nf-core · christopher-mohr · Dec 23, 2022 · Dec 19, 2022 · Dec 22, 2022 · Dec 22, 2022
diff --git a/.github/workflows/ci-external.yml b/.github/workflows/ci-external.yml
@@ -17,7 +17,7 @@ jobs:
       matrix:
         include:
           # Test pipeline minimum Nextflow version
-          - NXF_VER: "21.10.3"
+          - NXF_VER: "22.10.1"
             NXF_EDGE: ""
           # Test latest edge release of Nextflow
           - NXF_VER: ""

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -49,7 +49,7 @@ jobs:
       matrix:
         include:
           # Test pipeline minimum Nextflow version
-          - NXF_VER: "21.10.3"
+          - NXF_VER: "22.10.1"
             NXF_EDGE: ""
           # Test latest edge release of Nextflow
           - NXF_VER: ""
@@ -90,7 +90,7 @@ jobs:
       matrix:
         include:
           # Test pipeline minimum Nextflow version
-          - NXF_VER: "21.10.3"
+          - NXF_VER: "22.10.1"
             NXF_EDGE: ""
           # Test latest edge release of Nextflow
           - NXF_VER: ""

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
@@ -17,6 +17,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#180](https://github.com/nf-core/epitopeprediction/pull/180) - Update to nf-core template `2.6`
 - [#180](https://github.com/nf-core/epitopeprediction/pull/180) - Improve runtime for VCF-based predictions
 - [#187](https://github.com/nf-core/epitopeprediction/pull/187) - Update to nf-core template `2.7.1`
+- [#189](https://github.com/nf-core/epitopeprediction/pull/189) - Update to nf-core template `2.7.2`
 
 ### `Fixed`
 

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.json b/modules.json
@@ -7,17 +7,17 @@
                 "nf-core": {
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
                         "installed_by": ["modules"]
                     },
                     "gunzip": {
                         "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/cat_files.nf b/modules/local/cat_files.nf
@@ -1,7 +1,7 @@
 process CAT_FILES {
     label 'process_low'
 
-    conda (params.enable_conda ? "conda-forge:sed=4.8" : null)
+    conda "conda-forge:sed=4.8"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/cat:5.2.3--hdfd78af_1' :
         'quay.io/biocontainers/cat:5.2.3--hdfd78af_1' }"

diff --git a/modules/local/csvtk_concat.nf b/modules/local/csvtk_concat.nf
@@ -1,7 +1,7 @@
 process CSVTK_CONCAT {
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::csvtk=0.23.0" : null)
+    conda "bioconda::csvtk=0.23.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/csvtk:0.23.0--h9ee0642_0' :
         'quay.io/biocontainers/csvtk:0.23.0--h9ee0642_0' }"

diff --git a/modules/local/csvtk_split.nf b/modules/local/csvtk_split.nf
@@ -1,7 +1,7 @@
 process CSVTK_SPLIT {
     label 'process_low'
 
-    conda (params.enable_conda ? "conda-forge::sed=4.7 bioconda::csvtk=0.23.0" : null)
+    conda "conda-forge::sed=4.7 bioconda::csvtk=0.23.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/csvtk:0.23.0--h9ee0642_0' :
         'quay.io/biocontainers/csvtk:0.23.0--h9ee0642_0' }"

diff --git a/modules/local/epytope_check_requested_models.nf b/modules/local/epytope_check_requested_models.nf
@@ -1,7 +1,7 @@
 process EPYTOPE_CHECK_REQUESTED_MODELS {
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::epytope=3.1.0" : null)
+    conda "bioconda::epytope=3.1.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/epytope:3.1.0--pyh5e36f6f_0' :
         'quay.io/biocontainers/epytope:3.1.0--pyh5e36f6f_0' }"

diff --git a/modules/local/epytope_generate_peptides.nf b/modules/local/epytope_generate_peptides.nf
@@ -2,7 +2,7 @@ process EPYTOPE_GENERATE_PEPTIDES {
     label 'process_low'
     tag "${meta.sample}"
 
-    conda (params.enable_conda ? "bioconda::epytope=3.1.0" : null)
+    conda "bioconda::epytope=3.1.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/epytope:3.1.0--pyh5e36f6f_0' :
         'quay.io/biocontainers/epytope:3.1.0--pyh5e36f6f_0' }"

diff --git a/modules/local/epytope_peptide_prediction.nf b/modules/local/epytope_peptide_prediction.nf
@@ -1,7 +1,7 @@
 process EPYTOPE_PEPTIDE_PREDICTION {
     label 'process_low'
 
-    conda (params.enable_conda ? "conda-forge::coreutils=9.1 conda-forge::tcsh=6.20.00 bioconda::epytope=3.1.0 conda-forge::gawk=5.1.0 conda-forge::perl=5.32.1" : null)
+    conda "conda-forge::coreutils=9.1 conda-forge::tcsh=6.20.00 bioconda::epytope=3.1.0 conda-forge::gawk=5.1.0 conda-forge::perl=5.32.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-11bbf0d242ea96f7b9c08d5b5bc26f2cd5ac5943:3419f320edefe6077631798f50d7bd4f8dc4763f-0' :
         'quay.io/biocontainers/mulled-v2-11bbf0d242ea96f7b9c08d5b5bc26f2cd5ac5943:3419f320edefe6077631798f50d7bd4f8dc4763f-0' }"

diff --git a/modules/local/epytope_show_supported_models.nf b/modules/local/epytope_show_supported_models.nf
@@ -1,7 +1,7 @@
 process EPYTOPE_SHOW_SUPPORTED_MODELS {
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::epytope=3.1.0" : null)
+    conda "bioconda::epytope=3.1.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/epytope:3.1.0--pyh5e36f6f_0' :
         'quay.io/biocontainers/epytope:3.1.0--pyh5e36f6f_0' }"

diff --git a/modules/local/external_tools_import.nf b/modules/local/external_tools_import.nf
@@ -4,7 +4,7 @@
 process EXTERNAL_TOOLS_IMPORT {
     label 'process_low'
 
-    conda (params.enable_conda ? "conda-forge::coreutils=9.1" : null)
+    conda "conda-forge::coreutils=9.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' :
         'biocontainers/biocontainers:v1.2.0_cv1' }"

diff --git a/modules/local/get_prediction_versions.nf b/modules/local/get_prediction_versions.nf
@@ -1,7 +1,7 @@
 process GET_PREDICTION_VERSIONS {
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::epytope=3.1.0" : null)
+    conda "bioconda::epytope=3.1.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/epytope:3.1.0--pyh5e36f6f_0' :
         'quay.io/biocontainers/epytope:3.1.0--pyh5e36f6f_0' }"

diff --git a/modules/local/merge_json.nf b/modules/local/merge_json.nf
@@ -1,7 +1,7 @@
 process MERGE_JSON {
     label 'process_low'
 
-    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/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/local/snpsift_split.nf b/modules/local/snpsift_split.nf
@@ -1,7 +1,7 @@
 process SNPSIFT_SPLIT {
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::snpsift=4.2" : null)
+    conda "bioconda::snpsift=4.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/snpsift:4.2--hdfd78af_5' :
         'quay.io/biocontainers/snpsift:4.2--hdfd78af_5' }"

diff --git a/modules/local/split_peptides.nf b/modules/local/split_peptides.nf
@@ -1,7 +1,7 @@
 process SPLIT_PEPTIDES {
     label 'process_low'
 
-    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/local/variant_split.nf b/modules/local/variant_split.nf
@@ -1,7 +1,7 @@
 process VARIANT_SPLIT {
     label 'process_low'
 
-    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/gunzip/main.nf b/modules/nf-core/gunzip/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
@@ -70,21 +70,8 @@ params {
     validate_params            = true
     show_hidden_params         = false
     schema_ignore_params       = 'genomes'
-    enable_conda               = false
     igenomes_ignore            = true
 
-    // Max resource options
-    // Defaults only, expecting to be overwritten
-    max_memory = 128.GB
-    max_cpus = 16
-    max_time = 240.h
-
-    // MultiQC options
-    multiqc_config             = null
-    multiqc_title              = null
-    max_multiqc_email_size     = '25.MB'
-
-
     // Config options
     custom_config_version      = 'master'
     custom_config_base         = "https://github.com/nf-core/configs/${params.custom_config_version}"
@@ -93,6 +80,8 @@ params {
     config_profile_url         = null
     config_profile_name        = null
 
+    conda.enabled = false
+
     // Max resource options
     // Defaults only, expecting to be overwritten
     max_memory                 = '128.GB'
@@ -123,7 +112,6 @@ try {
 profiles {
     debug { process.beforeScript = 'echo $HOSTNAME' }
     conda {
-        params.enable_conda    = true
         conda.enabled          = true
         docker.enabled         = false
         singularity.enabled    = false
@@ -132,7 +120,6 @@ profiles {
         charliecloud.enabled   = false
     }
     mamba {
-        params.enable_conda    = true
         conda.enabled          = true
         conda.useMamba         = true
         docker.enabled         = false