Merge branch 'dev' into handle-ssh-git-paths

.github/workflows/pytest.yml

@@ -184,7 +184,7 @@ jobs:
  coverage report
  coverage xml
 
- - uses: codecov/codecov-action@84508663e988701840491b86de86b666e8a86bed # v4
+ - uses: codecov/codecov-action@5ecb98a3c6b747ed38dc09f787459979aebb39be # v4
  with:
  files: coverage.xml
  env:

CHANGELOG.md

@@ -2,8 +2,6 @@
 
 ## v2.13.2dev
 
-- Handle more complete list of possible git URL forms (ssh:// and ftp:// prefixes specifically)
-
 ### Template
 
 - Remove fasta default from nextflow.config ([#2828](https://github.com/nf-core/tools/pull/2828))
@@ -15,6 +13,10 @@
 - Update python to 3.12 ([#2805](https://github.com/nf-core/tools/pull/2805))
 - Remove `pyproject.toml` from template root
 - Shorten lines in pipeline template ([#2908](https://github.com/nf-core/tools/pull/2908))
+- Permanently activated pipeline-specific institutional configs support for all pipelines without need for manual intervention ([#2936](https://github.com/nf-core/tools/pull/2936))
+- Template config: `conda.channels`, not `channels` ([#2950](https://github.com/nf-core/tools/pull/2950))
+- Handles multiple DOIs + doi.org resolver from manifest.doi ([#2946](https://github.com/nf-core/tools/pull/2946))
+- Update included components ([#2949](https://github.com/nf-core/tools/pull/2949))
 
 ### Linting
 
@@ -28,6 +30,8 @@
 
 ### Components
 
+- Handle more complete list of possible git URL forms (ssh:// and ftp:// prefixes specifically) ([#2945](https://github.com/nf-core/tools/pull/2945))
+
 ### General
 
 - Update CI to use nf-core/setup-nextflow v2
@@ -63,7 +67,9 @@
 - Update gitpod/workspace-base Docker digest to 5aeb24f ([#2929](https://github.com/nf-core/tools/pull/2929))
 - Update pre-commit hook pre-commit/mirrors-mypy to v1.10.0 ([#2933](https://github.com/nf-core/tools/pull/2933))
 - Update GitHub Actions ([#2939](https://github.com/nf-core/tools/pull/2939))
-- Components: Handle extended set of git path prefixes ([#2945](https://github.com/nf-core/tools/pull/2945))
+- Update codecov/codecov-action digest to 5ecb98a ([#2948](https://github.com/nf-core/tools/pull/2948))
+- Update gitpod/workspace-base Docker digest to 124f2b8 ([#2943](https://github.com/nf-core/tools/pull/2943))
+- fix(collectfile): sort true for methods_description_mqc.yaml ([#2947](https://github.com/nf-core/tools/pull/2947))
 
 ## [v2.13.1 - Tin Puppy Patch](https://github.com/nf-core/tools/releases/tag/2.13) - [2024-02-29]
 

Dockerfile

@@ -1,4 +1,4 @@
-FROM python:3.12-slim@sha256:541d45d3d675fb8197f534525a671e2f8d66c882b89491f9dda271f4f94dcd06
+FROM python:3.12-slim@sha256:2be8daddbb82756f7d1f2c7ece706aadcb284bf6ab6d769ea695cc3ed6016743
 LABEL authors="phil.ewels@seqera.io,erik.danielsson@scilifelab.se" \
  description="Docker image containing requirements for nf-core/tools"
 

nf_core/gitpod/gitpod.Dockerfile

@@ -1,7 +1,7 @@
 # Test build locally before making a PR
 # docker build -t gitpod:test -f nf_core/gitpod/gitpod.Dockerfile .
 
-FROM gitpod/workspace-base@sha256:5aeb24f9994e8226744a200b8316d5d429c0ac98e0b49d1c05ee7d376d8420c5
+FROM gitpod/workspace-base@sha256:124f2b8cbefe9b4abbb6a14538da8846770dde20b93f038d9551b6230aec1d1c
 
 USER root
 

nf_core/pipeline-template/docs/usage.md

@@ -163,6 +163,8 @@ If `-profile` is not specified, the pipeline will run locally and expect all sof
  - A generic configuration profile to be used with [Charliecloud](https://hpc.github.io/charliecloud/)
 - `apptainer`
  - A generic configuration profile to be used with [Apptainer](https://apptainer.org/)
+- `wave`
+ - A generic configuration profile to enable [Wave](https://seqera.io/wave/) containers. Use together with one of the above (requires Nextflow ` 24.03.0-edge` or later).
 - `conda`
  - A generic configuration profile to be used with [Conda](https://conda.io/docs/). Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity, Podman, Shifter, Charliecloud, or Apptainer.
 

nf_core/pipeline-template/modules.json

@@ -7,7 +7,7 @@
  "nf-core": {
  "fastqc": {
  "branch": "master",
- "git_sha": "f4ae1d942bd50c5c0b9bd2de1393ce38315ba57c",
+ "git_sha": "285a50500f9e02578d90b3ce6382ea3c30216acd",
  "installed_by": ["modules"]
  },
  "multiqc": {
@@ -26,7 +26,7 @@
  },
  "utils_nfcore_pipeline": {
  "branch": "master",
- "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
+ "git_sha": "92de218a329bfc9a9033116eb5f65fd270e72ba3",
  "installed_by": ["subworkflows"]
  },
  "utils_nfvalidation_plugin": {

nf_core/pipeline-template/nextflow.config

@@ -76,105 +76,111 @@ try {
 }
 
 // Load {{ name }} custom profiles from different institutions.
-// Warning: Uncomment only if a pipeline-specific institutional config already exists on nf-core/configs!
-// try {
-// includeConfig "${params.custom_config_base}/pipeline/{{ short_name }}.config"
-// } catch (Exception e) {
-// System.err.println("WARNING: Could not load nf-core/config/{{ short_name }} profiles: ${params.custom_config_base}/pipeline/{{ short_name }}.config")
-// }
+try {
+ includeConfig "${params.custom_config_base}/pipeline/{{ short_name }}.config"
+} catch (Exception e) {
+ System.err.println("WARNING: Could not load nf-core/config/{{ short_name }} profiles: ${params.custom_config_base}/pipeline/{{ short_name }}.config")
+}
 {% endif -%}
 
 profiles {
  debug {
- dumpHashes = true
- process.beforeScript = 'echo $HOSTNAME'
- cleanup = false
+ dumpHashes  = true
+ process.beforeScript  = 'echo $HOSTNAME'
+ cleanup  = false
  nextflow.enable.configProcessNamesValidation = true
  }
  conda {
- conda.enabled = true
- docker.enabled = false
- singularity.enabled = false
- podman.enabled = false
- shifter.enabled = false
- charliecloud.enabled = false
- channels  = ['conda-forge', 'bioconda', 'defaults']
- apptainer.enabled = false
+ conda.enabled  = true
+ docker.enabled  = false
+ singularity.enabled  = false
+ podman.enabled  = false
+ shifter.enabled  = false
+ charliecloud.enabled  = false
+ conda.channels = ['conda-forge', 'bioconda', 'defaults']
+ apptainer.enabled  = false
  }
  mamba {
- conda.enabled = true
- conda.useMamba = true
- docker.enabled = false
- singularity.enabled = false
- podman.enabled = false
- shifter.enabled = false
- charliecloud.enabled = false
- apptainer.enabled = false
+ conda.enabled  = true
+ conda.useMamba  = true
+ docker.enabled  = false
+ singularity.enabled  = false
+ podman.enabled  = false
+ shifter.enabled  = false
+ charliecloud.enabled  = false
+ apptainer.enabled  = false
  }
  docker {
- docker.enabled = true
- conda.enabled = false
- singularity.enabled = false
- podman.enabled = false
- shifter.enabled = false
- charliecloud.enabled = false
- apptainer.enabled = false
- docker.runOptions = '-u $(id -u):$(id -g)'
+ docker.enabled  = true
+ conda.enabled  = false
+ singularity.enabled  = false
+ podman.enabled  = false
+ shifter.enabled  = false
+ charliecloud.enabled  = false
+ apptainer.enabled  = false
+ docker.runOptions  = '-u $(id -u):$(id -g)'
  }
  arm {
- docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64'
+ docker.runOptions  = '-u $(id -u):$(id -g) --platform=linux/amd64'
  }
  singularity {
- singularity.enabled = true
- singularity.autoMounts = true
- conda.enabled = false
- docker.enabled = false
- podman.enabled = false
- shifter.enabled = false
- charliecloud.enabled = false
- apptainer.enabled = false
+ singularity.enabled  = true
+ singularity.autoMounts  = true
+ conda.enabled  = false
+ docker.enabled  = false
+ podman.enabled  = false
+ shifter.enabled  = false
+ charliecloud.enabled  = false
+ apptainer.enabled  = false
  }
  podman {
- podman.enabled = true
- conda.enabled = false
- docker.enabled = false
- singularity.enabled = false
- shifter.enabled = false
- charliecloud.enabled = false
- apptainer.enabled = false
+ podman.enabled  = true
+ conda.enabled  = false
+ docker.enabled  = false
+ singularity.enabled  = false
+ shifter.enabled  = false
+ charliecloud.enabled  = false
+ apptainer.enabled  = false
  }
  shifter {
- shifter.enabled = true
- conda.enabled = false
- docker.enabled = false
- singularity.enabled = false
- podman.enabled = false
- charliecloud.enabled = false
- apptainer.enabled = false
+ shifter.enabled  = true
+ conda.enabled  = false
+ docker.enabled  = false
+ singularity.enabled  = false
+ podman.enabled  = false
+ charliecloud.enabled  = false
+ apptainer.enabled  = false
  }
  charliecloud {
- charliecloud.enabled = true
- conda.enabled = false
- docker.enabled = false
- singularity.enabled = false
- podman.enabled = false
- shifter.enabled = false
- apptainer.enabled = false
+ charliecloud.enabled  = true
+ conda.enabled  = false
+ docker.enabled  = false
+ singularity.enabled  = false
+ podman.enabled  = false
+ shifter.enabled  = false
+ apptainer.enabled  = false
  }
  apptainer {
- apptainer.enabled = true
- apptainer.autoMounts = true
- conda.enabled = false
- docker.enabled = false
- singularity.enabled = false
- podman.enabled = false
- shifter.enabled = false
- charliecloud.enabled = false
+ apptainer.enabled = true
+ apptainer.autoMounts = true
+ conda.enabled = false
+ docker.enabled = false
+ singularity.enabled = false
+ podman.enabled = false
+ shifter.enabled = false
+ charliecloud.enabled = false
+ }
+ wave {
+ apptainer.ociAutoPull = true
+ singularity.ociAutoPull = true
+ wave.enabled = true
+ wave.freeze = true
+ wave.strategy = 'conda,container'
  }
  gitpod {
- executor.name = 'local'
- executor.cpus = 4
- executor.memory = 8.GB
+ executor.name  = 'local'
+ executor.cpus  = 4
+ executor.memory  = 8.GB
  }
  test { includeConfig 'conf/test.config' }
  test_full { includeConfig 'conf/test_full.config' }

nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf

@@ -243,8 +243,16 @@ def methodsDescriptionText(mqc_methods_yaml) {
  meta["manifest_map"] = workflow.manifest.toMap()
 
  // Pipeline DOI
- meta["doi_text"] = meta.manifest_map.doi ? "(doi: <a href=\'https://doi.org/${meta.manifest_map.doi}\'>${meta.manifest_map.doi}</a>)" : ""
- meta["nodoi_text"] = meta.manifest_map.doi ? "": "<li>If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used. </li>"
+ if (meta.manifest_map.doi) {
+ // Using a loop to handle multiple DOIs
+ // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers
+ // Removing ` ` since the manifest.doi is a string and not a proper list
+ def temp_doi_ref = ""
+ String[] manifest_doi = meta.manifest_map.doi.tokenize(",")
+ for (String doi_ref: manifest_doi) temp_doi_ref += "(doi: <a href=\'https://doi.org/${doi_ref.replace("https://doi.org/", "").replace(" ", "")}\'>${doi_ref.replace("https://doi.org/", "").replace(" ", "")}</a>), "
+ meta["doi_text"] = temp_doi_ref.substring(0, temp_doi_ref.length() - 2)
+ } else meta["doi_text"] = ""
+ meta["nodoi_text"] = meta.manifest_map.doi ? "" : "<li>If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used. </li>"
 
  // Tool references
  meta["tool_citations"] = ""

nf_core/pipeline-template/workflows/pipeline.nf

@@ -75,7 +75,7 @@ workflow {{ short_name|upper }} {
  ch_multiqc_files = ch_multiqc_files.mix(
  ch_methods_description.collectFile(
  name: 'methods_description_mqc.yaml',
- sort: false
+ sort: true
  )
  )