Fixes for a parity release

.devcontainer/devcontainer.json

@@ -14,7 +14,11 @@
             },
 
             // Add the IDs of extensions you want installed when the container is created.
-            "extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"]
+            "extensions": [
+                "ms-python.python",
+                "ms-python.vscode-pylance",
+                "nf-core.nf-core-extensionpack"
+            ]
         }
     }
 }

.github/CONTRIBUTING.md

@@ -16,7 +16,7 @@ If you'd like to write some code for mskcc/neoantigenpipeline, the standard work
 1. Check that there isn't already an issue about your idea in the [mskcc/neoantigenpipeline issues](https://github.com/mskcc/neoantigenpipeline/issues) to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this
 2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [mskcc/neoantigenpipeline repository](https://github.com/mskcc/neoantigenpipeline) to your GitHub account
 3. Make the necessary changes / additions within your forked repository following [Pipeline conventions](#pipeline-contribution-conventions)
-4. Use `nf-core schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10).
+4. Use `nf-core pipelines schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10).
 5. Submit a Pull Request against the `dev` branch and wait for the code to be reviewed and merged
 
 If you're not used to this workflow with git, you can start with some [docs from GitHub](https://help.github.com/en/github/collaborating-with-issues-and-pull-requests) or even their [excellent `git` resources](https://try.github.io/).
@@ -37,7 +37,7 @@ There are typically two types of tests that run:
 ### Lint tests
 
 `nf-core` has a [set of guidelines](https://nf-co.re/developers/guidelines) which all pipelines must adhere to.
-To enforce these and ensure that all pipelines stay in sync, we have developed a helper tool which runs checks on the pipeline code. This is in the [nf-core/tools repository](https://github.com/nf-core/tools) and once installed can be run locally with the `nf-core lint <pipeline-directory>` command.
+To enforce these and ensure that all pipelines stay in sync, we have developed a helper tool which runs checks on the pipeline code. This is in the [nf-core/tools repository](https://github.com/nf-core/tools) and once installed can be run locally with the `nf-core pipelines lint <pipeline-directory>` command.
 
 If any failures or warnings are encountered, please follow the listed URL for more documentation.
 
@@ -68,7 +68,7 @@ If you wish to contribute a new step, please use the following coding standards:
 2. Write the process block (see below).
 3. Define the output channel if needed (see below).
 4. Add any new parameters to `nextflow.config` with a default (see below).
-5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core schema build` tool).
+5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core pipelines schema build` tool).
 6. Add sanity checks and validation for all relevant parameters.
 7. Perform local tests to validate that the new code works as expected.
 8. If applicable, add a new test command in `.github/workflow/ci.yml`.
@@ -79,11 +79,11 @@ If you wish to contribute a new step, please use the following coding standards:
 
 Parameters should be initialised / defined with default values in `nextflow.config` under the `params` scope.
 
-Once there, use `nf-core schema build` to add to `nextflow_schema.json`.
+Once there, use `nf-core pipelines schema build` to add to `nextflow_schema.json`.
 
 ### Default processes resource requirements
 
-Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/master/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels.
+Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/main/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels.
 
 The process resources can be passed on to the tool dynamically within the process with the `${task.cpus}` and `${task.memory}` variables in the `script:` block.
 
@@ -96,7 +96,7 @@ Please use the following naming schemes, to make it easy to understand what is g
 
 ### Nextflow version bumping
 
-If you are using a new feature from core Nextflow, you may bump the minimum required version of nextflow in the pipeline with: `nf-core bump-version --nextflow . [min-nf-version]`
+If you are using a new feature from core Nextflow, you may bump the minimum required version of nextflow in the pipeline with: `nf-core pipelines bump-version --nextflow . [min-nf-version]`
 
 ### Images and figures
 

.github/PULL_REQUEST_TEMPLATE.md

@@ -16,7 +16,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/mskcc/neoant
 - [ ] This comment contains a description of changes (with reason).
 - [ ] If you've fixed a bug or added code that should be tested, add tests!
 - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/mskcc/neoantigenpipeline/tree/master/.github/CONTRIBUTING.md)
-- [ ] Make sure your code lints (`nf-core lint`).
+- [ ] Make sure your code lints (`nf-core pipelines lint`).
 - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
 - [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir <OUTDIR>`).
 - [ ] Usage Documentation in `docs/usage.md` is updated.

.github/workflows/ci.yml

@@ -25,7 +25,7 @@ jobs:
     strategy:
       matrix:
         NXF_VER:
-          - "23.04.0"
+          - "23.10.0"
           - "latest-everything"
     steps:
       - name: Check out pipeline code

.github/workflows/linting.yml

@@ -1,6 +1,6 @@
 name: nf-core linting
 # This workflow is triggered on pushes and PRs to the repository.
-# It runs the `nf-core lint` and markdown lint tests to ensure
+# It runs the `nf-core pipelines lint` and markdown lint tests to ensure
 # that the code meets the nf-core guidelines.
 on:
   push:
@@ -41,17 +41,32 @@ jobs:
           python-version: "3.12"
           architecture: "x64"
 
+      - name: read .nf-core.yml
+        uses: pietrobolcato/[email protected]
+        id: read_yml
+        with:
+          config: ${{ github.workspace }}/.nf-core.yml
+
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install nf-core
+          pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }}
+
+      - name: Run nf-core pipelines lint
+        if: ${{ github.base_ref != 'master' }}
+        env:
+          GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }}
+        run: nf-core -l lint_log.txt pipelines lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md
 
-      - name: Run nf-core lint
+      - name: Run nf-core pipelines lint --release
+        if: ${{ github.base_ref == 'master' }}
         env:
           GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }}
-        run: nf-core -l lint_log.txt lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md
+        run: nf-core -l lint_log.txt pipelines lint --release --dir ${GITHUB_WORKSPACE} --markdown lint_results.md
 
       - name: Save PR number
         if: ${{ always() }}

.github/workflows/linting_comment.yml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Download lint results
-        uses: dawidd6/action-download-artifact@09f2f74827fd3a8607589e5ad7f9398816f540fe # v3
+        uses: dawidd6/action-download-artifact@bf251b5aa9c2f7eeb574a96ee720e24f801b7c11 # v6
         with:
           workflow: linting.yml
           workflow_conclusion: completed

.gitignore

@@ -6,3 +6,4 @@ results/
 testing/
 testing*
 *.pyc
+null/

.nf-core.yml

@@ -1,4 +1,4 @@
-nf_core_version: 2.14.1
+nf_core_version: 3.0.2
 lint:
   files_exist:
     - CODE_OF_CONDUCT.md
@@ -16,9 +16,7 @@ lint:
     - .github/ISSUE_TEMPLATE/bug_report.yml
   multiqc_config:
     - report_comment
-  nextflow_config:
-    - manifest.name
-    - manifest.homePage
+  nextflow_config: false
 repository_type: pipeline
 template:
   prefix: mskcc

.prettierignore

@@ -11,3 +11,6 @@ testing*
 *.pyc
 bin/
 README.md
+modules/nf-core/*
+.github/*
+subworkflows/nf-core/*

.prettierrc

@@ -0,0 +1 @@
+{}

README.md

@@ -1,6 +1,6 @@
 > [![GitHub Actions CI Status](https://github.com/mskcc/neoantigen-pipeline/actions/workflows/ci.yml/badge.svg)](https://github.com/mskcc/neoantigen-pipeline/actions/workflows/ci.yml) > [![GitHub Actions Linting Status](https://github.com/mskcc/neoantigen-pipeline/actions/workflows/linting.yml/badge.svg)](https://github.com/mskcc/neoantigen-pipeline/actions/workflows/linting.yml) > [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
 
-[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/)
+[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.10.0-23aa62.svg)](https://www.nextflow.io/)
 [![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/)

conf/modules.config

@@ -11,7 +11,6 @@
 */
 
 process {
-
     publishDir = [
         path: { "${params.outdir}/${task.tag}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
         mode: params.publish_dir_mode,
@@ -22,12 +21,11 @@ process {
         ext.args = '-f facets'
     }
 
-
     withName: 'PHYLOWGS_MULTIEVOLVE' {
-        ext.args = "--burnin-samples ${params.phylo_burnin_samples} --mcmc-samples ${params.phylo_mcmc_samples}"
+        ext.args = "--burnin-samples ${params.phylo_burnin_samples} --mcmc-samples ${params.phylo_mcmc_samples} --num-chains ${params.phylo_num_chains}"
     }
 
     withName: 'PHYLOWGS_WRITERESULTS' {
-        ext.args = "--max-multiprimary 1.0"
+        ext.args = '--max-multiprimary 1.0'
     }
 }

conf/prod.config

@@ -29,11 +29,15 @@ params {
     max_memory = '10.GB'
     max_time   = '100.h'
 
+    netmhc3 = true
+
     // Genome references
     genome = 'GRCh37'
     phylo_burnin_samples = 1000
     phylo_mcmc_samples = 2500
-    iedbfasta = 'https://raw.githubusercontent.com/mskcc-omics-workflows/test-datasets/neoantigen/neoantigen/neoantigenEditing/data/iedb.fasta'
+    phylo_num_chains = 15
+
+    iedbfasta = 'https://raw.githubusercontent.com/mskcc/NeoantigenEditing/refs/heads/main/data/iedb.fasta'
     cds = 'https://github.com/mskcc-omics-workflows/test-datasets/raw/neoantigen/neoantigen/Homo_sapiens.GRCh37.75.cds.all.fa.gz'
     cdna = 'https://github.com/mskcc-omics-workflows/test-datasets/raw/neoantigen/neoantigen/Homo_sapiens.GRCh37.75.cdna.all.fa.gz'
 }

conf/test.config

@@ -28,6 +28,8 @@ params {
     genome = 'GRCh37'
     phylo_burnin_samples = 2
     phylo_mcmc_samples = 2
+    phylo_num_chains = 2
+    netmhc3 = true
 
     iedbfasta = 'https://raw.githubusercontent.com/mskcc-omics-workflows/test-datasets/neoantigen/neoantigen/neoantigenEditing/data/iedb.fasta'
     cds = 'https://github.com/mskcc-omics-workflows/test-datasets/raw/neoantigen/neoantigen/Homo_sapiens.GRCh37.75.cds.all.fa.gz'

main.nf

@@ -56,7 +56,8 @@ workflow MSKCC_NEOANTIGENPIPELINE {
     )
 
     emit:
-    out = NEOANTIGENPIPELINE.out.neo_out // channel: /path/to/multiqc_report.html
+    out = NEOANTIGENPIPELINE.out.neo_out
+    tsv = NEOANTIGENPIPELINE.out.tsv_out
 
 }
 /*

modules.json

@@ -7,62 +7,77 @@
                 "msk": {
                     "neoantigenediting/aligntoiedb": {
                         "branch": "develop",
-                        "git_sha": "cac9c047e374ee259fb612ba5816e7e6aae6b86f",
-                        "installed_by": ["neoantigen_editing"]
+                        "git_sha": "34505c4c67eabebab927561d3a8fca87c9efe788",
+                        "installed_by": ["modules", "neoantigen_editing"]
                     },
                     "neoantigenediting/computefitness": {
                         "branch": "develop",
-                        "git_sha": "1f65c2ecdc5010549055ff7f4e6b8bccee48d4ae",
-                        "installed_by": ["neoantigen_editing"]
+                        "git_sha": "05e49188ee9407e1b51dfb1a49d8b6133e9276bc",
+                        "installed_by": ["modules", "neoantigen_editing"]
+                    },
+                    "neoantigenutils/convertannotjson": {
+                        "branch": "develop",
+                        "git_sha": "34505c4c67eabebab927561d3a8fca87c9efe788",
+                        "installed_by": ["modules"]
                     },
                     "neoantigenutils/formatnetmhcpan": {
                         "branch": "develop",
-                        "git_sha": "c5d1252252e15555abcc82ea537cebeb281a1856",
-                        "installed_by": ["netmhcstabandpan"]
+                        "git_sha": "e6bbb12a2dc237b9ea18163e96dbe9d780ddce5f",
+                        "installed_by": ["modules", "netmhcstabandpan"]
                     },
                     "neoantigenutils/generatehlastring": {
                         "branch": "develop",
-                        "git_sha": "33f0bd33095fa15016ee24f4fb4d61e896dbb970",
-                        "installed_by": ["netmhcstabandpan"]
+                        "git_sha": "34505c4c67eabebab927561d3a8fca87c9efe788",
+                        "installed_by": ["modules", "netmhcstabandpan"]
                     },
                     "neoantigenutils/generatemutfasta": {
                         "branch": "develop",
-                        "git_sha": "bb7975c796ab9a2d7a45ef733a6a226a0f5ad74a",
-                        "installed_by": ["netmhcstabandpan"]
+                        "git_sha": "e6bbb12a2dc237b9ea18163e96dbe9d780ddce5f",
+                        "installed_by": ["modules", "netmhcstabandpan"]
                     },
                     "neoantigenutils/neoantigeninput": {
-                        "branch": "neoantigen",
-                        "git_sha": "d66d3e2c7d132efe8bbde0c7e8a072b0f974b085",
+                        "branch": "develop",
+                        "git_sha": "003587a171d6cfa80bc894950d212add9f206f88",
                         "installed_by": ["modules"]
                     },
-                    "netmhcpan": {
+                    "netmhc3": {
                         "branch": "develop",
+                        "git_sha": "9baf08c136733d9e4c0b16c169b7eebfb98d3291",
+                        "installed_by": ["modules", "netmhcstabandpan"]
+                    },
+                    "netmhcpan": {
+                        "branch": "main",
                         "git_sha": "503abeb67260f060d8228221b07d743aa4180345",
+                        "installed_by": ["modules"]
+                    },
+                    "netmhcpan4": {
+                        "branch": "develop",
+                        "git_sha": "e64e6e100302131d575881363a9632936499918d",
                         "installed_by": ["modules", "netmhcstabandpan"]
                     },
                     "netmhcstabpan": {
                         "branch": "develop",
-                        "git_sha": "c1a473f8bc08f778269a36ab62d5adf24357225f",
+                        "git_sha": "3c39dd8d3d0a92aa33fda4352749e35fc22d3e87",
                         "installed_by": ["modules", "netmhcstabandpan"]
                     },
                     "phylowgs/createinput": {
                         "branch": "develop",
-                        "git_sha": "b031249dcf4279606c25e626da2a628756e75e8a",
+                        "git_sha": "05e49188ee9407e1b51dfb1a49d8b6133e9276bc",
                         "installed_by": ["phylowgs"]
                     },
                     "phylowgs/multievolve": {
                         "branch": "develop",
-                        "git_sha": "535662d391a3533dea3b11c462c14799227e08b2",
+                        "git_sha": "980c1328a92a6cc547834ccc361c5187d0927944",
                         "installed_by": ["phylowgs"]
                     },
                     "phylowgs/parsecnvs": {
                         "branch": "develop",
-                        "git_sha": "8471691d7c29bc2f5f4fb92279c94fb2640b6c38",
+                        "git_sha": "34505c4c67eabebab927561d3a8fca87c9efe788",
                         "installed_by": ["phylowgs"]
                     },
                     "phylowgs/writeresults": {
                         "branch": "develop",
-                        "git_sha": "6d27f08bf649e8680ace321d3127dcdf0e210973",
+                        "git_sha": "34505c4c67eabebab927561d3a8fca87c9efe788",
                         "installed_by": ["phylowgs"]
                     }
                 }
@@ -76,7 +91,7 @@
                     },
                     "netmhcstabandpan": {
                         "branch": "develop",
-                        "git_sha": "d60211568e3709e9284bc06eef938e361d474d08",
+                        "git_sha": "bbd3f9da83852bb8a87a7540a16b185cf28877ea",
                         "installed_by": ["subworkflows"]
                     },
                     "phylowgs": {
@@ -92,7 +107,7 @@
                 "nf-core": {
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "b80f5fd12ff7c43938f424dd76392a2704fa2396",
+                        "git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d",
                         "installed_by": ["modules"]
                     }
                 }

modules/msk/neoantigenediting/aligntoiedb/environment.yml

@@ -1,9 +1,7 @@
 ---
 # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
-name: "neoantigenediting_aligntoiedb"
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
-  - "NEOANTIGENEDITING"
+  - "YOUR-TOOL=HERE"