Revert Master

.github/workflows/test_pr_hybrid_docker.yml

@@ -0,0 +1,37 @@
+name: Testing hybrid / docker from PR
+on:
+  pull_request:
+    branches: [ master ]
+    types: [ opened, synchronize, reopened ]
+
+jobs:
+  run_nextflow:
+    name: Run pipeline for the upcoming PR
+    runs-on: ubuntu-latest
+
+    steps:
+
+      - name: Check out pipeline code
+        uses: actions/checkout@v2
+
+      - name: Install Nextflow
+        env:
+          CAPSULE_LOG: none
+        run: |
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+
+      - name: Clean environment
+        run: |
+          sudo rm -rf /usr/local/lib/android # will release about 10 GB if you don't need Android
+          sudo rm -rf /usr/share/dotnet # will release about 20GB if you don't need .NET
+
+      - name: Run tests for hybrid
+        run: |
+          nextflow run main.nf -profile docker,test,hybrid
+          rm -r work .nextflow*
+
+      - name: View results
+        run: |
+          sudo apt-get install -y tree
+          tree hybrid_test

.github/workflows/test_pr_hybrid_singularity.yml

@@ -0,0 +1,42 @@
+name: Testing hybrid / singularity from PR
+on:
+  pull_request:
+    branches: [ master ]
+    types: [ opened, synchronize, reopened ]
+
+jobs:
+  run_nextflow:
+    name: Run pipeline for the upcoming PR
+    runs-on: ubuntu-latest
+
+    steps:
+
+      - name: Check out pipeline code
+        uses: actions/checkout@v2
+
+      - name: Install Singularity
+        uses: eWaterCycle/setup-singularity@v7
+        with:
+          singularity-version: 3.8.3
+
+      - name: Install Nextflow
+        env:
+          CAPSULE_LOG: none
+        run: |
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+
+      - name: Clean environment
+        run: |
+          sudo rm -rf /usr/local/lib/android # will release about 10 GB if you don't need Android
+          sudo rm -rf /usr/share/dotnet # will release about 20GB if you don't need .NET
+
+      - name: Run tests for hybrid
+        run: |
+          nextflow run main.nf -profile singularity,test,hybrid
+          rm -r work .nextflow*
+
+      - name: View results
+        run: |
+          sudo apt-get install -y tree
+          tree hybrid_test

.github/workflows/test_pr_illumina_docker.yml

@@ -0,0 +1,37 @@
+name: Testing illumina / docker from PR
+on:
+  pull_request:
+    branches: [ master, dev ]
+    types: [ opened, synchronize, reopened ]
+
+jobs:
+  run_nextflow:
+    name: Run pipeline for the upcoming PR
+    runs-on: ubuntu-latest
+
+    steps:
+
+      - name: Check out pipeline code
+        uses: actions/checkout@v2
+
+      - name: Install Nextflow
+        env:
+          CAPSULE_LOG: none
+        run: |
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+
+      - name: Clean environment
+        run: |
+          sudo rm -rf /usr/local/lib/android # will release about 10 GB if you don't need Android
+          sudo rm -rf /usr/share/dotnet # will release about 20GB if you don't need .NET
+
+      - name: Run tests for illumina
+        run: |
+          nextflow run main.nf -profile docker,test,sreads
+          rm -r work .nextflow*
+
+      - name: View results
+        run: |
+          sudo apt-get install -y tree
+          tree sreads_test

.github/workflows/test_pr_illumina_singularity.yml

@@ -0,0 +1,42 @@
+name: Testing illumina / singularity from PR
+on:
+  pull_request:
+    branches: [ master, dev ]
+    types: [ opened, synchronize, reopened ]
+
+jobs:
+  run_nextflow:
+    name: Run pipeline for the upcoming PR
+    runs-on: ubuntu-latest
+
+    steps:
+
+      - name: Check out pipeline code
+        uses: actions/checkout@v2
+
+      - name: Install Singularity
+        uses: eWaterCycle/setup-singularity@v7
+        with:
+          singularity-version: 3.8.3
+
+      - name: Install Nextflow
+        env:
+          CAPSULE_LOG: none
+        run: |
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+
+      - name: Clean environment
+        run: |
+          sudo rm -rf /usr/local/lib/android # will release about 10 GB if you don't need Android
+          sudo rm -rf /usr/share/dotnet # will release about 20GB if you don't need .NET
+
+      - name: Run tests for illumina
+        run: |
+          nextflow run main.nf -profile singularity,test,sreads
+          rm -r work .nextflow*
+
+      - name: View results
+        run: |
+          sudo apt-get install -y tree
+          tree sreads_test

.github/workflows/test_pr_lreads_docker_ont.yml

@@ -0,0 +1,37 @@
+name: Testing long-reads / docker (ONT) from PR
+on:
+  pull_request:
+    branches: [ master, dev ]
+    types: [ opened, synchronize, reopened ]
+
+jobs:
+  run_nextflow:
+    name: Run pipeline for the upcoming PR
+    runs-on: ubuntu-latest
+
+    steps:
+
+      - name: Check out pipeline code
+        uses: actions/checkout@v2
+
+      - name: Install Nextflow
+        env:
+          CAPSULE_LOG: none
+        run: |
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+
+      - name: Clean environment
+        run: |
+          sudo rm -rf /usr/local/lib/android # will release about 10 GB if you don't need Android
+          sudo rm -rf /usr/share/dotnet # will release about 20GB if you don't need .NET
+
+      - name: Run tests for long-reads (ont)
+        run: |
+          nextflow run main.nf -profile docker,test,lreads,ont --max_memory '6.GB' --max_cpus 2 --skip_flye --skip_canu
+          rm -r work .nextflow*
+
+      - name: View results
+        run: |
+          sudo apt-get install -y tree
+          tree lreads_test_ont

.github/workflows/test_pr_lreads_singularity_ont.yml

@@ -0,0 +1,48 @@
+name: Testing long-reads / singularity (ONT) from PR
+on:
+  pull_request:
+    branches: [ master, dev ]
+    types: [ opened, synchronize, reopened ]
+
+jobs:
+  run_nextflow:
+    name: Run pipeline for the upcoming PR
+    runs-on: macos-latest
+
+    steps:
+
+      - name: 'Set up latest Oracle JDK 17'
+        uses: oracle-actions/setup-java@v1
+        with:
+          website: oracle.com
+          release: 17
+
+      - name: Check out pipeline code
+        uses: actions/checkout@v2
+
+      - name: Install Singularity
+        uses: eWaterCycle/setup-singularity@v7
+        with:
+          singularity-version: 3.8.3
+
+      - name: Install Nextflow
+        env:
+          CAPSULE_LOG: none
+        run: |
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+
+      - name: Clean environment
+        run: |
+          sudo rm -rf /usr/local/lib/android # will release about 10 GB if you don't need Android
+          sudo rm -rf /usr/share/dotnet # will release about 20GB if you don't need .NET
+
+      - name: Run tests for long-reads (ont)
+        run: |
+          nextflow run main.nf -profile singularity,test,lreads,ont
+          rm -r work .nextflow*
+
+      - name: View results
+        run: |
+          sudo apt-get install -y tree
+          tree lreads_test_ont

.zenodo.json

@@ -2,7 +2,7 @@
     "description": "<p>MpGAP is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. It is an easy to use pipeline that adopts well known software for _de novo_ genome assembly of Illumina, Pacbio and Oxford Nanopore sequencing data through illumina only, long reads only or hybrid modes.</p>",
     "license": "other-open", 
     "title": "fmalmeida/MpGAP: A generic multi-platform genome assembly pipeline", 
-    "version": "v3.1.4", 
+    "version": "v3.2", 
     "upload_type": "software",
     "creators": [
         {

Dockerfile

@@ -1,28 +1,34 @@
-FROM nfcore/base
+FROM mambaorg/micromamba
 LABEL authors="Felipe Almeida" \
       description="Docker image containing all software requirements for the fmalmeida/mpgap pipeline"
 
 # Install the conda environment
-RUN conda install -y -c conda-forge mamba
 COPY environment.yml /
-RUN mamba env create --quiet -f /environment.yml && mamba clean -a
+RUN micromamba env create --quiet -f /environment.yml --yes && micromamba clean -a
 
 # Add conda installation dir to PATH (instead of doing 'conda activate')
-ENV PATH /opt/conda/envs/mpgap-3.1/bin:$PATH
+ENV PATH /opt/conda/envs/mpgap-3.2/bin:$PATH
 
 # Dump the details of the installed packages to a file for posterity
-RUN conda env export --name mpgap-3.1 > mpgap-3.1.yml
+RUN micromamba env export --name mpgap-3.2 > mpgap-3.2.yml
+
+# check problematic installation
+RUN medaka --help
 
 # download busco dbs
 ENV CONDA_PREFIX=/opt/conda
-RUN mkdir -p $CONDA_PREFIX/envs/mpgap-3.1/lib/python3.6/site-packages/quast_libs/busco/
-RUN wget -O $CONDA_PREFIX/envs/mpgap-3.1/lib/python3.6/site-packages/quast_libs/busco/bacteria.tar.gz https://busco.ezlab.org/v2/datasets/bacteria_odb9.tar.gz
-RUN wget -O $CONDA_PREFIX/envs/mpgap-3.1/lib/python3.6/site-packages/quast_libs/busco/eukaryota.tar.gz https://busco.ezlab.org/v2/datasets/eukaryota_odb9.tar.gz
-RUN wget -O $CONDA_PREFIX/envs/mpgap-3.1/lib/python3.6/site-packages/quast_libs/busco/fungi.tar.gz https://busco.ezlab.org/v2/datasets/fungi_odb9.tar.gz
-RUN mkdir -p $CONDA_PREFIX/envs/mpgap-3.1/lib/python3.6/site-packages/quast_libs/augustus3.2.3 && wget -O $CONDA_PREFIX/envs/mpgap-3.1/lib/python3.6/site-packages/quast_libs/augustus3.2.3/augustus.tar.gz http://bioinf.uni-greifswald.de/augustus/binaries/old/augustus-3.2.3.tar.gz
+RUN mkdir -p $CONDA_PREFIX/envs/mpgap-3.2/lib/python3.8/site-packages/quast_libs/busco/
+RUN wget -O $CONDA_PREFIX/envs/mpgap-3.2/lib/python3.8/site-packages/quast_libs/busco/bacteria.tar.gz https://busco.ezlab.org/v2/datasets/bacteria_odb9.tar.gz
+RUN wget -O $CONDA_PREFIX/envs/mpgap-3.2/lib/python3.8/site-packages/quast_libs/busco/eukaryota.tar.gz https://busco.ezlab.org/v2/datasets/eukaryota_odb9.tar.gz
+RUN wget -O $CONDA_PREFIX/envs/mpgap-3.2/lib/python3.8/site-packages/quast_libs/busco/fungi.tar.gz https://busco.ezlab.org/v2/datasets/fungi_odb9.tar.gz
+RUN mkdir -p $CONDA_PREFIX/envs/mpgap-3.2/lib/python3.8/site-packages/quast_libs/augustus3.2.3 && wget -O $CONDA_PREFIX/envs/mpgap-3.2/lib/python3.8/site-packages/quast_libs/augustus3.2.3/augustus.tar.gz http://bioinf.uni-greifswald.de/augustus/binaries/old/augustus-3.2.3.tar.gz
 
 # fix permissions
-RUN chmod -R 777 $CONDA_PREFIX/envs/mpgap-3.1/lib/python3.6/site-packages/quast_libs/busco
-RUN chmod -R 777 $CONDA_PREFIX/envs/mpgap-3.1/lib/python3.6/site-packages/quast_libs/augustus3.2.3
-RUN chmod -R 777 $CONDA_PREFIX/envs/mpgap-3.1/lib/python3.6/site-packages/medaka
+RUN chmod -R 777 $CONDA_PREFIX/envs/mpgap-3.2/lib/python3.8/site-packages/quast_libs/busco
+RUN chmod -R 777 $CONDA_PREFIX/envs/mpgap-3.2/lib/python3.8/site-packages/quast_libs/augustus3.2.3
+RUN chmod -R 777 $CONDA_PREFIX/envs/mpgap-3.2/lib/python3.8/site-packages/medaka
 
+# install ps
+USER root
+RUN apt-get update && apt-get install -y procps && rm -rf /var/lib/apt/lists/*
+USER mambauser