Merge pull request #45 from mskcc/feature/netmhc_refactor

Feature/netmhc refactor

.editorconfig

@@ -24,6 +24,19 @@ end_of_line = unset
 insert_final_newline = unset
 trim_trailing_whitespace = unset
 indent_style = unset
+[/modules/msk/**]
+charset = unset
+end_of_line = unset
+insert_final_newline = unset
+trim_trailing_whitespace = unset
+indent_style = unset
+[/subworkflows/msk/**]
+charset = unset
+end_of_line = unset
+insert_final_newline = unset
+trim_trailing_whitespace = unset
+indent_style = unset
+
 
 [/assets/email*]
 indent_size = unset

.github/PULL_REQUEST_TEMPLATE.md

@@ -17,7 +17,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/mskcc/neoant
 - [ ] 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`).
-- [ ] Ensure the test suite passes (`nf-test test main.nf.test -profile test,docker`).
+- [ ] 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.
 - [ ] Output Documentation in `docs/output.md` is updated.

.github/workflows/download_pipeline.yml

@@ -11,14 +11,14 @@ on:
         description: "The specific branch you wish to utilize for the test execution of nf-core download."
         required: true
         default: "dev"
-  pull_request:
-    types:
-      - opened
-    branches:
-      - master
-  pull_request_target:
-    branches:
-      - master
+#  pull_request:
+#    types:
+#      - opened
+#    branches:
+#      - master
+#  pull_request_target:
+#    branches:
+#      - master
 
 env:
   NXF_ANSI_LOG: false

.github/workflows/linting.yml

@@ -14,13 +14,12 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
 
-      - name: Set up Python 3.11
-        uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - name: Set up Python 3.12
+        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
-          python-version: 3.11
-          cache: "pip"
+          python-version: "3.12"
 
       - name: Install pre-commit
         run: pip install pre-commit
@@ -32,14 +31,14 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
+        uses: nf-core/setup-nextflow@v2
 
-      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
-          python-version: "3.11"
+          python-version: "3.12"
           architecture: "x64"
 
       - name: Install dependencies
@@ -60,7 +59,7 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4
+        uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4
         with:
           name: linting-logs
           path: |

.github/workflows/linting_comment.yml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Download lint results
-        uses: dawidd6/action-download-artifact@f6b0bace624032e30a85a8fd9c1a7f8f611f5737 # v3
+        uses: dawidd6/action-download-artifact@09f2f74827fd3a8607589e5ad7f9398816f540fe # v3
         with:
           workflow: linting.yml
           workflow_conclusion: completed

.gitignore

@@ -6,6 +6,3 @@ results/
 testing/
 testing*
 *.pyc
-.nf-test/
-out/*
-.nf-test.log

.nf-core.yml

@@ -1,3 +1,4 @@
+nf_core_version: 2.14.1
 lint:
   files_exist:
     - CODE_OF_CONDUCT.md

CITATIONS.md

@@ -10,13 +10,20 @@
 
 ## Pipeline tools
 
-- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
+- [Phylowgs](https://github.com/morrislab/phylowgs)
 
-  > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].
+  > Deshwar, A. G., Vembu, S., Yung, C. K., Jang, G. H., Stein, L., & Morris, Q. (2015). PhyloWGS: reconstructing subclonal composition and evolution from whole-genome sequencing of tumors. Genome biology, 16(1), 35. https://doi.org/10.1186/s13059-015-0602-8
 
-- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
+- [NetMHCPan-4](https://services.healthtech.dtu.dk/services/NetMHCpan-4.1/)
 
-  > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.
+  > Jurtz, V., Paul, S., Andreatta, M., Marcatili, P., Peters, B., & Nielsen, M. (2017). NetMHCpan-4.0: Improved Peptide-MHC Class I Interaction Predictions Integrating Eluted Ligand and Peptide Binding Affinity Data. Journal of immunology (Baltimore, Md. : 1950), 199(9), 3360–3368. https://doi.org/10.4049/jimmunol.1700893
+
+- [NeoantigenEditing](https://github.com/LukszaLab/NeoantigenEditing)
+
+  > Łuksza, M., Sethna, Z.M., Rojas, L.A. et al. Neoantigen quality predicts immunoediting in survivors of pancreatic cancer. Nature 606, 389–395 (2022). https://doi.org/10.1038/s41586-022-04735-9
+
+- [NetMHCPanStab](https://services.healthtech.dtu.dk/services/NetMHCstabpan-1.0/)
+  > Rasmussen, M., Fenoy, E., Harndahl, M., Kristensen, A. B., Nielsen, I. K., Nielsen, M., & Buus, S. (2016). Pan-Specific Prediction of Peptide-MHC Class I Complex Stability, a Correlate of T Cell Immunogenicity. Journal of immunology (Baltimore, Md. : 1950), 197(4), 1517–1524. https://doi.org/10.4049/jimmunol.1600582
 
 ## Software packaging/containerisation tools