WorkflowAssembly/streamflow.yml at main · qBioTurin/WorkflowAssembly · GitHub

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#!/usr/bin/env streamflow
version: v1.0
workflows:
  workflow:
    type: cwl
    config:
      file: workflow.cwl
      settings: config.yml
      docker:
        - step: /
          deployment:
            type: none
            config: {}
    bindings:
      - step: /assembly_evaluation/assembly/hifiasm/hifiasm
        target:
          deployment: c3sfr1-slurm
          service: hifiasm
      - step: /assembly_evaluation/assembly/hifiasm/any2fasta
        target:
          deployment: c3sfr1-slurm
          service: any2fasta
      - step: /assembly_evaluation/assembly/hifiasm/medaka_hifiasm
        target:
          deployment: c3sfr1-slurm
          service: medaka
      - step: /assembly_evaluation/assembly/canu/canu
        target:
          deployment: c3sfr1-slurm
          service: canu
      - step: /assembly_evaluation/assembly/canu/medaka_canu
        target:
          deployment: c3sfr1-slurm
          service: medaka
      - step: /assembly_evaluation/assembly/flye/flye
        target:
          deployment: c3sfr1-slurm
          service: flye
      - step: /assembly_evaluation/assembly/flye/medaka_flye
        target:
          deployment: c3sfr1-slurm
          service: medaka
      - step: /assembly_evaluation/assembly/wtdbg2/wtdbg2
        target:
          deployment: c3sfr1-slurm
          service: wtdbg2
      - step: /assembly_evaluation/assembly/wtdbg2/wtpoa-cns
        target:
          deployment: c3sfr1-slurm
          service: wtdbg2
      - step: /assembly_evaluation/assembly/wtdbg2/medaka_wtdbg2
        target:
          deployment: c3sfr1-slurm
          service: medaka
      - step: /assembly_evaluation/assembly/quickmerge
        target:
          deployment: c3sfr1-slurm
          service: quickmerge
      - step: /assembly_evaluation/evaluation/busco
        target:
          deployment: c3sfr1-slurm
          service: busco
      - step: /assembly_evaluation/lrge
        target:
          deployment: c3sfr1-slurm
          service: lrge
      - step: /assembly_evaluation/best-result
        target:
          deployment: c3sfr1-slurm
          service: best-result
      - step: /assembly_evaluation/geneprediction/gene-prediction-eukaryotic/transposon/repeatmodeler-buildDatabase
        target:
          deployment: c3sfr1-slurm
          service: repeatmodeler
      - step: /assembly_evaluation/geneprediction/gene-prediction-eukaryotic/transposon/repeatmodeler-run
        target:
          deployment: c3sfr1-slurm
          service: repeatmodeler
      - step: /assembly_evaluation/geneprediction/gene-prediction-eukaryotic/transposon/repeatclassifier
        target:
          deployment: c3sfr1-slurm
          service: repeatmodeler
      - step: /assembly_evaluation/geneprediction/gene-prediction-eukaryotic/transposon/repeatmasker
        target:
          deployment: c3sfr1-slurm
          service: repeatmodeler
      - step: /assembly_evaluation/geneprediction/gene-prediction-eukaryotic/transposon/transposonpsi
        target:
          deployment: c3sfr1-slurm
          service: transposonpsi
      - step: /assembly_evaluation/geneprediction/gene-prediction-eukaryotic/transposon/transposonpsi-bedtools
        target:
          deployment: c3sfr1-slurm
          service: bedtools
      - step: /assembly_evaluation/geneprediction/gene-prediction-eukaryotic/transposon/edta
        target:
          deployment: c3sfr1-slurm
          service: edta
      - step: /assembly_evaluation/geneprediction/gene-prediction-eukaryotic/transposon/vsearch
        target:
          deployment: c3sfr1-slurm
          service: vsearch
      - step: /assembly_evaluation/geneprediction/gene-prediction-prokaryotic/bakta
        target:
          deployment: c3sfr1-slurm
          service: bakta
      - step: /assembly_evaluation/geneprediction/gene-prediction-prokaryotic/amrfinder
        target:
          deployment: c3sfr1-slurm
          service: amrfinder
      - step: /assembly_evaluation/geneprediction/antismash
        target:
          deployment: c3sfr1-slurm
          service: antismash
      - step: /assembly_evaluation/evaluation-prediction/busco
        target:
          deployment: c3sfr1-slurm
          service: busco
      - step: /assembly_evaluation/geneprediction/gene-prediction-eukaryotic/gene-prediction-eukaryotic
        target:
          deployment: c3sfr1-slurm
          service: braker3
      - step: /assembly_evaluation/clean-proteins
        target:
          deployment: c3sfr1-slurm
          service: interpro
      - step: /assembly_evaluation/interpro
        target:
          deployment: c3sfr1-slurm
          service: interpro
      - step: /assembly_evaluation/go_enrich
        target:
          deployment: c3sfr1-slurm
          service: interpro
      - step: /assembly_evaluation/postprocessing
        target:
          deployment: c3sfr1-slurm
          service: postprocessing

database:
  type: sqlite
  config:
    connection: ./database/test

deployments:
  c3sfr1-ssh:
    type: ssh
    config:
      nodes:
        - c3sfr1.di.unito.it
      username: scontald
      sshKey: key/id_rsa
    workdir: /beegfs/home/scontald/sf/assembly
  c3sfr1-slurm:
    type: slurm
    config:
      maxConcurrentJobs: 40
      services:
        canu:
          file: sbatch/canu.sh
        flye:
          file: sbatch/flye.sh
        wtdbg2:
          file: sbatch/wtdbg2.sh
        medaka:
          file: sbatch/medaka.sh
        quickmerge:
          file: sbatch/quickmerge.sh
        busco:
          file: sbatch/busco.sh
        bakta:
          file: sbatch/bakta.sh
        braker3:
          file: sbatch/braker3.sh
        best-result:
          file: sbatch/bestResult.sh
        interpro:
          file: sbatch/interpro.sh
        postprocessing:
          file: sbatch/postprocessing.sh
        repeatmodeler:
          file: sbatch/repeatmodeler.sh
        transposonpsi:
          file: sbatch/transposonpsi.sh
        bedtools:
          file: sbatch/bedtools.sh
        edta:
          file: sbatch/edta.sh
        vsearch:
          file: sbatch/vsearch.sh
        lrge:
          file: sbatch/lrge.sh
        hifiasm:
          file: sbatch/hifiasm.sh
        any2fasta:
          file: sbatch/any2fasta.sh
        antismash:
          file: sbatch/antismash.sh
        amrfinder:
          file: sbatch/amrfinder.sh
    wraps: c3sfr1-ssh