Nextflow Workflow Diagrams #319

chasemc · 2023-03-31T14:02:14Z

chasemc
Mar 31, 2023
Maintainer

/*
    test_dir=`mktemp -d -p "$DIR"`
    echo $test_dir

    nextflow run . \
        -profile test_example_1,docker \
        --outdir $test_dir \
        --input "" \
        -preview
*/
params {
    unclustered_recruitment     = true
    taxonomy_aware              = true
    large_downloads_permission  = true
}

flowchart TD
    p0((Channel.empty))
    p1((Channel.fromList))
    p2((Channel.empty))
    p3((Channel.empty))
    p4((Channel.empty))
    p5((Channel.fromPath))
    p6((Channel.empty))
    p7[AUTOMETA:PROCESS_METAGENOME:INPUT_CHECK:SAMPLESHEET_CHECK]
    p8([mix])
    p9([splitCsv])
    p10([map])
    p11([splitCsv])
    p12([map])
    p13([splitCsv])
    p14([map])
    p15([mix])
    p16[AUTOMETA:PROCESS_METAGENOME:SEQKIT_FILTER]
    p17([mix])
    p18([join])
    p19([mix])
    p20((Channel.empty))
    p21((Channel.empty))
    p22[AUTOMETA:COVERAGE:CALCULATE_COVERAGE:ALIGN_READS]
    p23(( ))
    p24([mix])
    p25[AUTOMETA:COVERAGE:CALCULATE_COVERAGE:BEDTOOLS_GENOMECOV]
    p26([mix])
    p27[AUTOMETA:COVERAGE:CALCULATE_COVERAGE:PARSE_BED]
    p28([mix])
    p29([mix])
    p30([filter])
    p31[AUTOMETA:COVERAGE:SPADES_KMER_COVERAGE]
    p32([mix])
    p33([mix])
    p34([mix])
    p35([mix])
    p36(( ))
    p37[AUTOMETA:PRODIGAL]
    p38(( ))
    p39(( ))
    p40(( ))
    p41([mix])
    p42((Channel.empty))
    p43((Channel.empty))
    p44[AUTOMETA:TAXON_ASSIGNMENT:PREPARE_TAXONOMY_DATABASES:DOWNLOAD_TAXDUMP]
    p45([mix])
    p46[AUTOMETA:TAXON_ASSIGNMENT:PREPARE_TAXONOMY_DATABASES:DOWNLOAD_ACESSION2TAXID]
    p47([mix])
    p48([mix])
    p49((Channel.empty))
    p50[AUTOMETA:TAXON_ASSIGNMENT:PREPARE_NR_DB:DOWNLOAD_NR]
    p51(( ))
    p52([mix])
    p53(( ))
    p54[AUTOMETA:TAXON_ASSIGNMENT:PREPARE_NR_DB:DIAMOND_MAKEDB]
    p55([mix])
    p56([mix])
    p57[AUTOMETA:TAXON_ASSIGNMENT:DIAMOND_BLASTP]
    p58([mix])
    p59((Channel.empty))
    p60[AUTOMETA:TAXON_ASSIGNMENT:LCA:PREP_DBS]
    p61([mix])
    p62[AUTOMETA:TAXON_ASSIGNMENT:LCA:REDUCE]
    p63(( ))
    p64(( ))
    p65([mix])
    p66([mix])
    p67[AUTOMETA:TAXON_ASSIGNMENT:MAJORITY_VOTE]
    p68([mix])
    p69([join])
    p70[AUTOMETA:TAXON_ASSIGNMENT:SPLIT_KINGDOMS]
    p71([mix])
    p72([transpose])
    p73([multiMap])
    p74([collect])
    p75([flatten])
    p76([combine])
    p77([map])
    p78([mix])
    p79((Channel.empty))
    p80[AUTOMETA:KMERS:COUNT]
    p81([mix])
    p82[AUTOMETA:KMERS:NORMALIZE]
    p83([mix])
    p84[AUTOMETA:KMERS:EMBED]
    p85([mix])
    p86([mix])
    p87([combine])
    p88([map])
    p89([combine])
    p90([map])
    p91([combine])
    p92([map])
    p93[AUTOMETA:MARKERS]
    p94(( ))
    p95([mix])
    p96([join])
    p97([join])
    p98([join])
    p99([join])
    p100[AUTOMETA:BINNING]
    p101(( ))
    p102([mix])
    p103([join])
    p104([join])
    p105([join])
    p106([join])
    p107[AUTOMETA:UNCLUSTERED_RECRUIT]
    p108(( ))
    p109(( ))
    p110([mix])
    p111((Channel.of))
    p112([join])
    p113([join])
    p114([combine])
    p115[AUTOMETA:BINNING_SUMMARY]
    p116(( ))
    p117(( ))
    p118(( ))
    p119([mix])
    p120([combine])
    p121([map])
    p122([combine])
    p123([map])
    p124([join])
    p125([join])
    p126(( ))
    p127[AUTOMETA:MOCK_DATA_REPORT]
    p128(( ))
    p129([mix])
    p130([unique])
    p131([collectFile])
    p132[AUTOMETA:CUSTOM_DUMPSOFTWAREVERSIONS]
    p133(( ))
    p134(( ))
    p135(( ))
    p0 -->|ch_versions| p19
    p1 -->|ch_taxa_with_marker_sets| p87
    p2 -->|ch_versions| p15
    p3 -->|assembly_to_locus| p120
    p4 -->|assembly_report| p122
    p5 -->|samplesheet| p7
    p6 -->|ch_versions| p8
    p7 --> p9
    p7 --> p8
    p8 -->|versions| p15
    p9 --> p10
    p10 -->|reads| p18
    p7 --> p11
    p11 --> p12
    p12 -->|raw_metagenome_fasta| p16
    p7 --> p13
    p13 --> p14
    p14 -->|user_provided_coverage_table| p33
    p15 -->|ch_versions| p17
    p16 -->|filtered_metagenome_fasta| p18
    p16 -->|filtered_metagenome_gc_content| p89
    p16 --> p17
    p17 -->|versions| p19
    p18 -->|metagenome_reads_ch| p22
    p19 -->|ch_versions| p35
    p20 -->|ch_versions| p29
    p21 -->|ch_versions| p24
    p22 -->|bam| p25
    p22 --> p23
    p22 --> p24
    p24 -->|ch_versions| p26
    p25 -->|bed| p27
    p25 --> p26
    p26 -->|ch_versions| p28
    p27 -->|coverage| p33
    p27 --> p28
    p28 -->|versions| p29
    p29 -->|ch_versions| p32
    p16 -->|filtered_metagenome_fasta| p30
    p30 -->|ch_for_spades_cov| p31
    p31 --> p34
    p31 --> p32
    p32 -->|versions| p35
    p33 --> p34
    p34 -->|ch_coverage| p87
    p35 -->|ch_versions| p41
    p16 -->|filtered_metagenome_fasta| p37
    p36 -->|output_format| p37
    p37 --> p40
    p37 --> p39
    p37 -->|merged_prodigal| p57
    p37 --> p38
    p37 --> p41
    p41 -->|ch_versions| p78
    p42 -->|ch_versions| p48
    p43 -->|ch_versions| p45
    p44 -->|ch_taxdump_files| p60
    p44 --> p45
    p45 -->|ch_versions| p47
    p46 -->|prot_accession2taxid| p62
    p46 --> p47
    p47 -->|versions| p48
    p48 -->|ch_versions| p56
    p49 -->|ch_versions| p52
    p50 --> p54
    p50 --> p51
    p50 --> p52
    p52 -->|ch_versions| p55
    p53 -->|dbname| p54
    p54 -->|diamond_db| p57
    p54 --> p55
    p55 -->|versions| p56
    p56 -->|ch_versions| p58
    p57 -->|blastp_results| p62
    p57 --> p58
    p58 -->|ch_versions| p66
    p59 -->|ch_versions| p61
    p60 -->|cache| p62
    p60 --> p61
    p61 -->|ch_versions| p65
    p44 -->|ch_taxdump_files| p62
    p62 -->|orf_votes| p67
    p62 -->|error_taxid| p64
    p62 -->|sseqid_to_taxids| p63
    p62 --> p65
    p65 -->|versions| p66
    p66 -->|ch_versions| p68
    p44 -->|ch_taxdump_files| p67
    p67 -->|contig_votes| p69
    p67 --> p68
    p68 -->|ch_versions| p71
    p16 -->|filtered_metagenome_fasta| p69
    p69 -->|split_kingdoms_input| p70
    p44 -->|ch_taxdump_files| p70
    p70 --> p76
    p70 --> p72
    p70 --> p71
    p71 -->|versions| p78
    p72 --> p73
    p73 --> p74
    p73 -->|fasta| p80
    p74 --> p75
    p75 -->|ch_found_taxa_list| p76
    p76 --> p77
    p77 -->|ch_taxonomy_results| p99
    p78 -->|ch_versions| p86
    p79 -->|ch_versions| p81
    p80 -->|counts| p82
    p80 --> p81
    p81 -->|ch_versions| p83
    p82 -->|ch_kmers_normalized| p84
    p82 --> p83
    p83 -->|ch_versions| p85
    p84 -->|ch_kmers_embedded| p96
    p84 --> p85
    p85 -->|versions| p86
    p86 -->|ch_versions| p95
    p87 --> p88
    p88 -->|new_ch_coverage| p96
    p1 -->|ch_taxa_with_marker_sets| p89
    p89 --> p90
    p90 -->|ch_new_filtered_metagenome_gc_content| p97
    p37 -->|merged_prodigal| p91
    p1 -->|ch_taxa_with_marker_sets| p91
    p91 --> p92
    p92 -->|ch_new_orf| p93
    p93 -->|ch_markers| p98
    p93 --> p94
    p93 --> p95
    p95 -->|ch_versions| p102
    p96 --> p97
    p97 --> p98
    p98 -->|ch_binning| p99
    p99 -->|ch_binning| p100
    p100 --> p101
    p100 --> p104
    p100 --> p102
    p102 -->|ch_versions| p110
    p82 -->|ch_kmers_normalized| p103
    p88 -->|new_ch_coverage| p103
    p103 --> p104
    p104 --> p105
    p93 -->|ch_markers| p105
    p105 -->|recruitment_ch| p106
    p77 -->|ch_taxonomy_results| p106
    p106 -->|recruitment_ch| p107
    p107 --> p109
    p107 -->|ch_binning_results| p112
    p107 --> p108
    p107 --> p110
    p110 -->|ch_versions| p119
    p111 -->|binning_col| p114
    p93 -->|ch_markers| p112
    p112 --> p113
    p73 -->|fasta| p113
    p113 --> p114
    p114 -->|binning_summary_ch| p115
    p44 -->|ch_taxdump_files| p115
    p115 --> p118
    p115 --> p117
    p115 --> p116
    p115 --> p119
    p119 -->|ch_versions| p129
    p1 -->|ch_taxa_with_marker_sets| p120
    p120 --> p121
    p121 -->|ch_new_assembly_to_locus| p124
    p1 -->|ch_taxa_with_marker_sets| p122
    p122 --> p123
    p123 -->|ch_new_assembly_report| p125
    p107 -->|ch_binning_results| p124
    p124 --> p125
    p125 -->|ch_mock_input| p127
    p126 -->|rmarkdown_file| p127
    p127 --> p128
    p127 --> p129
    p129 -->|ch_versions| p130
    p130 --> p131
    p131 --> p132
    p132 --> p135
    p132 --> p134
    p132 --> p133

chasemc · 2023-03-31T14:03:45Z

chasemc
Mar 31, 2023
Maintainer Author

/*
    test_dir=`mktemp -d -p "$DIR"`
    echo $test_dir

    nextflow run . \
        -profile test_example_1,docker \
        --outdir $test_dir \
        --input "" \
        -preview

    # remember to uncomment the line below to cleanup :)
    # rm -r $test_dir
*/
params {
    unclustered_recruitment     = true
    taxonomy_aware              = false
    large_downloads_permission  = false
}

flowchart TD
    p0((Channel.empty))
    p1((Channel.fromList))
    p2((Channel.empty))
    p3((Channel.empty))
    p4((Channel.empty))
    p5((Channel.fromPath))
    p6((Channel.empty))
    p7[AUTOMETA:PROCESS_METAGENOME:INPUT_CHECK:SAMPLESHEET_CHECK]
    p8([mix])
    p9([splitCsv])
    p10([map])
    p11([splitCsv])
    p12([map])
    p13([splitCsv])
    p14([map])
    p15([mix])
    p16[AUTOMETA:PROCESS_METAGENOME:SEQKIT_FILTER]
    p17([mix])
    p18([join])
    p19([mix])
    p20((Channel.empty))
    p21((Channel.empty))
    p22[AUTOMETA:COVERAGE:CALCULATE_COVERAGE:ALIGN_READS]
    p23(( ))
    p24([mix])
    p25[AUTOMETA:COVERAGE:CALCULATE_COVERAGE:BEDTOOLS_GENOMECOV]
    p26([mix])
    p27[AUTOMETA:COVERAGE:CALCULATE_COVERAGE:PARSE_BED]
    p28([mix])
    p29([mix])
    p30([filter])
    p31[AUTOMETA:COVERAGE:SPADES_KMER_COVERAGE]
    p32([mix])
    p33([mix])
    p34([mix])
    p35([mix])
    p36(( ))
    p37[AUTOMETA:PRODIGAL]
    p38(( ))
    p39(( ))
    p40(( ))
    p41([mix])
    p42((Channel.fromPath))
    p43((Channel.fromPath))
    p44((Channel.empty))
    p45[AUTOMETA:KMERS:COUNT]
    p46([mix])
    p47[AUTOMETA:KMERS:NORMALIZE]
    p48([mix])
    p49[AUTOMETA:KMERS:EMBED]
    p50([mix])
    p51([mix])
    p52((Channel.fromList))
    p53([combine])
    p54([map])
    p55((Channel.fromList))
    p56([combine])
    p57([map])
    p58((Channel.fromList))
    p59([combine])
    p60([map])
    p61([combine])
    p62([map])
    p63([combine])
    p64([map])
    p65([combine])
    p66([map])
    p67[AUTOMETA:MARKERS]
    p68(( ))
    p69([mix])
    p70([join])
    p71([join])
    p72([join])
    p73([combine])
    p74[AUTOMETA:BINNING]
    p75(( ))
    p76([mix])
    p77([join])
    p78([join])
    p79([join])
    p80([combine])
    p81[AUTOMETA:UNCLUSTERED_RECRUIT]
    p82(( ))
    p83(( ))
    p84([mix])
    p85((Channel.of))
    p86([join])
    p87([join])
    p88([combine])
    p89[AUTOMETA:BINNING_SUMMARY]
    p90(( ))
    p91(( ))
    p92(( ))
    p93([mix])
    p94([combine])
    p95([map])
    p96([combine])
    p97([map])
    p98([join])
    p99([join])
    p100(( ))
    p101[AUTOMETA:MOCK_DATA_REPORT]
    p102(( ))
    p103([mix])
    p104([unique])
    p105([collectFile])
    p106[AUTOMETA:CUSTOM_DUMPSOFTWAREVERSIONS]
    p107(( ))
    p108(( ))
    p109(( ))
    p0 -->|ch_versions| p19
    p1 -->|ch_taxa_with_marker_sets| p61
    p2 -->|ch_versions| p15
    p3 -->|assembly_to_locus| p94
    p4 -->|assembly_report| p96
    p5 -->|samplesheet| p7
    p6 -->|ch_versions| p8
    p7 --> p9
    p7 --> p8
    p8 -->|versions| p15
    p9 --> p10
    p10 -->|reads| p18
    p7 --> p11
    p11 --> p12
    p12 -->|raw_metagenome_fasta| p16
    p7 --> p13
    p13 --> p14
    p14 -->|user_provided_coverage_table| p33
    p15 -->|ch_versions| p17
    p16 -->|fasta| p18
    p16 -->|filtered_metagenome_gc_content| p63
    p16 --> p17
    p17 -->|versions| p19
    p18 -->|metagenome_reads_ch| p22
    p19 -->|ch_versions| p35
    p20 -->|ch_versions| p29
    p21 -->|ch_versions| p24
    p22 -->|bam| p25
    p22 --> p23
    p22 --> p24
    p24 -->|ch_versions| p26
    p25 -->|bed| p27
    p25 --> p26
    p26 -->|ch_versions| p28
    p27 -->|coverage| p33
    p27 --> p28
    p28 -->|versions| p29
    p29 -->|ch_versions| p32
    p16 -->|fasta| p30
    p30 -->|ch_for_spades_cov| p31
    p31 --> p34
    p31 --> p32
    p32 -->|versions| p35
    p33 --> p34
    p34 -->|ch_coverage| p61
    p35 -->|ch_versions| p41
    p16 -->|fasta| p37
    p36 -->|output_format| p37
    p37 --> p40
    p37 --> p39
    p37 -->|orfs_ch| p65
    p37 --> p38
    p37 --> p41
    p41 -->|ch_versions| p51
    p42 -->|ch_taxonomy_results| p73
    p43 -->|ch_taxdump_files| p89
    p44 -->|ch_versions| p46
    p16 -->|fasta| p45
    p45 -->|counts| p47
    p45 --> p46
    p46 -->|ch_versions| p48
    p47 -->|normalized| p49
    p47 --> p48
    p48 -->|ch_versions| p50
    p49 -->|embedded| p53
    p49 --> p50
    p50 -->|versions| p51
    p51 -->|ch_versions| p69
    p52 --> p53
    p53 --> p54
    p54 -->|ch_kmers_embedded| p70
    p55 --> p56
    p47 -->|normalized| p56
    p56 --> p57
    p57 -->|ch_kmers_normalized| p77
    p58 --> p59
    p16 -->|fasta| p59
    p59 --> p60
    p60 -->|ch_kmers_input_fasta| p87
    p61 --> p62
    p62 -->|new_ch_coverage| p70
    p1 -->|ch_taxa_with_marker_sets| p63
    p63 --> p64
    p64 -->|ch_new_filtered_metagenome_gc_content| p71
    p1 -->|ch_taxa_with_marker_sets| p65
    p65 --> p66
    p66 -->|ch_new_orf| p67
    p67 -->|ch_markers| p72
    p67 --> p68
    p67 --> p69
    p69 -->|ch_versions| p76
    p70 --> p71
    p71 --> p72
    p72 -->|ch_binning| p73
    p73 -->|ch_binning| p74
    p74 --> p75
    p74 --> p78
    p74 --> p76
    p76 -->|ch_versions| p84
    p62 -->|new_ch_coverage| p77
    p77 --> p78
    p78 --> p79
    p67 -->|ch_markers| p79
    p79 -->|recruitment_ch| p80
    p42 -->|ch_taxonomy_results| p80
    p80 -->|recruitment_ch| p81
    p81 --> p83
    p81 -->|ch_binning_results| p86
    p81 --> p82
    p81 --> p84
    p84 -->|ch_versions| p93
    p85 -->|binning_col| p88
    p67 -->|ch_markers| p86
    p86 --> p87
    p87 --> p88
    p88 -->|binning_summary_ch| p89
    p89 --> p92
    p89 --> p91
    p89 --> p90
    p89 --> p93
    p93 -->|ch_versions| p103
    p1 -->|ch_taxa_with_marker_sets| p94
    p94 --> p95
    p95 -->|ch_new_assembly_to_locus| p98
    p1 -->|ch_taxa_with_marker_sets| p96
    p96 --> p97
    p97 -->|ch_new_assembly_report| p99
    p81 -->|ch_binning_results| p98
    p98 --> p99
    p99 -->|ch_mock_input| p101
    p100 -->|rmarkdown_file| p101
    p101 --> p102
    p101 --> p103
    p103 -->|ch_versions| p104
    p104 --> p105
    p105 --> p106
    p106 --> p109
    p106 --> p108
    p106 --> p107

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Nextflow Workflow Diagrams #319

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Nextflow Workflow Diagrams #319

chasemc Mar 31, 2023 Maintainer

Replies: 1 comment

chasemc Mar 31, 2023 Maintainer Author

chasemc
Mar 31, 2023
Maintainer

chasemc
Mar 31, 2023
Maintainer Author