virprof/pipelines.yml at master · seiboldlab/virprof · GitHub

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pipelines:
  ### Sub-Pipelines ###
  # Trimming and FastQC
  qc:
    stages:
      - qc_fastqc
      - trim_bbmapAQ10L70
      - qc_fastqc

  # Keep *only* reads matching last *.fasta.gz (from ref)
  enrich:
    stages:
      - map_bbmapS:
          hide: true
      - extract_readsG12

  # Remove reads matching last bowtie2 and hisat2 indicies (from ref)
  deplete:
    stages:
      - get_unmapped_vp:
          hide: true
      - map_bowtie2:
          hide: true
      - extract_readsf12

  deplete2:
    stages:
      - get_unmapped_vp:
          hide: true
      - map_bowtie2:
          hide: true
      - extract_readsf12
      - filter_trf

  # Assemble (by sample) using Spades Single Cell mode and remove short contigs
  assemble_single:
    stages:
      - group_sample
      - assemble_spadesSc:
          hide: true
      - format_bbmapL200

  # Assemble (by sample) using Spades Metagenomic mode and remove short contigs
  # (removes low entropy reads prior to assembly)
  assemble_meta:
    stages:
      - dust_bbmapE60:
          hide: true
      - group_sample
      - assemble_spadesMeta:
          hide: true
      - format_bbmapL200

  # Compute coverage and sorted bam file using bowtie2
  coverage:
    stages:
      - index_bowtie2:
          hide: true
      - map_bowtie2S:
          hide: true
      - sort_bam:
          hide: true
      - markdup_sambambaRM
      - coverage_samtools
      - basecov_bedtools

  # Remove human contigs and create classified bins using BLAST
  blastbin:
    stages:
      - annotate_blastE2MegaBest:
          hide: true
      - fastaqc_vp:
          hide: true
      - blastfilter_vpU200:
          hide: true
      - ref_NT:
          hide: true
      - annotate_blastE10Best:
          hide: true
      - ref_NcbiTaxonomy:
          hide: true
      - group_sample:
          hide: true
      - blastbin_vp

  scaffold:
    stages:
      - scaffold_vp
      - coverage:
          hide: true
      - group_sample
      - polish_pilonSIL:
          hide: true
      - coverage
      - fastaqc_vp
      - group_ALL
      - bin_vpSpecies

  summarize:
    stages:
      - collect_vp
      - qc_multiqc
      - ref_VHDB
      - group_ALL
      - summarize_vp
      - group_ALL
      - report_pathogen_vp

  # Re-Assemble created bins (unused)
  reassemble:
    stages:
      - enrich:
          hide: true
      - group_sample
      - group_BIN
      - assemble_spadesSc:
          hide: true
      - group_sample
      - format_bbmapL200

  # Reference guidedworkflow
  targeted_virus:
    stages:
      - qc
      - enrich
      - assemble_single
      - coverage
      - blastbin

  rnaseq_report:
    stages:
      - group_ALL
      - qc_multiqc
      - group_ALL
      - tximport_vp
      - group_ALL
      - report_vp

  rnaseq_salmon:
    stages:
      - qc
      - quant_salmon_sa
      - rnaseq_report

  rnaseq_star_rsem:
    stages:
      - qc
      - map_starT
      - quant_rsem
      - rnaseq_report

  rnaseq_star_salmon:
    stages:
      - qc
      - map_starT
      - quant_salmonG
      - rnaseq_report

  umimap_starT:
    stages:
      - map_starT
      - sort_txbam
      - dedup_umi_vp
      - collate_txbam
      - fix_umi_vp

  rnaseq_umi_star_salmon:
    stages:
      - extract_umi_vp
      - qc
      - umimap_starT
      - quant_salmonG
      - rnaseq_report

  rnaseq_star_umi_salmon:
    stages:
      - qc
      - umimap_starT
      - quant_salmonG
      - rnaseq_report

  rnaseq_umi_star_rsem:
    stages:
      - extract_umi_vp
      - qc
      - umimap_starT
      - quant_rsem
      - rnaseq_report

  rnaseq_star_exon:
    stages:
      - qc
      - map_starT
      - quant_exon_vp
      - rnaseq_report

  virus:
    stages:
      - deplete
      - assemble_meta
      - coverage
      - blastbin
      - scaffold
      - summarize

  pathogen:
    stages:
      - deplete2
      - assemble_meta
      - coverage
      - blastbin
      - scaffold
      - summarize