nf-core · ggabernet · Jan 27, 2023 · Dec 19, 2022 · Jan 27, 2023 · Jan 27, 2023
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/CHANGELOG.md b/CHANGELOG.md
@@ -13,15 +13,28 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 - Added pipeline overview diagram and metro map.
 - Added full logs to `enchantr report filesize` process.
 - Template update to nf-core tools v2.7.1
+- Template update to nf-core tools v2.7.2
 
 ### `Fixed`
 
 - Fixed bug arising when not providing `--index_file FALSE` for some input options not requiring index files.
 
 ### `Dependencies`
 
+| Dependency | Old version | New version |
+| ---------- | ----------- | ----------- |
+| multiqc    | 1.13        | 1.14        |
+| pandas     | 1.1.5       | 1.5.3       |
+| presto     | 0.7.0       | 0.7.1       |
+| changeo    | 1.2.0       | 1.3.0       |
+| igblast    | 1.17.1      | 1.19.0      |
+| r-enchantr |             | 0.0.6       |
+| r-plotly   |             | 4.10.1      |
+
 ### `Deprecated`
 
+- Deprecated param `enable_conda`
+
 ## [2.4.0] 2022-12-05 "Aparecium"
 
 ### `Added`

diff --git a/LICENSE b/LICENSE
@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) Gisela Gabernet, Simon Heumos, Alexander Peltzer
+Copyright (c) Gisela Gabernet, Susanna Marquez, Alexander Peltzer, Simon Heumos
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy
@@ -71,7 +71,7 @@ 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/local/fetch_databases.nf b/modules/local/fetch_databases.nf
@@ -3,10 +3,10 @@ process FETCH_DATABASES {
     label 'process_low'
     label 'immcantation'
 
-    conda "bioconda::changeo=1.2.0 bioconda::igblast=1.17.1 conda-forge::wget=1.20.1"
+    conda "bioconda::changeo=1.3.0 bioconda::igblast=1.19.0 conda-forge::wget=1.20.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-7d8e418eb73acc6a80daea8e111c94cf19a4ecfd:e7f88c6f7da46a5407f261ca406c050d5bd12dea-0' :
-        'quay.io/biocontainers/mulled-v2-7d8e418eb73acc6a80daea8e111c94cf19a4ecfd:e7f88c6f7da46a5407f261ca406c050d5bd12dea-0' }"
+        'https://depot.galaxyproject.org/singularity/mulled-v2-7d8e418eb73acc6a80daea8e111c94cf19a4ecfd:00534555924705cdf2f7ac48b4b8b4083527ca58-1' :
+        'quay.io/biocontainers/mulled-v2-7d8e418eb73acc6a80daea8e111c94cf19a4ecfd:00534555924705cdf2f7ac48b4b8b4083527ca58-1' }"
 
     output:
     path("igblast_base"), emit: igblast

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 "conda-forge::pandas=1.1.5"
+    conda "conda-forge::pandas=1.5.3"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/pandas:1.1.5' :
         'quay.io/biocontainers/pandas:1.1.5' }"

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -407,21 +407,6 @@
             },
             "fa_icon": "far fa-file-code"
         },
-        "software_packaging_options": {
-            "title": "Software packaging options",
-            "type": "object",
-            "description": "Options for software packaging",
-            "default": "",
-            "properties": {
-                "enable_conda": {
-                    "type": "boolean",
-                    "fa_icon": "fas fa-box",
-                    "description": "Enable conda to run pipeline with conda environment."
-                }
-            },
-            "help_text": "Software packaging options",
-            "fa_icon": "fas fa-angle-double-right"
-        },
         "reference_genome_options": {
             "title": "Reference genome options",
             "type": "object",
@@ -670,9 +655,6 @@
         {
             "$ref": "#/definitions/report_options"
         },
-        {
-            "$ref": "#/definitions/software_packaging_options"
-        },
         {
             "$ref": "#/definitions/reference_genome_options"
         },