Merge pull request #2131 from mirpedrol/conda-enable

Remove params.enable_conda
nf-core · Dec 16, 2022 · b33d0c7 · b33d0c7
2 parents ee6725a + 81fc966
commit b33d0c7
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Showing 13 changed files with 93 additions and 85 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -19,6 +19,7 @@
 ### General
 
 - Only check that a pipeline name doesn't contain dashes if the name is provided by prompt of `--name`. Don't check if a template file is used. ([#2123](https://github.com/nf-core/tools/pull/2123))
+- Deprecate `--enable_conda` parameter. Use `conda.enable` instead ([#2131](https://github.com/nf-core/tools/pull/2131))
 
 ## [v2.7.1 - Mercury Eagle Patch](https://github.com/nf-core/tools/releases/tag/2.7.1) - [2022-12-08]
 

diff --git a/nf_core/lint/nextflow_config.py b/nf_core/lint/nextflow_config.py
@@ -146,6 +146,7 @@ def nextflow_config(self):
         "params.singleEnd",
         "params.igenomesIgnore",
         "params.name",
+        "params.enable_conda",
     ]
 
     # Remove field that should be ignored according to the linting config

diff --git a/nf_core/module-template/modules/main.nf b/nf_core/module-template/modules/main.nf
@@ -23,7 +23,7 @@ process {{ tool_name_underscore|upper }} {
     //               Software MUST be pinned to channel (i.e. "bioconda"), version (i.e. "1.10").
     //               For Conda, the build (i.e. "h9402c20_2") must be EXCLUDED to support installation on different operating systems.
     // TODO nf-core: See section in main README for further information regarding finding and adding container addresses to the section below.
-    conda (params.enable_conda ? "{{ bioconda if bioconda else 'YOUR-TOOL-HERE' }}" : null)
+    conda "{{ bioconda if bioconda else 'YOUR-TOOL-HERE' }}"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         '{{ singularity_container if singularity_container else 'https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE' }}':
         '{{ docker_container if docker_container else 'quay.io/biocontainers/YOUR-TOOL-HERE' }}' }"

diff --git a/nf_core/pipeline-template/lib/WorkflowMain.groovy b/nf_core/pipeline-template/lib/WorkflowMain.groovy
@@ -76,7 +76,7 @@ class WorkflowMain {
         NfcoreTemplate.checkConfigProvided(workflow, log)
 
         // Check that conda channels are set-up correctly
-        if (params.enable_conda) {
+        if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
             Utils.checkCondaChannels(log)
         }
 

diff --git a/nf_core/pipeline-template/modules.json b/nf_core/pipeline-template/modules.json
@@ -7,17 +7,17 @@
                 "nf-core": {
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
                         "installed_by": ["modules"]
                     },
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
                         "installed_by": ["modules"]
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
                         "installed_by": ["modules"]
                     }
                 }

diff --git a/nf_core/pipeline-template/modules/local/samplesheet_check.nf b/nf_core/pipeline-template/modules/local/samplesheet_check.nf
@@ -2,7 +2,7 @@ process SAMPLESHEET_CHECK {
     tag "$samplesheet"
     label 'process_single'
 
-    conda (params.enable_conda ? "conda-forge::python=3.8.3" : null)
+    conda "conda-forge::python=3.8.3"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/python:3.8.3' :
         'quay.io/biocontainers/python:3.8.3' }"

diff --git a/nf_core/pipeline-template/modules/nf-core/custom/dumpsoftwareversions/main.nf b/nf_core/pipeline-template/modules/nf-core/custom/dumpsoftwareversions/main.nf
diff --git a/...ne-template/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py b/...ne-template/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
diff --git a/nf_core/pipeline-template/modules/nf-core/fastqc/main.nf b/nf_core/pipeline-template/modules/nf-core/fastqc/main.nf
diff --git a/nf_core/pipeline-template/modules/nf-core/multiqc/main.nf b/nf_core/pipeline-template/modules/nf-core/multiqc/main.nf
diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config
@@ -41,7 +41,6 @@ params {
     validate_params            = true
     show_hidden_params         = false
     schema_ignore_params       = 'genomes'
-    enable_conda               = false
 {% if nf_core_configs %}
 
     // Config options
@@ -84,7 +83,6 @@ try {
 profiles {
     debug { process.beforeScript = 'echo $HOSTNAME' }
     conda {
-        params.enable_conda    = true
         conda.enabled          = true
         docker.enabled         = false
         singularity.enabled    = false
@@ -93,7 +91,6 @@ profiles {
         charliecloud.enabled   = false
     }
     mamba {
-        params.enable_conda    = true
         conda.enabled          = true
         conda.useMamba         = true
         docker.enabled         = false

diff --git a/nf_core/pipeline-template/nextflow_schema.json b/nf_core/pipeline-template/nextflow_schema.json
@@ -263,12 +263,6 @@
                     "description": "Show all params when using `--help`",
                     "hidden": true,
                     "help_text": "By default, parameters set as _hidden_ in the schema are not shown on the command line when a user runs with `--help`. Specifying this option will tell the pipeline to show all parameters."
-                },
-                "enable_conda": {
-                    "type": "boolean",
-                    "description": "Run this workflow with Conda. You can also use '-profile conda' instead of providing this parameter.",
-                    "hidden": true,
-                    "fa_icon": "fas fa-bacon"
                 }
             }
         }

diff --git a/tests/modules/update.py b/tests/modules/update.py
@@ -303,6 +303,12 @@ def test_update_only_show_differences(self, mock_prompt):
     modules_json = ModulesJson(self.pipeline_dir)
     update_obj = ModuleUpdate(self.pipeline_dir, update_all=True, show_diff=True)
 
+    # Update modules to a fixed old SHA
+    update_old = ModuleUpdate(
+        self.pipeline_dir, update_all=True, show_diff=False, sha="5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+    )
+    update_old.update()
+
     tmpdir = tempfile.mkdtemp()
     shutil.rmtree(tmpdir)
     shutil.copytree(Path(self.pipeline_dir, "modules", NF_CORE_MODULES_NAME), tmpdir)
@@ -329,6 +335,12 @@ def test_update_only_show_differences_when_patch(self, mock_prompt):
     modules_json = ModulesJson(self.pipeline_dir)
     update_obj = ModuleUpdate(self.pipeline_dir, update_all=True, show_diff=True)
 
+    # Update modules to a fixed old SHA
+    update_old = ModuleUpdate(
+        self.pipeline_dir, update_all=True, show_diff=False, sha="5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+    )
+    update_old.update()
+
     # Modify fastqc module, it will have a patch which will be applied during update
     # We modify fastqc because it's one of the modules that can be updated and there's another one before it (custom/dumpsoftwareversions)
     module_path = Path(self.pipeline_dir, "modules", "nf-core", "fastqc")