Merge branch 'release/1.0.0' into master

.github/workflows/test_bam_collapsing.yaml

@@ -0,0 +1,59 @@
+name: test_bam_collapsing
+on:
+  push:
+    paths-ignore:
+    - 'docs/**'
+    - '**.md'
+  pull_request:
+    paths-ignore:
+    - 'docs/**'
+    - '**.md'
+jobs:
+  test_bam_collapsing:
+    runs-on: ${{ matrix.platform }}
+    if: "!contains(github.event.head_commit.message, 'ci skip')"
+    strategy:
+      max-parallel: 1
+      matrix:
+        platform: [ubuntu-latest]
+        python-version: [3.6]
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v2
+        with:
+          ref: ${{ github.head_ref }}
+          submodules: recursive
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        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" 
+          [ -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   
+        uses: docker-practice/actions-setup-docker@master
+        with:
+          docker_channel: nightly
+        # this value please see https://github.com/AkihiroSuda/moby-snapshot/releases
+          docker_nightly_version: snapshot-20201109
+        env:
+          PLATFORM: ${{ matrix.platform }}
+      - name: Login to GitHub Container Registry
+        uses: docker/login-action@v1
+        with:
+          registry: ghcr.io
+          username: ${{ github.repository_owner }}
+          password: ${{ secrets.RS_PAT }}
+      - name: Install Python dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install tox tox-gh-actions
+      - name: Test with tox
+        id: run-tox
+        run: tox -vv
+        env:
+          PLATFORM: ${{ matrix.platform }}

.pyup.yml

@@ -1,8 +1,9 @@
-Update: all
+Update: insecure
 Search: True
 Pin: True
-Default Branch: master
+Default Branch: develop
 Branch pre-fix: pyup-
 Close PRs: True
 Label PRs: True
 Update hashes: True
+schedule: "every month"

.travis.yml

@@ -1,9 +1,8 @@
 language: python
 python:
-- 3.7
-- 2.7
+- 3.6
 install: pip install -U tox-travis
-script: travis_wait 120 tox
+script: tox
 deploy:
   provider: pypi
   distributions: sdist bdist_wheel
@@ -15,4 +14,4 @@ deploy:
   on:
     tags: true
     repo: msk-access/bam_collapsing
-    python: 2.7
+    python: 3.6

README.md

@@ -1,44 +1,31 @@
 ---
-description: Collapsing of reads a  aligned to the genome having same unique molecular identifier.
+description: >-
+    Collapsing of reads a  aligned to the genome having same unique molecular
+    identifier.
 ---
 
-# MSK-ACCESS BAM collapsing workflow
+# BAM Collapsing
 
-[![PyPI version](https://badge.fury.io/py/bam-collapsing.svg)](https://badge.fury.io/py/bam-collapsing)
-[![Build Status](https://travis-ci.org/msk-access/bam_collapsing.svg?branch=master)](https://travis-ci.org/msk-access/bam_collapsing)
-[![Updates](https://pyup.io/repos/github/msk-access/bam_collapsing/shield.svg)](https://pyup.io/repos/github/msk-access/bam_collapsing/)
-[![Python 3](https://pyup.io/repos/github/msk-access/bam_collapsing/python-3-shield.svg)](https://pyup.io/repos/github/msk-access/bam_collapsing/)
+[![PyPI version](https://badge.fury.io/py/bam-collapsing.svg)](https://badge.fury.io/py/bam-collapsing) [![Build Status](https://travis-ci.org/msk-access/bam_collapsing.svg?branch=master)](https://travis-ci.org/msk-access/bam_collapsing) [![Updates](https://pyup.io/repos/github/msk-access/bam_collapsing/shield.svg)](https://pyup.io/repos/github/msk-access/bam_collapsing/) [![Python 3](https://pyup.io/repos/github/msk-access/bam_collapsing/python-3-shield.svg)](https://pyup.io/repos/github/msk-access/bam_collapsing/)
 
-The bam collapsing workflow for MSK-ACCESS assay takes in a standard processed bam from standard processing workflow available [here](https://github.com/msk-access/standard_bam_processing). 
+The bam collapsing workflow for MSK-ACCESS assay takes in a standard processed bam from standard processing workflow available [here](https://github.com/msk-access/uncollapsed_bam_generation).
 
-- Free software: Apache Software License 2.0
-- Documentation: https://msk-access.gitbook.io/bam-collapsing.
+-   Free software: Apache Software License 2.0
+-   Documentation: [https://msk-access.gitbook.io/bam-collapsing](https://msk-access.gitbook.io/bam-collapsing)
 
-## Features
-
-Given a standard bam file:
-
-1. Generate a pileup using Waltz.
-
-2. Using the pileup with the bam file run Marianas bam collapsing, thus generating collapsed fastq.
+![Workflow](/docs/.gitbook/assets/fgbio_bam_collapsing.png)
 
-3. Using the collapsed fastq align and indel realign the reads generating unfiltered bam files.
-
-4. Using the unfiltered bam file with help of Marianas separate them into duplex and simplex bam.
-
-5. Calculate alignment metrics for unfiltered, duplex and simplex bam file.
-
-## Installation
+## Features
 
-Clone the repository:
+Given a uncollapsed Unique Molecular Index (UMI) tagged BAM file:
 
-```
-git clone --depth 50 https://github.com/msk-access/bam_collapsing.git
-```
+1. Group Reads using UMI and generate a BAM file
+2. Call Duplex Consensus Reads from the BAM and generate an unmapped BAM file
+3. Convert unmapped BAM to FASTQ and do standard BAM alignment.
+4. Merge the unmapped BAM with the aligned BAM and this generated the collapsed BAM.
+5. Generate Duplex and Simplex BAM files from the collapsed BAM.
 
 ## Credits
 
-- CMO MSK-ACCESS Informatics Team
-- This package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template.
-  - Cookiecutter: https://github.com/audreyr/cookiecutter
-  - `audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage
+- CMO cfDNA Informatics Team
+- This package was created with Cookiecutter _and the `audreyr/cookiecutter-pypackage`_ project template.