peak_call.yaml

peak_call:
  - music[tool]:
    - narrow[peak_type]:
      - music_narrow:
          inputs:
            prefix:
              param_name: prefix
            control.bed:
              param_name: control.bed
            signal.bed:
              param_name: signal.bed
          outputs:
            sorted_scale_129_all.bed:
              param_name: scale_129.bed
              final_result: true
            sorted_scale_194_all.bed:
              param_name: scale_194.bed
              final_result: true
            sorted_scale_291_all.bed:
              param_name: scale_291.bed
              final_result: true
    - punctate[peak_type]:
      - music_punctate:
          inputs:
            prefix:
              param_name: prefix
            control.bed:
              param_name: control.bed
            signal.bed:
              param_name: signal.bed
          outputs:
            sorted_scale_129_all.bed:
              param_name: scale_129.bed
              final_result: true
            sorted_scale_194_all.bed:
              param_name: scale_194.bed
              final_result: true
            sorted_scale_291_all.bed:
              param_name: scale_291.bed
              final_result: true
            sorted_scale_437_all.bed:
              param_name: scale_437.bed
              final_result: true
            sorted_scale_656_all.bed:
              param_name: scale_656.bed
              final_result: true
            sorted_scale_985_all.bed:
              param_name: scale_985.bed
              final_result: true
            sorted_scale_1477_all.bed:
              param_name: scale_1477.bed
              final_result: true
            sorted_scale_2216_all.bed:
              param_name: scale_2216.bed
              final_result: true
    - broad[peak_type]:
      - music_broad:
          inputs:
            prefix:
              param_name: prefix
            control.bed:
              param_name: control.bed
            signal.bed:
              param_name: signal.bed
          outputs:
            sorted_scale_1459_all.bed:
              param_name: scale_1459.bed
              final_result: true
            sorted_scale_2189_all.bed:
              param_name: scale_2189.bed
              final_result: true
            sorted_scale_3284_all.bed:
              param_name: scale_3284.bed
              final_result: true
            sorted_scale_4926_all.bed:
              param_name: scale_4926.bed
              final_result: true
            sorted_scale_7389_all.bed:
              param_name: scale_7389.bed
              final_result: true
            sorted_scale_11084_all.bed:
              param_name: scale_11084.bed
              final_result: true
            sorted_scale_16626_all.bed:
              param_name: scale_16626.bed
              final_result: true
  - peakranger[tool]:
    - narrow[peak_type]:
      - peakranger_callpeak:
          inputs:
            prefix:
              param_name: prefix
            control.bed:
              param_name: control.bed
            signal.bed:
              param_name: signal.bed
          outputs:
            region.bed:
              param_name: region_bed
            summit.bed:
              param_name: summit_bed
            details:
              param_name: details
            peakranger.log:
              param_name: log
      - peakranger_format_bed:
          inputs:
            region.bed:
              param_name: result_peaks
          outputs:
            region_sorted.bed:
              param_name: sorted_peaks
              final_result: true
      - peakranger_format_bed:
          inputs:
            summit.bed:
              param_name: result_peaks
          outputs:
            summit_sorted.bed:
              param_name: sorted_peaks
              final_result: true
  - ccat[tool]:
    - broad[peak_type]:
      - ccat_callpeak:
          inputs:
            prefix:
              param_name: prefix
            control.bed:
              param_name: control.bed
            signal.bed:
              param_name: signal.bed
            chrom.sizes:
              param_name: chrom.sizes
          outputs:
            significant.peak:
              param_name: significant_peak
              prefix_join: "."
            significant.region:
              param_name: significant_region
              prefix_join: "."
            top100000.peak:
              param_name: top_100000_peak
              prefix_join: "."
            log:
              param_name: ccat_log
              prefix_join: "."
      - ccat_format_bed:
          inputs:
            significant.region:
              param_name: result_peaks
          outputs:
            region_sorted.bed:
              param_name: sorted_peaks
              final_result: true
      - ccat_format_bed:
          inputs:
            significant.peak:
              param_name: result_peaks
          outputs:
            peak_sorted.bed:
              param_name: sorted_peaks
              final_result: true
  - gem[tool]:
    - narrow[peak_type]:
      - gem_callpeak:
          inputs:
            prefix:
              param_name: prefix
            chrom.sizes:
              param_name: chrom.sizes
            signal.bed:
              param_name: signal.bed
            control.bed:
              param_name: control.bed
            genome_dir:
              param_name: genome
            chr_fasta:
              param_name: chr_fasta
          outputs:
            GEM_events.narrowPeak:
              param_name: gem_peak_result
              name_template: "$prefix$/$prefix$_GEM_events.narrowPeak"
            GPS_events.narrowPeak:
              param_name: gps_peak_result
              name_template: "$prefix$/$prefix$_GPS_events.narrowPeak"
      - sort_awk_sort_peaks:
          inputs:
            GEM_events.narrowPeak:
              param_name: result_peaks
          outputs:
            results_GEM_sorted.bed:
              param_name: sorted_peaks
              final_result: true
      - sort_awk_sort_peaks:
          inputs:
            GPS_events.narrowPeak:
              param_name: result_peaks
          outputs:
            results_GPS_sorted.bed:
              param_name: sorted_peaks
              final_result: true
  - spp[tool]:
    - cp:
        inputs:
          signal.bed:
            param_name: input_file
        outputs:
          signal.tagAlign:
            param_name: output_file
    - cp:
        inputs:
          control.bed:
            param_name: input_file
        outputs:
          control.tagAlign:
            param_name: output_file
    - narrow[peak_type]:
      - spp_nodups_narrow:
          inputs:
            signal.tagAlign:
              param_name: signal.tagAlign
            control.tagAlign:
              param_name: control.tagAlign
          outputs:
            results.narrowPeak.gz:
              param_name: result_peaks
            results.pdf:
              param_name: plots_pdf
            results.ccscore:
              param_name: score
      - sort_awk_sort_peaks:
          inputs:
            results.narrowPeak.gz:
              param_name: result_peaks
          outputs:
            results_sorted.bed:
              param_name: sorted_peaks
              final_result: true
    - broad[peak_type]:
      - spp_nodups_broad:
          inputs:
            signal.tagAlign:
              param_name: signal.tagAlign
            control.tagAlign:
              param_name: control.tagAlign
          outputs:
            results.broadPeak.gz:
              param_name: result_peaks
            results.pdf:
              param_name: plots_pdf
            results.ccscore:
              param_name: score
      - sort_awk_sort_peaks:
          inputs:
            results.broadPeak.gz:
              param_name: result_peaks
          outputs:
            results_sorted.bed:
              param_name: sorted_peaks
              final_result: true
  - macs2[tool]:
    - narrow[peak_type]:
      - macs2_narrow:
          inputs:
            prefix:
              param_name: prefix
            control.bed:
              param_name: control.bed
            signal.bed:
              param_name: signal.bed
          outputs:
            peaks.narrowPeak:
              param_name: result_peaks
            peaks.xls:
              param_name: result_excel
            summits.bed:
              param_name: result_summit
      - sort_awk_sort_peaks:
          inputs:
            peaks.narrowPeak:
              param_name: result_peaks
          outputs:
            results_sorted.bed:
              param_name: sorted_peaks
              final_result: true
    - broad[peak_type]:
      - macs2_broad:
          inputs:
            prefix:
              param_name: prefix
            control.bed:
              param_name: control.bed
            signal.bed:
              param_name: signal.bed
          outputs:
            peaks.broadPeak:
              param_name: result_peaks
            peaks.xls:
              param_name: result_excel
            summits.bed:
              param_name: result_summit
      - sort_awk_sort_peaks:
          inputs:
            peaks.broadPeak:
              param_name: result_peaks
          outputs:
            results_sorted.bed:
              param_name: sorted_peaks
              final_result: true
  - zerone[tool]:
    - broad[peak_type]:
      - zerone_callpeak:
          inputs:
            control.bam:
              param_name: control.bam
            signal.bam:
              param_name: signal.bam
          outputs:
            peaks.bed:
              param_name: result_peaks
      - zerone_format:
          inputs:
            peaks.bed:
              param_name: result_peaks
          outputs:
            results_sorted.bed:
              param_name: full_result
              final_result: true
  - hiddendomains[tool]:
    - broad[peak_type]:
      - hiddendomains_callpeak:
          inputs:
            control.bed:
              param_name: control.bed
            signal.bed:
              param_name: signal.bed
            chrom.sizes:
              param_name: chrom_sizes
            prefix:
              param_name: prefix
          outputs:
            analysis.bed:
              param_name: result_peaks
            vis.bed:
              param_name: enriched_bins
            domains.txt:
              param_name: domains
            control_bins.txt:
              param_name: control_bins
            treatment_bins.txt:
              param_name: treatment_bins
      - hiddendomains_format:
          inputs:
            analysis.bed:
              param_name: result_peaks
          outputs:
            results_sorted.bed:
              param_name: full_result
              final_result: true
  - pepr[tool]:
    - pepr_callpeak:
        inputs:
          control.bed:
            param_name: control.bed
          signal.bed:
            param_name: signal.bed
          prefix:
            param_name: prefix
          peak_type:
            param_name: peak_type
        outputs:
          results_sorted.bed:
            param_name: result_peaks
            final_result: true
          parameters.txt:
            param_name: pepr_params