Merge pull request #260 from nf-core/dev

Release 2.4.1

.devcontainer/devcontainer.json

@@ -0,0 +1,27 @@
+{
+    "name": "nfcore",
+    "image": "nfcore/gitpod:latest",
+    "remoteUser": "gitpod",
+
+    // Configure tool-specific properties.
+    "customizations": {
+        // Configure properties specific to VS Code.
+        "vscode": {
+            // Set *default* container specific settings.json values on container create.
+            "settings": {
+                "python.defaultInterpreterPath": "/opt/conda/bin/python",
+                "python.linting.enabled": true,
+                "python.linting.pylintEnabled": true,
+                "python.formatting.autopep8Path": "/opt/conda/bin/autopep8",
+                "python.formatting.yapfPath": "/opt/conda/bin/yapf",
+                "python.linting.flake8Path": "/opt/conda/bin/flake8",
+                "python.linting.pycodestylePath": "/opt/conda/bin/pycodestyle",
+                "python.linting.pydocstylePath": "/opt/conda/bin/pydocstyle",
+                "python.linting.pylintPath": "/opt/conda/bin/pylint"
+            },
+
+            // 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"]
+        }
+    }
+}

.gitattributes

@@ -1,3 +1,4 @@
 *.config linguist-language=nextflow
+*.nf.test linguist-language=nextflow
 modules/nf-core/** linguist-generated
 subworkflows/nf-core/** linguist-generated

.github/CONTRIBUTING.md

@@ -101,3 +101,19 @@ If you are using a new feature from core Nextflow, you may bump the minimum requ
 ### Images and figures
 
 For overview images and other documents we follow the nf-core [style guidelines and examples](https://nf-co.re/developers/design_guidelines).
+
+## GitHub Codespaces
+
+This repo includes a devcontainer configuration which will create a GitHub Codespaces for Nextflow development! This is an online developer environment that runs in your browser, complete with VSCode and a terminal.
+
+To get started:
+
+- Open the repo in [Codespaces](https://github.com/nf-core/mhcquant/codespaces)
+- Tools installed
+  - nf-core
+  - Nextflow
+
+Devcontainer specs:
+
+- [DevContainer config](.devcontainer/devcontainer.json)
+- [Dockerfile](.devcontainer/Dockerfile)

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -42,7 +42,7 @@ body:
     attributes:
       label: System information
       description: |
-        * Nextflow version _(eg. 21.10.3)_
+        * Nextflow version _(eg. 22.10.1)_
         * Hardware _(eg. HPC, Desktop, Cloud)_
         * Executor _(eg. slurm, local, awsbatch)_
         * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter or Charliecloud)_

.github/workflows/ci.yml

@@ -11,6 +11,10 @@ on:
 env:
   NXF_ANSI_LOG: false
 
+concurrency:
+  group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
+  cancel-in-progress: true
+
 jobs:
   test:
     name: Run pipeline with test data
@@ -20,11 +24,11 @@ jobs:
     strategy:
       matrix:
         NXF_VER:
-          - "21.10.3"
+          - "22.10.1"
           - "latest-everything"
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1
@@ -33,7 +37,7 @@ jobs:
 
       - name: Run pipeline with test data
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --spectrum_batch_size 5000 --outdir ./results
 
   test_additional_params:
     name: Run pipeline with additional params
@@ -45,7 +49,7 @@ jobs:
         # Nextflow versions
         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: ""
@@ -66,6 +70,4 @@ jobs:
 
       - name: Run pipeline with additional params
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --predict_class_1 --predict_class_2 --predict_RT --outdir ./results
-
-#
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --predict_class_1 --predict_class_2 --predict_RT --spectrum_batch_size 2000 --outdir ./results

.github/workflows/fix-linting.yml

@@ -24,7 +24,7 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
-      - uses: actions/setup-node@v2
+      - uses: actions/setup-node@v3
 
       - name: Install Prettier
         run: npm install -g prettier @prettier/plugin-php
@@ -34,9 +34,9 @@ jobs:
         id: prettier_status
         run: |
           if prettier --check ${GITHUB_WORKSPACE}; then
-            echo "::set-output name=result::pass"
+            echo "result=pass" >> $GITHUB_OUTPUT
           else
-            echo "::set-output name=result::fail"
+            echo "result=fail" >> $GITHUB_OUTPUT
           fi
 
       - name: Run 'prettier --write'

.github/workflows/linting.yml

@@ -4,6 +4,8 @@ name: nf-core linting
 # that the code meets the nf-core guidelines.
 on:
   push:
+    branches:
+      - dev
   pull_request:
   release:
     types: [published]
@@ -12,9 +14,9 @@ jobs:
   EditorConfig:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: actions/setup-node@v2
+      - uses: actions/setup-node@v3
 
       - name: Install editorconfig-checker
         run: npm install -g editorconfig-checker
@@ -25,9 +27,9 @@ jobs:
   Prettier:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: actions/setup-node@v2
+      - uses: actions/setup-node@v3
 
       - name: Install Prettier
         run: npm install -g prettier
@@ -38,7 +40,7 @@ jobs:
   PythonBlack:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - name: Check code lints with Black
         uses: psf/black@stable
@@ -69,12 +71,12 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1
 
-      - uses: actions/setup-python@v3
+      - uses: actions/setup-python@v4
         with:
           python-version: "3.7"
           architecture: "x64"
@@ -97,7 +99,7 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v3
         with:
           name: linting-logs
           path: |

.github/workflows/linting_comment.yml

@@ -18,7 +18,7 @@ jobs:
 
       - name: Get PR number
         id: pr_number
-        run: echo "::set-output name=pr_number::$(cat linting-logs/PR_number.txt)"
+        run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT
 
       - name: Post PR comment
         uses: marocchino/sticky-pull-request-comment@v2

.prettierignore

@@ -1,5 +1,6 @@
 email_template.html
 adaptivecard.json
+slackreport.json
 .nextflow*
 work/
 data/
@@ -8,3 +9,4 @@ results/
 testing/
 testing*
 *.pyc
+bin/

CHANGELOG.md

@@ -3,6 +3,23 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## v2.4.1 nfcore/mhcquant "Maroon Gold Boxer" (patch) - 2023/04/04
+
+### `Added`
+
+- Added low resolution settings (e.g. Iontrap) [#254](https://github.com/nf-core/mhcquant/pull/254)
+
+### `Fixed`
+
+- Increased comet search, through altering the spectrum_batch_size from 500 to 0
+- [#249](https://github.com/nf-core/mhcquant/pull/249) - nf-core template update (version 2.7.2)
+- [#258](https://github.com/nf-core/mhcquant/pull/258) - Adjusted decoy strategy to reverse [#255](https://github.com/nf-core/mhcquant/issues/255) and made consistent fdr-level flags [#228](https://github.com/nf-core/mhcquant/issues/228)
+- [#845](https://github.com/nf-core/test-datasets/pull/845) - Adjusted nf-core test data set [#233](https://github.com/nf-core/mhcquant/issues/233)
+
+### `Dependencies`
+
+### `Deprecated`
+
 ## v2.4.0 nfcore/mhcquant "Maroon Gold Boxer" - 2022/12/02
 
 Initial release of nf-core/mhcquant, created with the [nf-core](https://nf-co.re/) template.

README.md

@@ -2,7 +2,7 @@
 
 [![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/mhcquant/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.1569909-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.1569909)
 
-[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A521.10.3-23aa62.svg)](https://www.nextflow.io/)
+[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A522.10.1-23aa62.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/)
@@ -26,7 +26,7 @@ On release, automated continuous integration tests run the pipeline on a full-si
 
 ## Quick Start
 
-1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=21.10.3`)
+1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=22.10.1`)
 
 2. Install any of [`Docker`](https://docs.docker.com/engine/installation/), [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/) (you can follow [this tutorial](https://singularity-tutorial.github.io/01-installation/)), [`Podman`](https://podman.io/), [`Shifter`](https://nersc.gitlab.io/development/shifter/how-to-use/) or [`Charliecloud`](https://hpc.github.io/charliecloud/) for full pipeline reproducibility _(you can use [`Conda`](https://conda.io/miniconda.html) both to install Nextflow itself and also to manage software within pipelines. Please only use it within pipelines as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))_.
 

assets/methods_description_template.yml

@@ -3,7 +3,6 @@ description: "Suggested text and references to use when describing pipeline usag
 section_name: "nf-core/mhcquant Methods Description"
 section_href: "https://github.com/nf-core/mhcquant"
 plot_type: "html"
-## TODO nf-core: Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline
 ## You inject any metadata in the Nextflow '${workflow}' object
 data: |
   <h4>Methods</h4>

assets/slackreport.json

@@ -0,0 +1,34 @@
+{
+    "attachments": [
+        {
+            "fallback": "Plain-text summary of the attachment.",
+            "color": "<% if (success) { %>good<% } else { %>danger<%} %>",
+            "author_name": "sanger-tol/readmapping v${version} - ${runName}",
+            "author_icon": "https://www.nextflow.io/docs/latest/_static/favicon.ico",
+            "text": "<% if (success) { %>Pipeline completed successfully!<% } else { %>Pipeline completed with errors<% } %>",
+            "fields": [
+                {
+                    "title": "Command used to launch the workflow",
+                    "value": "```${commandLine}```",
+                    "short": false
+                }
+                <%
+                    if (!success) { %>
+                    ,
+                    {
+                        "title": "Full error message",
+                        "value": "```${errorReport}```",
+                        "short": false
+                    },
+                    {
+                        "title": "Pipeline configuration",
+                        "value": "<% out << summary.collect{ k,v -> k == "hook_url" ? "_${k}_: (_hidden_)" : ( ( v.class.toString().contains('Path') || ( v.class.toString().contains('String') && v.contains('/') ) ) ? "_${k}_: `${v}`" : (v.class.toString().contains('DateTime') ? ("_${k}_: " + v.format(java.time.format.DateTimeFormatter.ofLocalizedDateTime(java.time.format.FormatStyle.MEDIUM))) : "_${k}_: ${v}") ) }.join(",\n") %>",
+                        "short": false
+                    }
+                    <% }
+                %>
+            ],
+            "footer": "Completed at <% out << dateComplete.format(java.time.format.DateTimeFormatter.ofLocalizedDateTime(java.time.format.FormatStyle.MEDIUM)) %> (duration: ${duration})"
+        }
+    ]
+}

bin/check_samplesheet.py

@@ -1,5 +1,7 @@
 #!/usr/bin/env python
 
+# Written by Marissa Dubbelaar and released under MIT license.
+
 """Provide a command line tool to validate and transform tabular samplesheets."""
 
 import os
@@ -147,7 +149,6 @@ def sniff_format(handle):
 
 
 def check_samplesheet(file_in, file_out):
-
     """
     Check that the tabular samplesheet has the structure expected by nf-core pipelines.
     Validate the general shape of the table, expected columns, and each row. Also add

bin/get_ion_annotations.py

@@ -1,5 +1,6 @@
 #!/usr/bin/env python
-__author__ = "Jonas Scheid"
+
+# Written by Jonas Scheid and released under MIT license.
 
 from typing import Tuple
 from pyopenms import *

bin/markdown_to_html.py

@@ -1,4 +1,5 @@
 #!/usr/bin/env python
+
 from __future__ import print_function
 import argparse
 import markdown

bin/mhcflurry_neoepitope_binding_prediction.py

@@ -1,4 +1,7 @@
 #!/usr/bin/env python
+
+# Written by Lukas Heumos and released under MIT license.
+
 import pandas as pd
 import numpy as np
 import logging

bin/mhcflurry_predict_mztab.py

@@ -1,4 +1,7 @@
 #!/usr/bin/env python
+
+# Written by Lukas Heumos and released under MIT license.
+
 import argparse
 import logging
 import pandas as pd

bin/mhcflurry_predict_mztab_for_filtering.py

@@ -1,4 +1,7 @@
 #!/usr/bin/env python
+
+# Written by Lukas Heumos and released under MIT license.
+
 from mhcflurry import Class1AffinityPredictor
 import logging
 import sys

bin/mhcnuggets_predict_peptides.py

@@ -1,4 +1,7 @@
 #!/usr/bin/env python
+
+# Written by Lukas Heumos and released under MIT license.
+
 from mhcnuggets.src.predict import predict
 import argparse
 import logging

bin/postprocess_neoepitopes_mhcnuggets.py

@@ -1,4 +1,7 @@
 #!/usr/bin/env python
+
+# Written by Lukas Heumos and released under MIT license.
+
 import argparse
 import sys
 import logging

bin/postprocess_peptides_mhcnuggets.py

@@ -1,4 +1,7 @@
 #!/usr/bin/env python
+
+# Written by Lukas Heumos and released under MIT license.
+
 import argparse
 import sys
 import logging

bin/preprocess_neoepitopes_mhcnuggets.py

@@ -1,4 +1,7 @@
 #!/usr/bin/env python
+
+# Written by Lukas Heumos and released under MIT license.
+
 import argparse
 import logging
 import sys

bin/preprocess_peptides_mhcnuggets.py

@@ -1,5 +1,7 @@
 #!/usr/bin/env python
 
+# Written by Lukas Heumos and released under MIT license.
+
 import argparse
 import logging
 import sys