Merge branch 'release/3.1.0'

.github/workflows/codeql.yml

@@ -0,0 +1,41 @@
+name: "CodeQL"
+
+on:
+  push:
+    branches: [ "master" ]
+  pull_request:
+    branches: [ "master" ]
+  schedule:
+    - cron: "49 21 * * 6"
+
+jobs:
+  analyze:
+    name: Analyze
+    runs-on: ubuntu-latest
+    permissions:
+      actions: read
+      contents: read
+      security-events: write
+
+    strategy:
+      fail-fast: false
+      matrix:
+        language: [ python ]
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+
+      - name: Initialize CodeQL
+        uses: github/codeql-action/init@v2
+        with:
+          languages: ${{ matrix.language }}
+          queries: +security-and-quality
+
+      - name: Autobuild
+        uses: github/codeql-action/autobuild@v2
+
+      - name: Perform CodeQL Analysis
+        uses: github/codeql-action/analyze@v2
+        with:
+          category: "/language:${{ matrix.language }}"

.github/workflows/test_nucleo.yaml

@@ -16,25 +16,25 @@ jobs:
       max-parallel: 1
       matrix:
         platform: [ubuntu-latest]
-        python-version: [3.6]
+        python-version: ['3.10']
     steps:
       - name: Checkout repo
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
         with:
           ref: ${{ github.head_ref }}
           submodules: recursive
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name : Set up NodeJS
         run: |
           curl -o- https://raw.githubusercontent.com/nvm-sh/nvm/v0.37.2/install.sh | bash
-          export NVM_DIR="$HOME/.nvm" 
+          export NVM_DIR="$HOME/.nvm"
           [ -s "$NVM_DIR/nvm.sh" ] && \. "$NVM_DIR/nvm.sh"  # This loads nvm
           [ -s "$NVM_DIR/bash_completion" ] && \. "$NVM_DIR/bash_completion"  # This loads nvm bash_completion
           nvm install node
-      - name: Setup Docker   
+      - name: Setup Docker
         uses: docker-practice/actions-setup-docker@master
         with:
           docker_channel: nightly
@@ -43,7 +43,7 @@ jobs:
         env:
           PLATFORM: ${{ matrix.platform }}
       - name: Login to GitHub Container Registry
-        uses: docker/login-action@v1
+        uses: docker/login-action@v3
         with:
           registry: ghcr.io
           username: ${{ github.repository_owner }}

.gitmodules

@@ -6,11 +6,11 @@
 	path = subworkflows
 	url = https://github.com/msk-access/cwl_subworkflows.git
 	branch = develop
-[submodule "bam_collapsing"]
-	path = bam_collapsing
-	url = https://github.com/msk-access/bam_collapsing.git
-	branch = develop
 [submodule "uncollapsed_bam_generation"]
 	path = uncollapsed_bam_generation
 	url = https://github.com/msk-access/uncollapsed_bam_generation.git
 	branch = develop
+[submodule "bam_collapsing"]
+	path = bam_collapsing
+	url = https://github.com/msk-access/bam_collapsing.git
+	branch = develop

.travis.yml

@@ -1,6 +1,6 @@
 language: python
 python:
-- 3.6
+- 3.10
 install: pip install -U tox-travis
 script: tox
 deploy:
@@ -14,4 +14,4 @@ deploy:
   on:
     tags: true
     repo: msk-access/nucleo
-    python: 3.6
+    python: 3.10

install_data.sh

@@ -5,23 +5,15 @@
 # https://drive.google.com/file/d/1GtT8jsBGwRoQC-5wHh06r8RFkiFBuirp/view?usp=sharing
 
 fileid=1GtT8jsBGwRoQC-5wHh06r8RFkiFBuirp
-
 filename=test_nucleo.tar.gz
-foldername=test_nucleo
-
-# Skip if already have test data
-[[ -f $filename ]] && exit 0
-[[ -d $foldername ]] && exit 0
-
-curl -c ./cookie -s -k -L "https://drive.google.com/uc?export=download&id=$fileid" > /dev/null
 
-curl -k -Lb ./cookie "https://drive.google.com/uc?export=download&confirm=`awk '/download/ {print $NF}' ./cookie`&id=${fileid}" -o ${filename}
+gdown https://drive.google.com/uc?id=$fileid 
 
 # Suppress linux warnings for MacOS tar.gz files
 if [[ "$OSTYPE" == "linux-gnu" ]]; then
-    tar --warning=no-unknown-keyword -xzvf $filename
+    tar --warning=no-unknown-keyword -xzvf $filename 
 elif [[ "$OSTYPE" == "darwin"* ]]; then
-    tar -xzvf $filename
+    tar -xzvf $filename 
 fi
 
-rm $filename
+rm $filename

requirements.txt

@@ -1,9 +1,10 @@
-toil[cwl]
-pytz
-bumpversion
-flake8
-tox
-twine
-pytest
-pytest-runner
-coloredlogs
+toil[cwl]==5.10.0
+pytz==2022.6
+bumpversion==0.6.0
+flake8==6.0.0
+tox==3.27.1
+twine==4.0.2
+pytest==7.2.0
+pytest-runner==6.0.0
+coloredlogs==15.0.1
+gdown

setup.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 3.0.4
+current_version = 3.1.0
 commit = True
 tag = True
 

setup.py

@@ -8,7 +8,7 @@
 with open('README.md') as readme_file:
     readme = readme_file.read()
 
-requirements = ['toil[cwl]==5.5.0', ]
+requirements = ['toil[cwl]==5.10.0', ]
 
 setup_requirements = ['pytest-runner', ]
 
@@ -22,7 +22,7 @@
         'Intended Audience :: Developers',
         'License :: OSI Approved :: Apache Software License',
         'Natural Language :: English',
-        'Programming Language :: Python :: 3.6',
+        'Programming Language :: Python :: 3.10',
     ],
     description="Workflow that creates all the bam files for the MSK-ACCESS fastq file",
     install_requires=requirements,
@@ -36,6 +36,6 @@
     test_suite='tests',
     tests_require=test_requirements,
     url='https://github.com/msk-access/nucleo',
-    version='3.0.4',
+    version='3.1.0',
     zip_safe=False,
 )

tox.ini

@@ -1,9 +1,9 @@
 [tox]
-envlist = py{36}-{linux}, flake8
+envlist = py{310}-{linux}, flake8
 
 [travis]
 python =
-    3.6: py36
+    3.10: py310
 
 [testenv:flake8]
 basepython = python
@@ -12,7 +12,7 @@ commands = flake8 nucleo
 
 [gh-actions]
 python =
-    3.6: py36
+    3.10: py310
 
 [gh-actions:env]
 PLATFORM =
@@ -32,14 +32,16 @@ deps =
 
 passenv = {gh-actions,pytest}
 
-whitelist_externals =
+allowlist_externals =
     wget
     chmod
     tar
     goodls
+    sh
+    bash
+    tar
 
-commands_pre = ./install_data.sh
+commands_pre = bash ./install_data.sh
 
 commands =
     py.test --capture=sys --basetemp={envtmpdir} tests
-