Release/0.1.1

.editorconfig

@@ -0,0 +1,15 @@
+root = true
+
+[*]
+charset = utf-8
+end_of_line = lf
+insert_final_newline = true
+trim_trailing_whitespace = true
+indent_size = 4
+indent_style = space
+
+[*.{md,yml,yaml,cff}]
+indent_size = 2
+
+[*.nf.test]
+insert_final_newline = false

.github/CODEOWNERS

@@ -1,2 +1,2 @@
-# Review from a member of the review-team is required 
+# Review from a member of the review-team is required
 * @mskcc-omics-workflows/reviewers

.github/workflows/gitbook-sync.yml

@@ -74,6 +74,9 @@ jobs:
 
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 2 # To retrieve the preceding commit.
       - run: echo "🎉 The job was automatically triggered by a ${{ github.event_name }} event."
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
       - name: setup python
@@ -109,6 +112,7 @@ jobs:
       - uses: jaywcjlove/github-action-read-file@main
         id: cat_file_module
         with:
+          branch: ${{ github.ref }}
           path: modules/msk/${{ env.SW_NAME }}/meta.yml
       - name: Write Module yaml to temp
         if: ${{ steps.cat_file_module.outputs.size }}
@@ -126,6 +130,7 @@ jobs:
         if: ${{ steps.cat_file_module.outputs.size == '' }}
         id: cat_file_subworkflow
         with:
+          branch: ${{ github.ref }}
           path: subworkflows/msk/${{ env.SW_NAME }}/meta.yml
       - name: Write Subworkflow yaml to temp
         if: ${{ steps.cat_file_subworkflow.outputs.size }}

.github/workflows/test.yml

@@ -173,6 +173,9 @@ jobs:
             "${{ fromJson(needs.nf-test-changes.outputs.modules) }}",
           ]
     steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 2 # To retrieve the preceding commit.
       - name: setup python
         uses: actions/setup-python@v4
         with:
@@ -193,9 +196,11 @@ jobs:
           TEMP_NAME=$(echo $MATRIX_FRAGMENT | sed 's/subworkflows\///g')
           SW_NAME=$(echo $TEMP_NAME | sed 's/modules\///g')
           echo "SW_NAME=$SW_NAME" >> $GITHUB_ENV
+          echo $SW_NAME
       - uses: jaywcjlove/github-action-read-file@main
         id: cat_file_module
         with:
+          branch: ${{ github.ref }}
           path: modules/msk/${{ env.SW_NAME }}/meta.yml
       - run: echo "${{ steps.cat_file_module.outputs.size }}"
       - name: Write Module yaml to temp
@@ -209,6 +214,7 @@ jobs:
         if: ${{ steps.cat_file_module.outputs.size == '' }}
         id: cat_file_subworkflow
         with:
+          branch: ${{ github.ref }}
           path: subworkflows/msk/${{ env.SW_NAME }}/meta.yml
       - name: Write Subworkflow yaml to temp
         if: ${{ steps.cat_file_subworkflow.outputs.size }}
@@ -352,8 +358,65 @@ jobs:
             tags: facets
           - profile: "conda"
             tags: mutect1
+          - profile: "conda"
+            tags: phylowgs/createinput
+          - profile: "conda"
+            tags: phylowgs/parsecnvs
+          - profile: "conda"
+            tags: phylowgs/multievolve
+          - profile: "conda"
+            tags: phylowgs/writeresults
+          - profile: "conda"
+            tags: netmhcpan
+          - profile: "conda"
+            tags: neoantigeninput
+          - profile: "conda"
+            tags: neoantigenediting/aligntoIEDB
+          - profile: "conda"
+            tags: neoantigenediting/computeFitness
+          - profile: "conda"
+            tags: subworkflows/neoantigen_editing
+          - profile: "conda"
+            tags: subworkflows/phylowgs
+          - profile: "conda"
+            tags: netmhcstabpan
           - profile: "conda"
             tags: ppflagfixer
+          - profile: "conda"
+            tags: neoantigenutils/generatemutfasta
+          - profile: "conda"
+            tags: neoantigenutils/formatnetmhcpan
+          - profile: "conda"
+            tags: neoantigenutils/generatehlastring
+          - profile: "conda"
+            tags: neoantigenutils/neoantigeninput
+          - profile: "conda"
+            tags: subworkflows/netmhcstabandpan
+          - profile: "conda"
+            tags: salmon/index
+          - profile: "conda"
+            tags: genomenexus/vcf2maf
+          - profile: "conda"
+            tags: genomenexus/annotationpipeline
+          - profile: "conda"
+            tags: ppflagfixer
+          - profile: "conda"
+            tags: pvmaf/tagtraceback
+          - profile: "conda"
+            tags: pvmaf/concat
+          - profile: "conda"
+            tags: genotypevariants/all
+          - profile: "conda"
+            tags: subworkflows/traceback
+          - profile: "conda"
+            tags: salmon/index
+          - profile: "conda"
+            tags: subworkflows/genome_nexus
+          - profile: "conda"
+            tags: salmon/quant
+          - profile: "conda"
+            tags: rediscoverte
+
     env:
       NXF_ANSI_LOG: false
       SENTIEON_LICENSE_BASE64: ${{ secrets.SENTIEON_LICENSE_BASE64 }}

.github/workflows/update_summary.py

@@ -1,19 +1,19 @@
 import sys
 
 def update_summary(origin: str, new_feature: str, feature_type: str):
-  out_summary = ""
-  with open(origin, 'r') as f:
-    for line in f.readlines():
-      if feature_type == "module" and line.startswith("## Subworkflows"):
-        out_summary += new_feature + '\n\n'
-      if line.strip():
-        out_summary += line
-  if feature_type == "subworkflow":
-    out_summary += new_feature
-  return out_summary
-        
+    out_summary = ""
+    with open(origin, 'r') as f:
+        for line in f.readlines():
+        if feature_type == "module" and line.startswith("## Subworkflows"):
+            out_summary += new_feature + '\n\n'
+        if line.strip():
+            out_summary += line
+    if feature_type == "subworkflow":
+        out_summary += new_feature
+    return out_summary
+
 if __name__ == "__main__":
-  origin_summary = sys.argv[1]
-  new_feature = sys.argv[2]
-  feature_type = sys.argv[3]
-  print(update_summary(origin_summary, new_feature, feature_type))
+    origin_summary = sys.argv[1]
+    new_feature = sys.argv[2]
+    feature_type = sys.argv[3]
+    print(update_summary(origin_summary, new_feature, feature_type))

.prettierignore

@@ -0,0 +1,19 @@
+includes/Maven_Pro/
+
+# gitignore
+.nextflow*
+work/
+results/
+test_output/
+output/
+.DS_Store
+*.code-workspace
+tests/data/
+.screenrc
+.*.sw?
+__pycache__
+*.pyo
+*.pyc
+.github/renovate.json5
+.github/workflows/update_summary.py
+distance_data/

.prettierrc

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

.prettierrc.yml

@@ -0,0 +1 @@
+printWidth: 120

README.md

@@ -0,0 +1,156 @@
+# mskcc-omics-workflows/modules
+
+adapted from [nf-core/modules/README.md](https://github.com/nf-core/modules/blob/master/README.md)
+
+[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A521.10.3-23aa62.svg?labelColor=000000)](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/)
+
+![GitHub Actions Coda Linting](https://github.com/nf-core/modules/workflows/Code%20Linting/badge.svg)
+
+> THIS REPOSITORY IS UNDER ACTIVE DEVELOPMENT. SYNTAX, ORGANISATION AND LAYOUT MAY CHANGE WITHOUT NOTICE!
+
+A repository for hosting [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) module files containing tool-specific process definitions and their associated documentation.
+
+## Table of contents
+
+- [mskcc-omics-workflows/modules](#mskcc-omics-workflowsmodules)
+  - [Table of contents](#table-of-contents)
+  - [Using existing modules](#using-existing-modules)
+  - [Adding new modules](#adding-new-modules)
+  - [Help](#help)
+  - [Citation](#citation)
+
+## Using existing modules
+
+The module files hosted in this repository define a set of processes for software tools such as `facets`, `gbcms`, `snppileup` etc. This allows you to share and add common functionality across multiple pipelines in a modular fashion.
+
+We use a helper command in the `nf-core/tools` package that uses the GitHub API to obtain the relevant information for the module files present in the [`modules/`](modules/) directory of this repository. This includes using `git` commit hashes to track changes for reproducibility purposes, and to download and install all of the relevant module files.
+
+1. Install the latest version of [`nf-core/tools`](https://github.com/nf-core/tools#installation) (`>=2.0`)
+2. List the available modules:
+
+   ```console
+   $ nf-core modules --git-remote [email protected]:mskcc-omics-workflows/modules.git list remote
+
+                                         ,--./,-.
+         ___     __   __   __   ___     /,-._.--~\
+   |\ | |__  __ /  ` /  \ |__) |__         }  {
+   | \| |       \__, \__/ |  \ |___     \`-._,-`-,
+                                         `._,._,'
+
+   nf-core/tools version 2.14.1 - https://nf-co.re
+
+   INFO     Modules available from [email protected]:mskcc-omics-workflows/modules.git (main):
+
+   ┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓
+   ┃ Module Name                    ┃
+   ┡━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩
+   │ custom/splitfastqbylane        │
+   │ facets                         │
+   │ gatk4/applybqsr                │
+   │ gbcms                          │
+   ..truncated..
+   ```
+
+3. Install the module in your pipeline directory:
+
+   ```console
+   $ nf-core modules --git-remote [email protected]:mskcc-omics-workflows/modules.git install facets
+
+                                         ,--./,-.
+         ___     __   __   __   ___     /,-._.--~\
+   |\ | |__  __ /  ` /  \ |__) |__         }  {
+   | \| |       \__, \__/ |  \ |___     \`-._,-`-,
+                                         `._,._,'
+
+    nf-core/tools version 2.14.1 - https://nf-co.re
+
+    INFO     Installing 'facets'
+    INFO     Use the following statement to include this module:
+
+     include { FACETS } from '../modules/msk/facets/main'
+   ```
+
+4. Import the module in your Nextflow script:
+
+   ```nextflow
+   #!/usr/bin/env nextflow
+
+   nextflow.enable.dsl = 2
+
+   include { FACETS } from '../modules/msk/facets/main'
+   ```
+
+5. Remove the module from the pipeline repository if required:
+
+   ```console
+   $ nf-core modules --git-remote [email protected]:mskcc-omics-workflows/modules.git remove facets
+
+                                         ,--./,-.
+         ___     __   __   __   ___     /,-._.--~\
+   |\ | |__  __ /  ` /  \ |__) |__         }  {
+   | \| |       \__, \__/ |  \ |___     \`-._,-`-,
+                                         `._,._,'
+
+    nf-core/tools version 2.14.1 - https://nf-co.re
+
+    INFO     Removed files for 'facets' and its dependencies 'facets'.
+   ```
+
+6. Check that a locally installed nf-core module is up-to-date compared to the one hosted in this repo:
+
+   ```console
+   $ nf-core modules --git-remote [email protected]:mskcc-omics-workflows/modules.git lint facets
+
+                                         ,--./,-.
+         ___     __   __   __   ___     /,-._.--~\
+   |\ | |__  __ /  ` /  \ |__) |__         }  {
+   | \| |       \__, \__/ |  \ |___     \`-._,-`-,
+                                         `._,._,'
+
+    nf-core/tools version 2.14.1 - https://nf-co.re
+
+    INFO     Linting pipeline: '.'
+    INFO     Linting module: 'facets'
+
+    ╭─ [!] 6 Module Test Warnings ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
+    │              ╷                             ╷                                                                                                                                          │
+    │ Module name  │ File path                   │ Test message                                                                                                                             │
+    │╶─────────────┼─────────────────────────────┼─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╴│
+    │ facets       │ modules/msk/facets/main.nf  │ Unable to connect to container registry, code:  403, url: <https://www.docker.com/mskcc/facets-suite:2.0.9>                                │
+    │ facets       │ modules/msk/facets/main.nf  │ Container versions do not match                                                                                                          │
+    │ facets       │ modules/msk/facets/meta.yml │ hisens_r_data  is present as an output in the main.nf, but missing in meta.yml                                                           │
+    │ facets       │ modules/msk/facets/meta.yml │ purity_r_data  is present as an output in the main.nf, but missing in meta.yml                                                           │
+    │ facets       │ modules/msk/facets/meta.yml │ hisens_rdata is present as an output in meta.yml but not in main.nf                                                                      │
+    │ facets       │ modules/msk/facets/meta.yml │ purity_rdata is present as an output in meta.yml but not in main.nf                                                                      │
+    │              ╵                             ╵                                                                                                                                          │
+    ╰───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
+    ╭───────────────────────╮
+    │ LINT RESULTS SUMMARY  │
+    ├───────────────────────┤
+    │ [✔]  59 Tests Passed  │
+    │ [!]   6 Test Warnings │
+    │ [✗]   0 Tests Failed  │
+   ```
+
+## Adding new modules
+
+If you wish to contribute a new module, please see the documentation on the [MSK Omics Workflow website](https://mskcc-omics-workflows.gitbook.io/omics-workflows/contributing).
+
+> Please be kind to our code reviewers and submit one pull request per module :)
+
+## Help
+
+For further information or help, don't hesitate to get in touch on [Slack `#mskcc-omics-workflows` channel](https://mskcc.enterprise.slack.com/archives/C040T4MFCHJ).
+
+## Citation
+
+If you use the module files in this repository for your analysis please you can cite the `nf-core` publication as follows:
+
+> **The nf-core framework for community-curated bioinformatics pipelines.**
+>
+> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.
+>
+> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).