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9ecdb612f6
Build pipeline: viash-hub.rnaseq.prepare-reads-9nvqs
Source commit: 2bd8e1becf
Source message: update mermaid
157 lines
4.9 KiB
Plaintext
157 lines
4.9 KiB
Plaintext
---
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title: rnaseq
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format: gfm
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---
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<!-- README.md is generated by running 'quarto render README.qmd' -->
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```{r, echo = FALSE, message = FALSE, error = FALSE, warning = FALSE}
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library(tidyverse)
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```
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## RNA-seq
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```{mermaid}
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flowchart TB
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subgraph inputs[Inputs]
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input_r1[Input R1 FastQ]
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input_r2[Input R2 FastQ]
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sample_metadata[Sample metadata]
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reference_fasta[Reference fasta]
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reference_gtf[Reference GTF]
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end
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inputs:::io
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input_r1 & input_r2 & sample_metadata --> prepare_reads --> processed_r1 & processed_r2 & processed_metadata
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prepare_reads[/prepare_reads/]:::comp
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reference_fasta & reference_gtf --> prepare_reference --> processed_fasta & processed_gtf & star_index
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prepare_reference[/prepare_reference/]:::comp
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processed_r1 & processed_r2 & star_index & processed_fasta & processed_gtf --> align_and_quant --> aligned_reads_bam & quant_matrix
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align_and_quant[/align_and_quant/]:::comp
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aligned_reads_bam --> postprocess_bam --> output_aligned_reads_bam
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postprocess_bam[/postprocess_bam/]:::comp
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quant_matrix & processed_metadata --> postprocess_mtx --> output_quant_matrix
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postprocess_mtx[/postprocess_mtx/]:::comp
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processed_metadata & output_quant_matrix & output_combined_qc_data --> conversion --> output_anndata & output_sce
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conversion[/conversion/]:::comp
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subgraph outputs[Outputs]
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output_aligned_reads_bam[Aligned reads]
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output_quant_matrix[Quant matrix]
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output_combined_qc_data[QC Data]
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output_combined_qc_report[QC Report]
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output_anndata[AnnData]
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output_sce[SCE]
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end
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outputs:::io
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subgraph legend[Legend]
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comp[/Component/]:::comp
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end
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legend:::info
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classDef info stroke-dasharray: 4 4
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```
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## RNA-seq (With reporting)
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```{mermaid}
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flowchart TB
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subgraph inputs[Inputs]
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input_r1[Input R1 FastQ]
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input_r2[Input R2 FastQ]
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sample_metadata[Sample metadata]
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reference_fasta[Reference fasta]
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reference_gtf[Reference GTF]
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end
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inputs:::io
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input_r1 & input_r2 & sample_metadata --> prepare_reads --> processed_r1 & processed_r2 & processed_metadata
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prepare_reads[/prepare_reads/]:::comp
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prepare_reads -.-> prepare_reads_qc_data
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reference_fasta & reference_gtf --> prepare_reference --> processed_fasta & processed_gtf & star_index
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prepare_reference[/prepare_reference/]:::comp
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prepare_reference -.-> prepare_reference_qc_data
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processed_r1 & processed_r2 & star_index & processed_fasta & processed_gtf --> align_and_quant --> aligned_reads_bam & quant_matrix
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align_and_quant[/align_and_quant/]:::comp
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align_and_quant -.-> align_and_quant_qc_data
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aligned_reads_bam --> postprocess_bam --> output_aligned_reads_bam
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postprocess_bam[/postprocess_bam/]:::comp
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postprocess_bam -.-> postprocess_bam_qc_data
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quant_matrix & processed_metadata --> postprocess_mtx --> output_quant_matrix
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postprocess_mtx[/postprocess_mtx/]:::comp
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postprocess_mtx -.-> postprocess_mtx_qc_data
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prepare_reads_qc_data & prepare_reference_qc_data & align_and_quant_qc_data & postprocess_bam_qc_data & postprocess_mtx_qc_data -.-> reporting -.-> output_combined_qc_data & output_combined_qc_report
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reporting[/reporting/]:::comp
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processed_metadata & output_quant_matrix & output_combined_qc_data --> conversion --> output_anndata & output_sce
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conversion[/conversion/]:::comp
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subgraph outputs[Outputs]
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output_aligned_reads_bam[Aligned reads]
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output_quant_matrix[Quant matrix]
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output_combined_qc_data[QC Data]
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output_combined_qc_report[QC Report]
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output_anndata[AnnData]
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output_sce[SCE]
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end
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outputs:::io
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subgraph legend[Legend]
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comp[/Component/]:::comp
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end
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legend:::info
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classDef info stroke-dasharray: 4 4
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```
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## Prepare reads
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```{mermaid}
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flowchart TB
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subgraph inputs[Inputs]
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input_r1[R1 reads]
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input_r2[R2 reads]
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input_strandedness[Strandedness]
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end
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input_r1 --> concat_text_r1[/concat_text/]:::comp
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input_r2 --> concat_text_r2[/concat_text/]:::comp
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concat_text_r1 & concat_text_r2 --> lint_fastq1[/lint_fastq/]:::comp --> trim_reads[/trim_reads/]:::comp --> lint_fastq2[/lint_fastq/]:::comp --> remove_genome_contaminants[/remove_genome_contaminants/]:::comp --> lint_fastq3[/lint_fastq/]:::comp --> remove_rRNA[/remove_rRNA/]:::comp --> lint_fastq4[/lint_fastq/]:::comp --> infer_strandedness[/infer_strandedness/]:::comp --> processed_r1 & processed_r2 & output_strandedness
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input_strandedness --> infer_strandedness
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concat_text_r1 & concat_text_r2 --> fastqc_raw[/fastqc_raw/]:::comp --> fastqc_raw_multiqc
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trim_reads --> fastqc_trimmed[/fastqc_trimmed/]:::comp --> fastqc_trimmed_multiqc
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infer_strandedness --> strandedness_multiqc
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fastqc_raw_multiqc & fastqc_trimmed_multiqc & strandedness_multiqc --> prepare_reads_multiqc
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subgraph outputs[Outputs]
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processed_r1[R1 reads]
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processed_r2[R2 reads]
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output_strandedness[Strandedness]
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prepare_reads_multiqc[MultiQC files]
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end
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classDef info stroke-dasharray: 4 4
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```
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