%%{
  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"]
    v96[" "]
    v142["Channel.of"]
    v145["Channel.fromPath"]
    v148["ch_workflow_summary"]
    v152["ch_methods_description"]
    v166["replace_names"]
    v167["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"])
    v53(["TRIMGALORE"])
    subgraph "NFCORE_METHYLSEQ:METHYLSEQ:FASTQ_ALIGN_DEDUP_BISMARK [FASTQ_ALIGN_DEDUP_BISMARK]"
    v88(["BISMARK_ALIGN"])
    v93(["BISMARK_DEDUPLICATE"])
    v97(["SAMTOOLS_SORT"])
    v102(["SAMTOOLS_INDEX"])
    v107(["BISMARK_METHYLATIONEXTRACTOR"])
    v111(["BISMARK_COVERAGE2CYTOSINE"])
    v118(["BISMARK_REPORT"])
    v126(["BISMARK_SUMMARY"])
    v90(( ))
    v92(( ))
    v94(( ))
    v120(( ))
    v124(( ))
    v125(( ))
    end
    v168(["MULTIQC"])
    v46(( ))
    v49(( ))
    v58(( ))
    v163(( ))
    v164(( ))
    v165(( ))
    v172(( ))
    end
    v8(( ))
    v24(( ))
    end
    subgraph " "
    v51["ch_fastqc_html"]
    v54[" "]
    v55[" "]
    v56[" "]
    v89[" "]
    v91["ch_alignment_reports"]
    v98[" "]
    v99[" "]
    v100[" "]
    v103[" "]
    v104[" "]
    v105["bai"]
    v108["methylation_calls"]
    v109["ch_bedgraph"]
    v112["coverage2cytosine_summary"]
    v113["coverage2cytosine_report"]
    v114["coverage2cytosine_coverage"]
    v169[" "]
    v170[" "]
    v171[" "]
    v174["versions"]
    v176[" "]
    end
    subgraph "PIPELINE_INITIALISATION [PIPELINE_INITIALISATION]"
    v3(( ))
    end
    subgraph "PIPELINE_COMPLETION [PIPELINE_COMPLETION]"
    v175(( ))
    end
    v2 --> v3
    v7 --> v8
    v18 --> v19
    v19 --> v18
    v19 --> v21
    v18 --> v22
    v22 --> v21
    v22 --> v58
    v46 --> v47
    v47 --> v46
    v47 --> v49
    v46 --> v50
    v50 --> v51
    v50 --> v49
    v46 --> v53
    v53 --> v56
    v53 --> v55
    v53 --> v54
    v53 --> v49
    v53 --> v58
    v58 --> v88
    v88 --> v93
    v88 --> v89
    v88 --> v90
    v88 --> v92
    v88 --> v94
    v88 --> v120
    v90 --> v91
    v93 --> v97
    v93 --> v107
    v93 --> v92
    v93 --> v94
    v96 --> v97
    v97 --> v102
    v97 --> v100
    v97 --> v99
    v97 --> v98
    v97 --> v92
    v102 --> v105
    v102 --> v104
    v102 --> v103
    v102 --> v92
    v58 --> v107
    v107 --> v109
    v107 --> v108
    v107 --> v111
    v107 --> v92
    v107 --> v94
    v107 --> v124
    v107 --> v125
    v58 --> v111
    v111 --> v114
    v111 --> v113
    v111 --> v112
    v111 --> v92
    v94 --> v118
    v118 --> v92
    v118 --> v94
    v94 --> v126
    v120 --> v126
    v124 --> v126
    v125 --> v126
    v126 --> v92
    v126 --> v94
    v142 --> v49
    v145 --> v163
    v148 --> v49
    v152 --> v49
    v166 --> v168
    v167 --> v168
    v49 --> v168
    v163 --> v168
    v164 --> v168
    v165 --> v168
    v168 --> v171
    v168 --> v170
    v168 --> v169
    v168 --> v172
    v24 --> v174
    v175 --> v176
    v3 --> v46
    v8 --> v18
    v18 --> v58
    v21 --> v24
    v49 --> v24
    v24 --> v49
    v92 --> v49
    v94 --> v49
    v172 --> v175