ansible-falcon.yaml

---
- name: Installing and running Falcon
  hosts: localhost
  vars_prompt:
  - name: dir
    prompt: "Enter your group directory"
    private: no
  - name: fasta_read_1
    prompt: "Enter the name of your fasta read 1 file (subreads1.fasta if doing demo)"
    private: no
  - name: fasta_read_2
    prompt: "Enter the name of your fasta read 2 file (subreads2.fasta if doing demo)"
    private: no
  - name: bam_read_1
    prompt: "Enter the name of your bam read 1 file (subreads1.bam if doing demo)"
    private: no
  - name: bam_read_2
    prompt: "Enter the name of your bam read 2 file (subreads2.bam if doing demo)" 
    private: no
  tasks:
  - name: Starting a Slurm interactive session
    command: salloc -n 1 -t 1:00:00 --account=$PAWSEY_PROJECT
  - name: Setting up Falcon
    shell: |
      cd {{ dir }}/ansible-falcon/falcon
      git clone https://github.com/cdunn2001/git-sym.git
      git clone https://github.com/pb-cdunn/FALCON-examples.git
      cd FALCON-examples
      ../git-sym/git-sym update run/greg200k-sv2
      mv run/greg200k-sv2/data/greg200k-sv2/subreads* {{ dir }}/ansible-falcon/falcon/
      cd {{ dir }}/ansible-falcon/falcon
      rm -rf FALCON-examples/ git-sym/
      echo '{{ dir }}/ansible-falcon/falcon/{{ fasta_read_1 }}' > subreads.fasta.fofn
      echo '{{ dir }}/ansible-falcon/falcon/{{ fasta_read_2 }}' >> subreads.fasta.fofn
      echo '{{ dir }}/ansible-falcon/falcon/{{ bam_read_1 }}' > subreads.bam.fofn
      echo '{{ dir }}/ansible-falcon/falcon/{{ bam_read_2 }}' >> subreads.bam.fofn      
      sed -i "s|project_dir|{{ dir }}|g" main.nf
      sed -i "s|project_dir|{{ dir }}|g" nextflow.config
      module load singularity
      singularity pull docker://quay.io/biocontainers/pbcore:1.7.1--py27_0
      wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
      bash Miniconda3-latest-Linux-x86_64.sh -b -p {{ dir }}/miniconda3
      rm Miniconda3-latest-Linux-x86_64.sh
  - name: Activating conda 
    shell: |  
      eval "$("{ dir }}/miniconda3/bin/conda" shell.bash hook)"
      conda config --set auto_activate_base false
      conda init
  - name: Running Falcon
    command: sbatch --account=$PAWSEY_PROJECT {{ dir }}/ansible-falcon/falcon/sbatch_nextflow.sh