Important! Template update for nf-core/tools v4.0.2

.github/workflows/download_pipeline.yml

@@ -38,6 +38,9 @@ jobs:
     runs-on: ubuntu-latest
     needs: configure
     steps:
+      - name: Check out pipeline code
+        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3
 
@@ -55,10 +58,9 @@ jobs:
           apptainer-version: 1.3.4
 
       - name: Read .nf-core.yml
-        uses: pietrobolcato/action-read-yaml@9f13718d61111b69f30ab4ac683e67a56d254e1d # 1.1.0
         id: read_yml
-        with:
-          config: ${{ github.workspace }}/.nf-core.yml
+        run: |
+          echo "nf_core_version=$(yq '.nf_core_version' ${{ github.workspace }}/.nf-core.yml)" >> "$GITHUB_OUTPUT"
 
       - name: Install dependencies
         run: |

.github/workflows/nf-test.yml

@@ -64,6 +64,7 @@ jobs:
     runs-on: # use self-hosted runners
       - runs-on=${{ github.run_id }}-nf-test
       - runner=4cpu-linux-x64
+      - volume=40gb
     strategy:
       fail-fast: false
       matrix:
@@ -78,8 +79,8 @@ jobs:
           - isMain: false
             profile: "singularity"
         NXF_VER:
-          - 26.04.0
-          - latest-everything
+          - "26.04.0"
+          - "latest-everything"
     env:
       NXF_ANSI_LOG: false
       TOTAL_SHARDS: ${{ needs.nf-test-changes.outputs.total_shards }}

.nf-core.yml

@@ -9,7 +9,7 @@ lint:
     - assets/nf-core-references_logo_light.png
     - docs/images/nf-core-references_logo_light.png
     - docs/images/nf-core-references_logo_dark.png
-nf_core_version: 4.0.1
+nf_core_version: 4.0.2
 repository_type: pipeline
 template:
   author: "@maxulysse"
@@ -22,4 +22,4 @@ template:
   skip_features:
     - fastqc
     - igenomes
-  version: "0.2"
+  version: "0.2dev"

README.md

@@ -11,7 +11,7 @@
 [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
 
 [![Nextflow](https://img.shields.io/badge/version-%E2%89%A526.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)
-[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.0.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.0.1)
+[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.0.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.0.2)
 [![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/)

assets/multiqc_config.yml

@@ -1,7 +1,5 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/references/releases/tag/0.2" target="_blank">nf-core/references</a>
-  analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/references/0.2/docs/output" target="_blank">documentation</a>.
+  This report has been generated by the <a href="https://github.com/nf-core/references/tree/dev" target="_blank">nf-core/references</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://nf-co.re/references/dev/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-references-methods-description":
     order: -1000

conf/containers_conda_lock_files_amd64.config

@@ -0,0 +1 @@
+process { withName: 'MULTIQC' { container = 'modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c17fb751507e9dfc_1.txt' } }

conf/containers_conda_lock_files_arm64.config

@@ -0,0 +1 @@
+process { withName: 'MULTIQC' { container = 'modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-5c84a5000a226ab5_1.txt' } }

conf/containers_docker_amd64.config

@@ -0,0 +1 @@
+process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.35--c17fb751507e9dfc' } }

conf/containers_docker_arm64.config

@@ -0,0 +1 @@
+process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.35--5c84a5000a226ab5' } }

conf/containers_singularity_https_amd64.config

@@ -0,0 +1 @@
+process { withName: 'MULTIQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c8/c8e346f4f6080eadf1253505e6ff09ef004454fc18e8d672006fd7b222cc412e/data' } }

conf/containers_singularity_https_arm64.config

@@ -0,0 +1 @@
+process { withName: 'MULTIQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/e4/e48aa28aebc881254a499b24c3e1ce77b8df1b85a5432699ed6f72eb17ac7fb5/data' } }

conf/containers_singularity_oras_amd64.config

@@ -0,0 +1 @@
+process { withName: 'MULTIQC' { container = 'oras://community.wave.seqera.io/library/multiqc:1.35--c680f2aea25ccec2' } }

conf/containers_singularity_oras_arm64.config

@@ -0,0 +1 @@
+process { withName: 'MULTIQC' { container = 'oras://community.wave.seqera.io/library/multiqc:1.35--c0468833d65b2f81' } }

modules.json

@@ -12,7 +12,7 @@
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "008f9d3e61209bf995edac3ba531f54e269e1215",
+                        "git_sha": "98403d15b0e50edae1f3fec5eae5e24982f1fade",
                         "installed_by": ["modules"]
                     },
                     "untar": {
@@ -36,126 +36,6 @@
                     }
                 }
             }
-        },
-        "https://github.com/nf-side/modules.git": {
-            "modules": {
-                "nf-side": {
-                    "bowtie/build": {
-                        "branch": "main",
-                        "git_sha": "86dd28d52838e684c2b11345df2f8937972e834d",
-                        "installed_by": ["prepare_genome_rnaseq"]
-                    },
-                    "bowtie2/build": {
-                        "branch": "main",
-                        "git_sha": "86dd28d52838e684c2b11345df2f8937972e834d",
-                        "installed_by": ["prepare_genome_rnaseq"]
-                    },
-                    "bwa/index": {
-                        "branch": "main",
-                        "git_sha": "86dd28d52838e684c2b11345df2f8937972e834d",
-                        "installed_by": ["prepare_genome_dnaseq"]
-                    },
-                    "bwamem2/index": {
-                        "branch": "main",
-                        "git_sha": "86dd28d52838e684c2b11345df2f8937972e834d",
-                        "installed_by": ["prepare_genome_dnaseq"]
-                    },
-                    "dragmap/hashtable": {
-                        "branch": "main",
-                        "git_sha": "86dd28d52838e684c2b11345df2f8937972e834d",
-                        "installed_by": ["prepare_genome_dnaseq"]
-                    },
-                    "gatk4/createsequencedictionary": {
-                        "branch": "main",
-                        "git_sha": "86dd28d52838e684c2b11345df2f8937972e834d",
-                        "installed_by": ["prepare_genome_dnaseq"]
-                    },
-                    "gawk": {
-                        "branch": "main",
-                        "git_sha": "86dd28d52838e684c2b11345df2f8937972e834d",
-                        "installed_by": ["prepare_genome_dnaseq"]
-                    },
-                    "gffread": {
-                        "branch": "main",
-                        "git_sha": "86dd28d52838e684c2b11345df2f8937972e834d",
-                        "installed_by": ["prepare_genome_rnaseq"]
-                    },
-                    "hisat2/build": {
-                        "branch": "main",
-                        "git_sha": "86dd28d52838e684c2b11345df2f8937972e834d",
-                        "installed_by": ["prepare_genome_rnaseq"]
-                    },
-                    "hisat2/extractsplicesites": {
-                        "branch": "main",
-                        "git_sha": "86dd28d52838e684c2b11345df2f8937972e834d",
-                        "installed_by": ["prepare_genome_rnaseq"]
-                    },
-                    "kallisto/index": {
-                        "branch": "main",
-                        "git_sha": "4b418e22f9fb3a5e753fcf4224baf12d445ff7b9",
-                        "installed_by": ["prepare_genome_rnaseq"]
-                    },
-                    "msisensorpro/scan": {
-                        "branch": "main",
-                        "git_sha": "86dd28d52838e684c2b11345df2f8937972e834d",
-                        "installed_by": ["prepare_genome_dnaseq"]
-                    },
-                    "rsem/preparereference": {
-                        "branch": "main",
-                        "git_sha": "86dd28d52838e684c2b11345df2f8937972e834d",
-                        "installed_by": ["prepare_genome_rnaseq"]
-                    },
-                    "salmon/index": {
-                        "branch": "main",
-                        "git_sha": "86dd28d52838e684c2b11345df2f8937972e834d",
-                        "installed_by": ["prepare_genome_rnaseq"]
-                    },
-                    "samtools/faidx": {
-                        "branch": "main",
-                        "git_sha": "86dd28d52838e684c2b11345df2f8937972e834d",
-                        "installed_by": ["prepare_genome_dnaseq", "prepare_genome_rnaseq"]
-                    },
-                    "snapaligner/index": {
-                        "branch": "main",
-                        "git_sha": "86dd28d52838e684c2b11345df2f8937972e834d",
-                        "installed_by": ["prepare_genome_dnaseq"]
-                    },
-                    "star/genomegenerate": {
-                        "branch": "main",
-                        "git_sha": "86dd28d52838e684c2b11345df2f8937972e834d",
-                        "installed_by": ["prepare_genome_rnaseq"]
-                    },
-                    "tabix/bgziptabix": {
-                        "branch": "main",
-                        "git_sha": "86dd28d52838e684c2b11345df2f8937972e834d",
-                        "installed_by": ["prepare_genome_dnaseq"]
-                    },
-                    "tabix/tabix": {
-                        "branch": "main",
-                        "git_sha": "86dd28d52838e684c2b11345df2f8937972e834d",
-                        "installed_by": ["prepare_genome_dnaseq"]
-                    }
-                }
-            },
-            "subworkflows": {
-                "nf-side": {
-                    "prepare_genome_dnaseq": {
-                        "branch": "main",
-                        "git_sha": "86dd28d52838e684c2b11345df2f8937972e834d",
-                        "installed_by": ["subworkflows"]
-                    },
-                    "prepare_genome_rnaseq": {
-                        "branch": "main",
-                        "git_sha": "4b418e22f9fb3a5e753fcf4224baf12d445ff7b9",
-                        "installed_by": ["subworkflows"]
-                    },
-                    "utils_references": {
-                        "branch": "main",
-                        "git_sha": "3f81209f8ae9b11925da2a9a8bc57bfdb5028eef",
-                        "installed_by": ["subworkflows"]
-                    }
-                }
-            }
         }
     }
 }