Template update for nf-core/tools version 2.7.2

nf-core · Dec 19, 2022 · e012a2a · e012a2a
1 parent e0c94db
commit e012a2a
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Showing 12 changed files with 82 additions and 88 deletions.
diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml
@@ -34,9 +34,9 @@ jobs:
         id: prettier_status
         run: |
           if prettier --check ${GITHUB_WORKSPACE}; then
-            echo "name=result::pass" >> $GITHUB_OUTPUT
+            echo "result=pass" >> $GITHUB_OUTPUT
           else
-            echo "name=result::fail" >> $GITHUB_OUTPUT
+            echo "result=fail" >> $GITHUB_OUTPUT
           fi
 
       - name: Run 'prettier --write'

diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml
@@ -18,7 +18,7 @@ jobs:
 
       - name: Get PR number
         id: pr_number
-        run: echo "name=pr_number::$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT
+        run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT
 
       - name: Post PR comment
         uses: marocchino/sticky-pull-request-comment@v2

diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy
@@ -72,7 +72,7 @@ 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/modules.json b/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/modules/local/samplesheet_check.nf b/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/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf
diff --git a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf
diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
diff --git a/nextflow.config b/nextflow.config
@@ -39,7 +39,6 @@ params {
     validate_params            = true
     show_hidden_params         = false
     schema_ignore_params       = 'genomes'
-    enable_conda               = false
 
 
     // Config options
@@ -81,7 +80,6 @@ try {
 profiles {
     debug { process.beforeScript = 'echo $HOSTNAME' }
     conda {
-        params.enable_conda    = true
         conda.enabled          = true
         docker.enabled         = false
         singularity.enabled    = false
@@ -90,7 +88,6 @@ profiles {
         charliecloud.enabled   = false
     }
     mamba {
-        params.enable_conda    = true
         conda.enabled          = true
         conda.useMamba         = true
         docker.enabled         = false

diff --git a/nextflow_schema.json b/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/workflows/epitopeprediction.nf b/workflows/epitopeprediction.nf
@@ -82,7 +82,7 @@ workflow EPITOPEPREDICTION {
     ch_versions = ch_versions.mix(FASTQC.out.versions.first())
 
     CUSTOM_DUMPSOFTWAREVERSIONS (
-        ch_versions.unique{ it.text }.collectFile(name: 'collated_versions.yml')
+        ch_versions.unique().collectFile(name: 'collated_versions.yml')
     )
 
     //