%%{ 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"] v93[" "] v139["Channel.of"] v142["Channel.fromPath"] v145["ch_workflow_summary"] v149["ch_methods_description"] v161["replace_names"] v162["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"]) subgraph "NFCORE_METHYLSEQ:METHYLSEQ:FASTQ_ALIGN_DEDUP_BISMARK [FASTQ_ALIGN_DEDUP_BISMARK]" v85(["BISMARK_ALIGN"]) v90(["BISMARK_DEDUPLICATE"]) v94(["SAMTOOLS_SORT"]) v99(["SAMTOOLS_INDEX"]) v104(["BISMARK_METHYLATIONEXTRACTOR"]) v108(["BISMARK_COVERAGE2CYTOSINE"]) v115(["BISMARK_REPORT"]) v123(["BISMARK_SUMMARY"]) v87(( )) v89(( )) v91(( )) v117(( )) v121(( )) v122(( )) end v163(["MULTIQC"]) v46(( )) v49(( )) v158(( )) v159(( )) v160(( )) v167(( )) end v8(( )) v24(( )) end subgraph " " v51["ch_fastqc_html"] v86[" "] v88["ch_alignment_reports"] v95[" "] v96[" "] v97[" "] v100[" "] v101[" "] v102["bai"] v105["methylation_calls"] v106["ch_bedgraph"] v109["coverage2cytosine_summary"] v110["coverage2cytosine_report"] v111["coverage2cytosine_coverage"] v164[" "] v165[" "] v166[" "] v169["versions"] v171[" "] end subgraph "PIPELINE_INITIALISATION [PIPELINE_INITIALISATION]" v3(( )) end subgraph "PIPELINE_COMPLETION [PIPELINE_COMPLETION]" v170(( )) end v2 --> v3 v7 --> v8 v18 --> v19 v19 --> v18 v19 --> v21 v18 --> v22 v22 --> v21 v22 --> v46 v46 --> v47 v47 --> v46 v47 --> v49 v46 --> v50 v50 --> v51 v50 --> v49 v46 --> v85 v85 --> v90 v85 --> v86 v85 --> v87 v85 --> v89 v85 --> v91 v85 --> v117 v87 --> v88 v90 --> v94 v90 --> v104 v90 --> v89 v90 --> v91 v93 --> v94 v94 --> v99 v94 --> v97 v94 --> v96 v94 --> v95 v94 --> v89 v99 --> v102 v99 --> v101 v99 --> v100 v99 --> v89 v46 --> v104 v104 --> v106 v104 --> v105 v104 --> v108 v104 --> v89 v104 --> v91 v104 --> v121 v104 --> v122 v46 --> v108 v108 --> v111 v108 --> v110 v108 --> v109 v108 --> v89 v91 --> v115 v115 --> v89 v115 --> v91 v91 --> v123 v117 --> v123 v121 --> v123 v122 --> v123 v123 --> v89 v123 --> v91 v139 --> v49 v142 --> v158 v145 --> v49 v149 --> v49 v161 --> v163 v162 --> v163 v49 --> v163 v158 --> v163 v159 --> v163 v160 --> v163 v163 --> v166 v163 --> v165 v163 --> v164 v163 --> v167 v24 --> v169 v170 --> v171 v3 --> v46 v8 --> v18 v18 --> v46 v21 --> v24 v49 --> v24 v24 --> v49 v89 --> v49 v91 --> v49 v167 --> v170