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77 changes: 77 additions & 0 deletions docs/images/seqinspector.mmd
Original file line number Diff line number Diff line change
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%%metro title: nf-core/seqinspector
%%metro style: dark
%%metro logo: docs/images/nf-core-seqinspector_logo_dark.png

%%metro line: run_folder | Run Folder | #1f77b4
%%metro line: fastq_files | FASTQ Files | #ff7f0e

%%metro file: rundir_in | RUNDIR
%%metro file: fastq_in | FASTQ
%%metro file: report_global | HTML
%%metro file: report_per_tag | HTML
%%metro direction: LR
%%metro entry: left | run_folder
%%metro entry: left | fastq_files
%%metro exit: left | fastq_files
%%metro exit: left | run_folder
%%metro legend: bl

graph LR
subgraph run_folder [Run Folder]
rundir_in[ ]

checkqc[CheckQC]
rundirparser[Rundirparser]

rundir_in -->|run_folder| checkqc
checkqc -->|run_folder| rundirparser
end

subgraph fastq_files [FASTQ Files]
fastq_in[ ]
bwamem2[BWAmem2]
fastp[FastP]
fastqc[FASTQC]
fastqe[FASTQE]
fastqscreen[FastQ Screen]
fq_lint[FQ Lint]
kraken2[Kraken2]
krona[Krona]
picard[Picard]
seqfu[SeqFu Stats]
seqtk[SeqTK]
toulligqc[ToulligQC]

fastq_in -->|fastq_files| fq_lint
fq_lint -->|fastq_files| seqtk

seqtk -->|fastq_files| bwamem2
seqtk -->|fastq_files| fastp
seqtk -->|fastq_files| fastqc
seqtk -->|fastq_files| fastqe
seqtk -->|fastq_files| fastqscreen
seqtk -->|fastq_files| kraken2
seqtk -->|fastq_files| seqfu

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seqfu takes input from fq_lint not seqtk.

seqtk -->|fastq_files| toulligqc

bwamem2 -->|fastq_files| picard
kraken2 -->|fastq_files| krona
end

subgraph multiqc [MultiQC]
multiqc[MultiQC]
report_global[Global report]
report_per_tag[Reports per tags]

fastp -->|fastq_files| multiqc
fastqc -->|fastq_files| multiqc
fastqe -->|fastq_files| multiqc
fastqscreen -->|fastq_files| multiqc
krona -->|fastq_files| multiqc
picard -->|fastq_files| multiqc
rundirparser -->|run_folder| multiqc
seqfu -->|fastq_files| multiqc
toulligqc -->|fastq_files| multiqc
multiqc -->|fastq_files| report_per_tag
multiqc -->|fastq_files,run_folder| report_global
end
Binary file added docs/images/seqinspector.png

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i guess you need to file a bug for the "reports per tags" overlap

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127 changes: 127 additions & 0 deletions docs/images/seqinspector.svg
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Binary file added docs/images/seqinspector_dark.png
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122 changes: 122 additions & 0 deletions docs/images/seqinspector_dark.svg
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Binary file added docs/images/seqinspector_light.png
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127 changes: 127 additions & 0 deletions docs/images/seqinspector_light.svg
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