prompts):
 @click.pass_context
 @click.argument("tool", type=str, required=False, metavar="<tool> or <tool/subtool>")
 @click.option("-d", "--dir", type=click.Path(exists=True), default=".", metavar="<pipeline/modules directory>")
+@click.option(
+    "-r", "--registry", type=str, metavar="<registry>", default="quay.io", help="Registry to use for containers"
+)
 @click.option("-k", "--key", type=str, metavar="<test>", multiple=True, help="Run only these lint tests")
 @click.option("-a", "--all", is_flag=True, help="Run on all modules")
 @click.option("-w", "--fail-warned", is_flag=True, help="Convert warn tests to failures")
@@ -821,7 +824,7 @@ def create_test_yml(ctx, tool, run_tests, output, force, no_prompts):
 )
 @click.option("--fix-version", is_flag=True, help="Fix the module version if a newer version is available")
 def lint(
-    ctx, tool, dir, key, all, fail_warned, local, passed, sort_by, fix_version
+    ctx, tool, dir, registry, key, all, fail_warned, local, passed, sort_by, fix_version
 ):  # pylint: disable=redefined-outer-name
     """
     Lint one or more modules in a directory.
@@ -846,6 +849,7 @@ def lint(
         )
         module_lint.lint(
             module=tool,
+            registry=registry,
             key=key,
             all_modules=all,
             print_results=True,
diff --git a/nf_core/modules/lint/__init__.py b/nf_core/modules/lint/__init__.py
index 24d673b1c..f288f1776 100644
--- a/nf_core/modules/lint/__init__.py
+++ b/nf_core/modules/lint/__init__.py
@@ -145,6 +145,7 @@ def get_all_lint_tests(is_pipeline):
     def lint(
         self,
         module=None,
+        registry="quay.io",
         key=(),
         all_modules=False,
         print_results=True,
@@ -227,11 +228,11 @@ def lint(
 
         # Lint local modules
         if local and len(local_modules) > 0:
-            self.lint_modules(local_modules, local=True, fix_version=fix_version)
+            self.lint_modules(local_modules, registry=registry, local=True, fix_version=fix_version)
 
         # Lint nf-core modules
         if len(remote_modules) > 0:
-            self.lint_modules(remote_modules, local=False, fix_version=fix_version)
+            self.lint_modules(remote_modules, registry=registry, local=False, fix_version=fix_version)
 
         if print_results:
             self._print_results(show_passed=show_passed, sort_by=sort_by)
@@ -264,12 +265,13 @@ def filter_tests_by_key(self, key):
         # If -k supplied, only run these tests
         self.lint_tests = [k for k in self.lint_tests if k in key]
 
-    def lint_modules(self, modules, local=False, fix_version=False):
+    def lint_modules(self, modules, registry, local=False, fix_version=False):
         """
         Lint a list of modules
 
         Args:
             modules ([NFCoreModule]): A list of module objects
+            registry (str): The container registry to use. Should be quay.io in most situations.
             local (boolean): Whether the list consist of local or nf-core modules
             fix_version (boolean): Fix the module version if a newer version is available
         """
@@ -290,9 +292,9 @@ def lint_modules(self, modules, local=False, fix_version=False):
 
             for mod in modules:
                 progress_bar.update(lint_progress, advance=1, test_name=mod.module_name)
-                self.lint_module(mod, progress_bar, local=local, fix_version=fix_version)
+                self.lint_module(mod, progress_bar, registry=registry, local=local, fix_version=fix_version)
 
-    def lint_module(self, mod, progress_bar, local=False, fix_version=False):
+    def lint_module(self, mod, progress_bar, registry, local=False, fix_version=False):
         """
         Perform linting on one module
 
@@ -311,7 +313,7 @@ def lint_module(self, mod, progress_bar, local=False, fix_version=False):
 
         # Only check the main script in case of a local module
         if local:
-            self.main_nf(mod, fix_version, progress_bar)
+            self.main_nf(mod, fix_version, registry, progress_bar)
             self.passed += [LintResult(mod, *m) for m in mod.passed]
             warned = [LintResult(mod, *m) for m in (mod.warned + mod.failed)]
             if not self.fail_warned:
@@ -323,7 +325,7 @@ def lint_module(self, mod, progress_bar, local=False, fix_version=False):
         else:
             for test_name in self.lint_tests:
                 if test_name == "main_nf":
-                    getattr(self, test_name)(mod, fix_version, progress_bar)
+                    getattr(self, test_name)(mod, fix_version, registry, progress_bar)
                 else:
                     getattr(self, test_name)(mod)
 
diff --git a/nf_core/modules/lint/main_nf.py b/nf_core/modules/lint/main_nf.py
index 73d1df365..18d95bd37 100644
--- a/nf_core/modules/lint/main_nf.py
+++ b/nf_core/modules/lint/main_nf.py
@@ -17,7 +17,7 @@
 log = logging.getLogger(__name__)
 
 
-def main_nf(module_lint_object, module, fix_version, progress_bar):
+def main_nf(module_lint_object, module, fix_version, registry, progress_bar):
     """
     Lint a ``main.nf`` module file
 
@@ -121,7 +121,7 @@ def main_nf(module_lint_object, module, fix_version, progress_bar):
         module.passed.append(("main_nf_script_outputs", "Process 'output' block found", module.main_nf))
 
     # Check the process definitions
-    if check_process_section(module, process_lines, fix_version, progress_bar):
+    if check_process_section(module, process_lines, registry, fix_version, progress_bar):
         module.passed.append(("main_nf_container", "Container versions match", module.main_nf))
     else:
         module.warned.append(("main_nf_container", "Container versions do not match", module.main_nf))
@@ -209,12 +209,20 @@ def check_when_section(self, lines):
     self.passed.append(("when_condition", "when: condition is unchanged", self.main_nf))
 
 
-def check_process_section(self, lines, fix_version, progress_bar):
-    """
-    Lint the section of a module between the process definition
+def check_process_section(self, lines, registry, fix_version, progress_bar):
+    """Lint the section of a module between the process definition
     and the 'input:' definition
     Specifically checks for correct software versions
     and containers
+
+    Args:
+        lines (List[str]): Content of process.
+        registry (str): Base Docker registry for containers. Typically quay.io.
+        fix_version (bool): Fix software version
+        progress_bar (ProgressBar): Progress bar to update.
+
+    Returns:
+        Optional[bool]: True if singularity and docker containers match, False otherwise. If process definition does not exist, None.
     """
     # Check that we have a process section
     if len(lines) == 0:
@@ -288,7 +296,7 @@ def check_process_section(self, lines, fix_version, progress_bar):
             else:
                 self.failed.append(("docker_tag", "Unable to parse docker tag", self.main_nf))
                 docker_tag = None
-            if l.startswith("quay.io/"):
+            if l.startswith(registry):
                 l_stripped = re.sub(r"\W+$", "", l)
                 self.failed.append(
                     (
@@ -303,7 +311,7 @@ def check_process_section(self, lines, fix_version, progress_bar):
             # Guess if container name is simple one (e.g. nfcore/ubuntu:20.04)
             # If so, add quay.io as default container prefix
             if l.count("/") == 1 and l.count(":") == 1:
-                l = "quay.io/" + l
+                l = "/".join([registry, l]).replace("//", "/")
             url = urlparse(l.split("'")[0])
 
         # lint double quotes
@@ -326,7 +334,7 @@ def check_process_section(self, lines, fix_version, progress_bar):
                 )
 
         # lint more than one container in the same line
-        if ("https://containers" in l or "https://depot" in l) and ("biocontainers/" in l or "quay.io/" in l):
+        if ("https://containers" in l or "https://depot" in l) and ("biocontainers/" in l or l.startswith(registry)):
             self.warned.append(
                 (
                     "container_links",
diff --git a/tests/modules/lint.py b/tests/modules/lint.py
index b7aaf610c..8e692e8ca 100644
--- a/tests/modules/lint.py
+++ b/tests/modules/lint.py
@@ -82,6 +82,16 @@ def test_modules_lint_multiple_remotes(self):
     assert len(module_lint.warned) >= 0
 
 
+def test_modules_lint_registry(self):
+    """Test linting the TrimGalore! module"""
+    self.mods_install.install("samtools")
+    module_lint = nf_core.modules.ModuleLint(dir=self.pipeline_dir)
+    module_lint.lint(print_results=False, registry="public.ecr.aws", module="samtools")
+    assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
+    assert len(module_lint.passed) > 0
+    assert len(module_lint.warned) >= 0
+
+
 def test_modules_lint_patched_modules(self):
     """
     Test creating a patch file and applying it to a new version of the the files

From 9b70efb5d1ce2d64ac770bebdff8c4bef827d1ec Mon Sep 17 00:00:00 2001
From: Adam Talbot <adam.talbot@seqera.io>
Date: Mon, 12 Jun 2023 10:34:01 +0100
Subject: [PATCH 21/36] Quick test update

---
 tests/modules/lint.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/modules/lint.py b/tests/modules/lint.py
index 8e692e8ca..66da0019d 100644
--- a/tests/modules/lint.py
+++ b/tests/modules/lint.py
@@ -83,7 +83,7 @@ def test_modules_lint_multiple_remotes(self):
 
 
 def test_modules_lint_registry(self):
-    """Test linting the TrimGalore! module"""
+    """Test linting the samtools module and alternative registry"""
     self.mods_install.install("samtools")
     module_lint = nf_core.modules.ModuleLint(dir=self.pipeline_dir)
     module_lint.lint(print_results=False, registry="public.ecr.aws", module="samtools")

From 464f0f75856ecedf3776d45c4d11a2d6ef14d3d5 Mon Sep 17 00:00:00 2001
From: Adam Talbot <adam.talbot@seqera.io>
Date: Mon, 12 Jun 2023 11:04:02 +0100
Subject: [PATCH 22/36] CHANGELOG

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

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 407e04ed4..be0ab9828 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -13,7 +13,7 @@
 - Fixed the Slack report to include the pipeline name ([#2291](https://github.com/nf-core/tools/pull/2291))
 - Fix link in the MultiQC report to point to exact version of output docs ([#2298](https://github.com/nf-core/tools/pull/2298))
 - Fix parsing of container directive when it is not typical nf-core format ([#2306](https://github.com/nf-core/tools/pull/2306))
-- Add ability to specify custom registry for linting modules, defaults to quay.io
+- Add ability to specify custom registry for linting modules, defaults to quay.io ([#2313](https://github.com/nf-core/tools/pull/2313))
 
 ### Download
 

From 5e52513f701540c78828d0c769a445e658b4cd21 Mon Sep 17 00:00:00 2001
From: Adam Talbot <adam.talbot@seqera.io>
Date: Mon, 12 Jun 2023 11:04:30 +0100
Subject: [PATCH 23/36] Added 'quay.io' as default for lint_modules

---
 nf_core/modules/lint/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nf_core/modules/lint/__init__.py b/nf_core/modules/lint/__init__.py
index f288f1776..ba3b3d18f 100644
--- a/nf_core/modules/lint/__init__.py
+++ b/nf_core/modules/lint/__init__.py
@@ -265,7 +265,7 @@ def filter_tests_by_key(self, key):
         # If -k supplied, only run these tests
         self.lint_tests = [k for k in self.lint_tests if k in key]
 
-    def lint_modules(self, modules, registry, local=False, fix_version=False):
+    def lint_modules(self, modules, registry="quay.io", local=False, fix_version=False):
         """
         Lint a list of modules
 

From 4fe8a043d686199240e16dd393d050626ed846a7 Mon Sep 17 00:00:00 2001
From: Adam Talbot <adam.talbot@seqera.io>
Date: Mon, 12 Jun 2023 13:28:38 +0100
Subject: [PATCH 24/36] Add test for quay.io and public.aws.ecr explicitly for
 a direct comparison

---
 tests/modules/lint.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/tests/modules/lint.py b/tests/modules/lint.py
index 66da0019d..5b2c25080 100644
--- a/tests/modules/lint.py
+++ b/tests/modules/lint.py
@@ -90,6 +90,10 @@ def test_modules_lint_registry(self):
     assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
     assert len(module_lint.passed) > 0
     assert len(module_lint.warned) >= 0
+    module_lint.lint(print_results=False, registry="quay.io", module="samtools")
+    assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
+    assert len(module_lint.passed) > 0
+    assert len(module_lint.warned) >= 0
 
 
 def test_modules_lint_patched_modules(self):

From e5716819de7d959377ad29b048a686a156066475 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Mon, 12 Jun 2023 15:49:29 +0200
Subject: [PATCH 25/36] add docs to commit new files before pytest

---
 README.md | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/README.md b/README.md
index dacb50ebc..5d5791c10 100644
--- a/README.md
+++ b/README.md
@@ -941,6 +941,8 @@ before_command: sed 's/1.13a/1.10/g' modules/multiqc/main.nf > modules/multiqc/m
 
 To run unit tests of a module that you have installed or the test created by the command [`nf-core modules create-test-yml`](#create-a-module-test-config-file), you can use `nf-core modules test` command. This command runs the tests specified in `modules/tests/software/<tool>/<subtool>/test.yml` file using [pytest](https://pytest-workflow.readthedocs.io/en/stable/).
 
+> This command uses the pytest argument `--git-aware` to avoid copying the whole `.git` directory and files ignored by `git`. This means that it will only include files listed by `git ls-files`. Remember to **commit your changes** after adding a new module to add the new files to your git index.
+
 You can specify the module name in the form TOOL/SUBTOOL in command line or provide it later by prompts.
 
 <!-- RICH-CODEX
@@ -1199,6 +1201,8 @@ extra_env:
 
 To run unit tests of a subworkflow that you have installed or the test created by the command [`nf-core subworkflow create-test-yml`](#create-a-subworkflow-test-config-file), you can use `nf-core subworkflows test` command. This command runs the tests specified in `tests/subworkflows/<subworkflow_name>/test.yml` file using [pytest](https://pytest-workflow.readthedocs.io/en/stable/).
 
+> This command uses the pytest argument `--git-aware` to avoid copying the whole `.git` directory and files ignored by `git`. This means that it will only include files listed by `git ls-files`. Remember to **commit your changes** after adding a new subworkflow to add the new files to your git index.
+
 You can specify the subworkflow name in the form TOOL/SUBTOOL in command line or provide it later by prompts.
 
 <!-- RICH-CODEX

From 202ee4e9ba756fcae4fe3df1d4d0d9236b6f68a2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= <mirp.julia@gmail.com>
Date: Mon, 12 Jun 2023 14:32:43 +0000
Subject: [PATCH 26/36] check for uncommitted changes

---
 nf_core/components/components_test.py | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/nf_core/components/components_test.py b/nf_core/components/components_test.py
index c2b9abf56..b8a0d724c 100644
--- a/nf_core/components/components_test.py
+++ b/nf_core/components/components_test.py
@@ -7,6 +7,7 @@
 import pytest
 import questionary
 import rich
+from git import Repo
 
 import nf_core.modules.modules_utils
 import nf_core.utils
@@ -179,6 +180,11 @@ def _run_pytests(self):
         console = rich.console.Console()
         console.rule(self.component_name, style="black")
 
+        # Check uncommitted changed
+        repo = Repo(self.dir)
+        if repo.is_dirty():
+            log.warning("You have uncommitted changes. Make sure to commit last changes before running the tests.")
+
         # Set pytest arguments
         tag = self.component_name
         if self.component_type == "subworkflows":

From b4e8f823428eec9701e5496d06130ee0af72199e Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Tue, 13 Jun 2023 16:01:08 +0200
Subject: [PATCH 27/36] catch InvalidGitRepositoryError

---
 nf_core/components/components_test.py | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/nf_core/components/components_test.py b/nf_core/components/components_test.py
index b8a0d724c..37e275aea 100644
--- a/nf_core/components/components_test.py
+++ b/nf_core/components/components_test.py
@@ -7,7 +7,7 @@
 import pytest
 import questionary
 import rich
-from git import Repo
+from git import InvalidGitRepositoryError, Repo
 
 import nf_core.modules.modules_utils
 import nf_core.utils
@@ -181,9 +181,12 @@ def _run_pytests(self):
         console.rule(self.component_name, style="black")
 
         # Check uncommitted changed
-        repo = Repo(self.dir)
-        if repo.is_dirty():
-            log.warning("You have uncommitted changes. Make sure to commit last changes before running the tests.")
+        try:
+            repo = Repo(self.dir)
+            if repo.is_dirty():
+                log.warning("You have uncommitted changes. Make sure to commit last changes before running the tests.")
+        except InvalidGitRepositoryError:
+            pass
 
         # Set pytest arguments
         tag = self.component_name

From 0eb32e33ef08ab3067cee36b6f22cc18767375da Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Tue, 13 Jun 2023 17:28:13 +0200
Subject: [PATCH 28/36] remove params.tracedir as it doesn't renders properly
 in tower

---
 nf_core/pipeline-template/nextflow.config      | 9 ++++-----
 nf_core/pipeline-template/nextflow_schema.json | 7 -------
 2 files changed, 4 insertions(+), 12 deletions(-)

diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config
index f8aa90b4e..c8bd1dca0 100644
--- a/nf_core/pipeline-template/nextflow.config
+++ b/nf_core/pipeline-template/nextflow.config
@@ -29,7 +29,6 @@ params {
 
     // Boilerplate options
     outdir                     = null
-    tracedir                   = "${params.outdir}/pipeline_info"
     publish_dir_mode           = 'copy'
     email                      = null
     email_on_fail              = null
@@ -214,19 +213,19 @@ process.shell = ['/bin/bash', '-euo', 'pipefail']
 def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
 timeline {
     enabled = true
-    file    = "${params.tracedir}/execution_timeline_${trace_timestamp}.html"
+    file    = "${params.outdir}/pipeline_info/execution_timeline_${trace_timestamp}.html"
 }
 report {
     enabled = true
-    file    = "${params.tracedir}/execution_report_${trace_timestamp}.html"
+    file    = "${params.outdir}/pipeline_info/execution_report_${trace_timestamp}.html"
 }
 trace {
     enabled = true
-    file    = "${params.tracedir}/execution_trace_${trace_timestamp}.txt"
+    file    = "${params.outdir}/pipeline_info/execution_trace_${trace_timestamp}.txt"
 }
 dag {
     enabled = true
-    file    = "${params.tracedir}/pipeline_dag_${trace_timestamp}.html"
+    file    = "${params.outdir}/pipeline_info/pipeline_dag_${trace_timestamp}.html"
 }
 
 manifest {
diff --git a/nf_core/pipeline-template/nextflow_schema.json b/nf_core/pipeline-template/nextflow_schema.json
index c2509faca..319503c37 100644
--- a/nf_core/pipeline-template/nextflow_schema.json
+++ b/nf_core/pipeline-template/nextflow_schema.json
@@ -249,13 +249,6 @@
                     "description": "Custom MultiQC yaml file containing HTML including a methods description.",
                     "fa_icon": "fas fa-cog"
                 },
-                "tracedir": {
-                    "type": "string",
-                    "description": "Directory to keep pipeline Nextflow logs and reports.",
-                    "default": "${params.outdir}/pipeline_info",
-                    "fa_icon": "fas fa-cogs",
-                    "hidden": true
-                },
                 "validate_params": {
                     "type": "boolean",
                     "description": "Boolean whether to validate parameters against the schema at runtime",

From 6a2adc15c72c500fa3297a1553d633d2bffc3eb6 Mon Sep 17 00:00:00 2001
From: Adam Talbot <adam.talbot@seqera.io>
Date: Tue, 13 Jun 2023 16:42:06 +0100
Subject: [PATCH 29/36] feat (2311): Infer docker.registry value from
 nextflow.config

Fixes #2311
---
 CHANGELOG.md                     |  1 +
 nf_core/__main__.py              |  9 +++++++--
 nf_core/modules/lint/__init__.py | 27 ++++++++++++++++++---------
 nf_core/utils.py                 |  9 +++++++--
 4 files changed, 33 insertions(+), 13 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index be0ab9828..d95e84f0a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -14,6 +14,7 @@
 - Fix link in the MultiQC report to point to exact version of output docs ([#2298](https://github.com/nf-core/tools/pull/2298))
 - Fix parsing of container directive when it is not typical nf-core format ([#2306](https://github.com/nf-core/tools/pull/2306))
 - Add ability to specify custom registry for linting modules, defaults to quay.io ([#2313](https://github.com/nf-core/tools/pull/2313))
+- Add ability to interpret `docker.registry` from `nextflow.config` file. If not found defaults to quay.io.
 
 ### Download
 
diff --git a/nf_core/__main__.py b/nf_core/__main__.py
index 00fba3631..f531108b1 100644
--- a/nf_core/__main__.py
+++ b/nf_core/__main__.py
@@ -808,7 +808,12 @@ def create_test_yml(ctx, tool, run_tests, output, force, no_prompts):
 @click.argument("tool", type=str, required=False, metavar="<tool> or <tool/subtool>")
 @click.option("-d", "--dir", type=click.Path(exists=True), default=".", metavar="<pipeline/modules directory>")
 @click.option(
-    "-r", "--registry", type=str, metavar="<registry>", default="quay.io", help="Registry to use for containers"
+    "-r",
+    "--registry",
+    type=str,
+    metavar="<registry>",
+    default=None,
+    help="Registry to use for containers. If not specified will interpret it from nextflow.config file at attribute docker.registry",
 )
 @click.option("-k", "--key", type=str, metavar="<test>", multiple=True, help="Run only these lint tests")
 @click.option("-a", "--all", is_flag=True, help="Run on all modules")
@@ -842,6 +847,7 @@ def lint(
         module_lint = ModuleLint(
             dir,
             fail_warned=fail_warned,
+            registry=ctx.params["registry"],
             remote_url=ctx.obj["modules_repo_url"],
             branch=ctx.obj["modules_repo_branch"],
             no_pull=ctx.obj["modules_repo_no_pull"],
@@ -849,7 +855,6 @@ def lint(
         )
         module_lint.lint(
             module=tool,
-            registry=registry,
             key=key,
             all_modules=all,
             print_results=True,
diff --git a/nf_core/modules/lint/__init__.py b/nf_core/modules/lint/__init__.py
index ba3b3d18f..81ec32a6a 100644
--- a/nf_core/modules/lint/__init__.py
+++ b/nf_core/modules/lint/__init__.py
@@ -69,6 +69,7 @@ def __init__(
         remote_url=None,
         branch=None,
         no_pull=False,
+        registry=None,
         hide_progress=False,
     ):
         super().__init__(
@@ -114,6 +115,7 @@ def __init__(
                     )
                     for m in self.get_local_components()
                 ]
+            self.config = nf_core.utils.fetch_wf_config(self.dir, cache_config=True)
         else:
             module_dir = Path(self.dir, self.default_modules_path)
             self.all_remote_modules = [
@@ -124,6 +126,15 @@ def __init__(
             if not self.all_remote_modules:
                 raise LookupError("No modules in 'modules' directory")
 
+            # This could be better, perhaps glob for all nextflow.config files in?
+            self.config = nf_core.utils.fetch_wf_config(Path(self.dir).joinpath("tests", "config"), cache_config=True)
+
+        if registry is None:
+            self.registry = self.config.get("docker.registry", "quay.io")
+        else:
+            self.registry = registry
+        log.debug(f"Registry set to {self.registry}")
+
         self.lint_config = None
         self.modules_json = None
 
@@ -145,7 +156,6 @@ def get_all_lint_tests(is_pipeline):
     def lint(
         self,
         module=None,
-        registry="quay.io",
         key=(),
         all_modules=False,
         print_results=True,
@@ -228,11 +238,11 @@ def lint(
 
         # Lint local modules
         if local and len(local_modules) > 0:
-            self.lint_modules(local_modules, registry=registry, local=True, fix_version=fix_version)
+            self.lint_modules(local_modules, local=True, fix_version=fix_version)
 
         # Lint nf-core modules
         if len(remote_modules) > 0:
-            self.lint_modules(remote_modules, registry=registry, local=False, fix_version=fix_version)
+            self.lint_modules(remote_modules, local=False, fix_version=fix_version)
 
         if print_results:
             self._print_results(show_passed=show_passed, sort_by=sort_by)
@@ -265,13 +275,12 @@ def filter_tests_by_key(self, key):
         # If -k supplied, only run these tests
         self.lint_tests = [k for k in self.lint_tests if k in key]
 
-    def lint_modules(self, modules, registry="quay.io", local=False, fix_version=False):
+    def lint_modules(self, modules, local=False, fix_version=False):
         """
         Lint a list of modules
 
         Args:
             modules ([NFCoreModule]): A list of module objects
-            registry (str): The container registry to use. Should be quay.io in most situations.
             local (boolean): Whether the list consist of local or nf-core modules
             fix_version (boolean): Fix the module version if a newer version is available
         """
@@ -292,9 +301,9 @@ def lint_modules(self, modules, registry="quay.io", local=False, fix_version=Fal
 
             for mod in modules:
                 progress_bar.update(lint_progress, advance=1, test_name=mod.module_name)
-                self.lint_module(mod, progress_bar, registry=registry, local=local, fix_version=fix_version)
+                self.lint_module(mod, progress_bar, local=local, fix_version=fix_version)
 
-    def lint_module(self, mod, progress_bar, registry, local=False, fix_version=False):
+    def lint_module(self, mod, progress_bar, local=False, fix_version=False):
         """
         Perform linting on one module
 
@@ -313,7 +322,7 @@ def lint_module(self, mod, progress_bar, registry, local=False, fix_version=Fals
 
         # Only check the main script in case of a local module
         if local:
-            self.main_nf(mod, fix_version, registry, progress_bar)
+            self.main_nf(mod, fix_version, self.registry, progress_bar)
             self.passed += [LintResult(mod, *m) for m in mod.passed]
             warned = [LintResult(mod, *m) for m in (mod.warned + mod.failed)]
             if not self.fail_warned:
@@ -325,7 +334,7 @@ def lint_module(self, mod, progress_bar, registry, local=False, fix_version=Fals
         else:
             for test_name in self.lint_tests:
                 if test_name == "main_nf":
-                    getattr(self, test_name)(mod, fix_version, registry, progress_bar)
+                    getattr(self, test_name)(mod, fix_version, self.registry, progress_bar)
                 else:
                     getattr(self, test_name)(mod)
 
diff --git a/nf_core/utils.py b/nf_core/utils.py
index 3ddce9b87..3d72b7fcb 100644
--- a/nf_core/utils.py
+++ b/nf_core/utils.py
@@ -258,7 +258,7 @@ def fetch_wf_config(wf_path, cache_config=True):
 
     if cache_basedir and cache_fn:
         cache_path = os.path.join(cache_basedir, cache_fn)
-        if os.path.isfile(cache_path):
+        if os.path.isfile(cache_path) and cache_config is True:
             log.debug(f"Found a config cache, loading: {cache_path}")
             with open(cache_path, "r") as fh:
                 try:
@@ -274,7 +274,7 @@ def fetch_wf_config(wf_path, cache_config=True):
         ul = l.decode("utf-8")
         try:
             k, v = ul.split(" = ", 1)
-            config[k] = v
+            config[k] = v.strip("'\"")
         except ValueError:
             log.debug(f"Couldn't find key=value config pair:\n  {ul}")
 
@@ -303,6 +303,11 @@ def fetch_wf_config(wf_path, cache_config=True):
     return config
 
 
+def parse_nf_config(wf_path, cache_config=True):
+    config = fetch_wf_config(wf_path=wf_path, cache_config=True)
+    return config
+
+
 def nextflow_cmd(cmd):
     """Run a Nextflow command and capture the output. Handle errors nicely"""
     try:

From 5d16c043202082d33ac779e2a55f365501c1ea9b Mon Sep 17 00:00:00 2001
From: Adam Talbot <adam.talbot@seqera.io>
Date: Tue, 13 Jun 2023 16:51:57 +0100
Subject: [PATCH 30/36] Update test

---
 tests/modules/lint.py | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/tests/modules/lint.py b/tests/modules/lint.py
index 5b2c25080..d31f2c321 100644
--- a/tests/modules/lint.py
+++ b/tests/modules/lint.py
@@ -85,12 +85,13 @@ def test_modules_lint_multiple_remotes(self):
 def test_modules_lint_registry(self):
     """Test linting the samtools module and alternative registry"""
     self.mods_install.install("samtools")
-    module_lint = nf_core.modules.ModuleLint(dir=self.pipeline_dir)
-    module_lint.lint(print_results=False, registry="public.ecr.aws", module="samtools")
+    module_lint = nf_core.modules.ModuleLint(dir=self.pipeline_dir, registry="public.ecr.aws")
+    module_lint.lint(print_results=False, module="samtools")
     assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
     assert len(module_lint.passed) > 0
     assert len(module_lint.warned) >= 0
-    module_lint.lint(print_results=False, registry="quay.io", module="samtools")
+    module_lint = nf_core.modules.ModuleLint(dir=self.pipeline_dir)
+    module_lint.lint(print_results=False, module="samtools")
     assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
     assert len(module_lint.passed) > 0
     assert len(module_lint.warned) >= 0

From a5f74b443196123534fea6f035b45941ee0a0bb3 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Tue, 13 Jun 2023 19:20:55 +0200
Subject: [PATCH 31/36] add hook_url

---
 nf_core/pipeline-template/.github/workflows/awsfulltest.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/nf_core/pipeline-template/.github/workflows/awsfulltest.yml b/nf_core/pipeline-template/.github/workflows/awsfulltest.yml
index 9511ea57b..95280215a 100644
--- a/nf_core/pipeline-template/.github/workflows/awsfulltest.yml
+++ b/nf_core/pipeline-template/.github/workflows/awsfulltest.yml
@@ -22,6 +22,7 @@ jobs:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
           compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
+          hook_url: "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}"
           workdir: s3://${{ secrets.AWS_S3_BUCKET }}{% endraw %}/work/{{ short_name }}/{% raw %}work-${{ github.sha }}{% endraw %}
           parameters: |
             {

From 0b374b52141cd2386968b256fc6017b1c7d28cc1 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Tue, 13 Jun 2023 19:53:50 +0200
Subject: [PATCH 32/36] it's a params

---
 nf_core/pipeline-template/.github/workflows/awsfulltest.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nf_core/pipeline-template/.github/workflows/awsfulltest.yml b/nf_core/pipeline-template/.github/workflows/awsfulltest.yml
index 95280215a..fa7f6cf3a 100644
--- a/nf_core/pipeline-template/.github/workflows/awsfulltest.yml
+++ b/nf_core/pipeline-template/.github/workflows/awsfulltest.yml
@@ -22,10 +22,10 @@ jobs:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
           compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
-          hook_url: "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}"
           workdir: s3://${{ secrets.AWS_S3_BUCKET }}{% endraw %}/work/{{ short_name }}/{% raw %}work-${{ github.sha }}{% endraw %}
           parameters: |
             {
+              "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
               "outdir": "s3://{% raw %}${{ secrets.AWS_S3_BUCKET }}{% endraw %}/{{ short_name }}/{% raw %}results-${{ github.sha }}{% endraw %}"
             }
           profiles: test_full

From 1d796dc13ac022a5d634e487cd5a2b4ca5b95169 Mon Sep 17 00:00:00 2001
From: Adam Talbot <adam.talbot@seqera.io>
Date: Wed, 14 Jun 2023 10:17:35 +0100
Subject: [PATCH 33/36] Update test to remove single quotes

---
 tests/test_download.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/test_download.py b/tests/test_download.py
index 4ee8d3ef6..332003c42 100644
--- a/tests/test_download.py
+++ b/tests/test_download.py
@@ -128,7 +128,7 @@ def test_wf_use_local_configs(self, tmp_path):
             # Test the function
             download_obj.wf_use_local_configs("workflow")
             wf_config = nf_core.utils.fetch_wf_config(os.path.join(test_outdir, "workflow"), cache_config=False)
-            assert wf_config["params.custom_config_base"] == f"'{test_outdir}/workflow/../configs/'"
+            assert wf_config["params.custom_config_base"] == f"{test_outdir}/workflow/../configs/"
 
     #
     # Tests for 'find_container_images'

From 56d0c3626e355fdcc5743dfdd05dab6e85373edf Mon Sep 17 00:00:00 2001
From: Adam Talbot <adam.talbot@seqera.io>
Date: Wed, 14 Jun 2023 10:22:01 +0100
Subject: [PATCH 34/36] better language around help text

---
 nf_core/__main__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nf_core/__main__.py b/nf_core/__main__.py
index f531108b1..32e8fc270 100644
--- a/nf_core/__main__.py
+++ b/nf_core/__main__.py
@@ -813,7 +813,7 @@ def create_test_yml(ctx, tool, run_tests, output, force, no_prompts):
     type=str,
     metavar="<registry>",
     default=None,
-    help="Registry to use for containers. If not specified will interpret it from nextflow.config file at attribute docker.registry",
+    help="Registry to use for containers. If not specified it will use docker.registry value in the nextflow.config file",
 )
 @click.option("-k", "--key", type=str, metavar="<test>", multiple=True, help="Run only these lint tests")
 @click.option("-a", "--all", is_flag=True, help="Run on all modules")

From 6c3a218e67d8589406cdae5cbad747bf30f46474 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= <mirp.julia@gmail.com>
Date: Thu, 15 Jun 2023 06:41:52 +0000
Subject: [PATCH 35/36] fix jinja error when parsing awsfultest.yml

---
 nf_core/pipeline-template/.github/workflows/awsfulltest.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nf_core/pipeline-template/.github/workflows/awsfulltest.yml b/nf_core/pipeline-template/.github/workflows/awsfulltest.yml
index e1e8adccc..2f83a0962 100644
--- a/nf_core/pipeline-template/.github/workflows/awsfulltest.yml
+++ b/nf_core/pipeline-template/.github/workflows/awsfulltest.yml
@@ -26,7 +26,7 @@ jobs:
           workdir: s3://${{ secrets.AWS_S3_BUCKET }}{% endraw %}/work/{{ short_name }}/{% raw %}work-${{ github.sha }}{% endraw %}
           parameters: |
             {
-              "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
+              "hook_url": "{% raw %}${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}{% endraw %}",
               "outdir": "s3://{% raw %}${{ secrets.AWS_S3_BUCKET }}{% endraw %}/{{ short_name }}/{% raw %}results-${{ github.sha }}{% endraw %}"
             }
           profiles: test_full

From 0ed72102306907d564b23f2b3063592f1a8df5df Mon Sep 17 00:00:00 2001
From: Adam Talbot <adam.talbot@seqera.io>
Date: Thu, 15 Jun 2023 12:30:06 +0100
Subject: [PATCH 36/36] Remove unused functioN

---
 nf_core/utils.py | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/nf_core/utils.py b/nf_core/utils.py
index 9fd8626f8..31738edab 100644
--- a/nf_core/utils.py
+++ b/nf_core/utils.py
@@ -303,11 +303,6 @@ def fetch_wf_config(wf_path, cache_config=True):
     return config
 
 
-def parse_nf_config(wf_path, cache_config=True):
-    config = fetch_wf_config(wf_path=wf_path, cache_config=True)
-    return config
-
-
 def nextflow_cmd(cmd):
     """Run a Nextflow command and capture the output. Handle errors nicely"""
     try: