%%{
  init: {
    'theme': 'base',
    'themeVariables': {
      'primaryColor': '#B6ECE2',
      'primaryTextColor': '#160F26',
      'primaryBorderColor': '#065647',
      'lineColor': '#545555',
      'clusterBkg': '#BABCBD22',
      'clusterBorder': '#DDDEDE',
      'fontFamily': 'arial'
    }
  }
}%%
flowchart TB
    subgraph " "
    v2["Channel.fromList"]
    v7["Channel.fromPath"]
    v98[" "]
    v140["Channel.of"]
    v143["Channel.fromPath"]
    v146["ch_workflow_summary"]
    v150["ch_methods_description"]
    v164["replace_names"]
    v165["sample_names"]
    end
    subgraph "NFCORE_METHYLSEQ [NFCORE_METHYLSEQ]"
    subgraph "NFCORE_METHYLSEQ:FASTA_INDEX_BISMARK_BWAMETH [FASTA_INDEX_BISMARK_BWAMETH]"
    v19(["GUNZIP"])
    v22(["BISMARK_GENOMEPREPARATION"])
    v18(( ))
    v21(( ))
    end
    subgraph "NFCORE_METHYLSEQ:METHYLSEQ [METHYLSEQ]"
    v47(["CAT_FASTQ"])
    v50(["FASTQC"])
    v55(["TRIMGALORE"])
    subgraph "NFCORE_METHYLSEQ:METHYLSEQ:FASTQ_ALIGN_DEDUP_BISMARK [FASTQ_ALIGN_DEDUP_BISMARK]"
    v90(["BISMARK_ALIGN"])
    v95(["BISMARK_DEDUPLICATE"])
    v99(["SAMTOOLS_SORT"])
    v104(["SAMTOOLS_INDEX"])
    v109(["BISMARK_METHYLATIONEXTRACTOR"])
    v116(["BISMARK_REPORT"])
    v124(["BISMARK_SUMMARY"])
    v92(( ))
    v94(( ))
    v96(( ))
    v118(( ))
    v122(( ))
    v123(( ))
    end
    v166(["MULTIQC"])
    v46(( ))
    v49(( ))
    v60(( ))
    v161(( ))
    v162(( ))
    v163(( ))
    v170(( ))
    end
    v8(( ))
    v24(( ))
    end
    subgraph " "
    v51["ch_fastqc_html"]
    v56[" "]
    v57[" "]
    v58[" "]
    v91[" "]
    v93["ch_alignment_reports"]
    v100[" "]
    v101[" "]
    v102[" "]
    v105[" "]
    v106[" "]
    v107["bai"]
    v110["methylation_coverage"]
    v111["methylation_calls"]
    v112["ch_bedgraph"]
    v167[" "]
    v168[" "]
    v169[" "]
    v172["versions"]
    v174[" "]
    end
    subgraph "PIPELINE_INITIALISATION [PIPELINE_INITIALISATION]"
    v3(( ))
    end
    subgraph "PIPELINE_COMPLETION [PIPELINE_COMPLETION]"
    v173(( ))
    end
    v2 --> v3
    v7 --> v8
    v18 --> v19
    v19 --> v18
    v19 --> v21
    v18 --> v22
    v22 --> v21
    v22 --> v60
    v46 --> v47
    v47 --> v46
    v47 --> v49
    v46 --> v50
    v50 --> v51
    v50 --> v49
    v46 --> v55
    v55 --> v58
    v55 --> v57
    v55 --> v56
    v55 --> v49
    v55 --> v60
    v60 --> v90
    v90 --> v95
    v90 --> v91
    v90 --> v92
    v90 --> v94
    v90 --> v96
    v90 --> v118
    v92 --> v93
    v95 --> v99
    v95 --> v109
    v95 --> v94
    v95 --> v96
    v98 --> v99
    v99 --> v104
    v99 --> v102
    v99 --> v101
    v99 --> v100
    v99 --> v94
    v104 --> v107
    v104 --> v106
    v104 --> v105
    v104 --> v94
    v60 --> v109
    v109 --> v112
    v109 --> v111
    v109 --> v110
    v109 --> v94
    v109 --> v96
    v109 --> v122
    v109 --> v123
    v96 --> v116
    v116 --> v94
    v116 --> v96
    v96 --> v124
    v118 --> v124
    v122 --> v124
    v123 --> v124
    v124 --> v94
    v124 --> v96
    v140 --> v49
    v143 --> v161
    v146 --> v49
    v150 --> v49
    v164 --> v166
    v165 --> v166
    v49 --> v166
    v161 --> v166
    v162 --> v166
    v163 --> v166
    v166 --> v169
    v166 --> v168
    v166 --> v167
    v166 --> v170
    v24 --> v172
    v173 --> v174
    v3 --> v46
    v8 --> v18
    v18 --> v60
    v21 --> v24
    v49 --> v24
    v24 --> v49
    v94 --> v49
    v96 --> v49
    v170 --> v173