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diff --git a/nextflow/README.md b/nextflow/README.md
index 0533b65..013286a 100644
--- a/nextflow/README.md
+++ b/nextflow/README.md
@@ -10,18 +10,226 @@ It is recommended that each workflow in `main.nf` is run sequentially to allow f
- The first workflow runs [`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) on the raw fastq files and then [`MultiQC`](http://multiqc.info/) on those results
- To run this workflow alone use: `nextflow run main.nf -params-file params.json -profile iris -entry FASTQC_FASTQ`
+```html
+
+
+
+
+
+
+flowchart TB
+ subgraph " "
+ v0["Channel.fromFilePairs"]
+ v1["Channel.fromPath"]
+ v3["adapterFASTA"]
+ v11["filename"]
+ end
+ subgraph " "
+ v2["adapter_ch"]
+ v5[" "]
+ v6[" "]
+ v13[" "]
+ end
+ subgraph FASTP_FASTQ
+ v4([RUN_FASTP])
+ v7([RUN_FASTQC_FASTP])
+ v12([RUN_MULTIQC_FASTP])
+ v8(( ))
+ end
+ v0 --> v4
+ v1 --> v2
+ v3 --> v4
+ v4 --> v7
+ v4 --> v6
+ v4 --> v5
+ v4 --> v8
+ v7 --> v8
+ v11 --> v12
+ v8 --> v12
+ v12 --> v13
+
+
+
+
+
+```
+
2. **Trimming and QC**
- The second workflow runs [`fastp`](https://github.com/OpenGene/fastp) to trim adapters and/or poly-X or poly-A tails, followed by [`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and [`MultiQC`](http://multiqc.info/)
- To run this workflow alone use: `nextflow run main.nf -params-file params.json -profile iris -entry FASTP_FASTQ`
+```html
+
+
+
+
+
+
+flowchart TB
+ subgraph " "
+ v0["Channel.fromFilePairs"]
+ v1["Channel.fromPath"]
+ v3["adapterFASTA"]
+ v11["filename"]
+ end
+ subgraph " "
+ v2["adapter_ch"]
+ v5[" "]
+ v6[" "]
+ v13[" "]
+ end
+ subgraph FASTP_FASTQ
+ v4([RUN_FASTP])
+ v7([RUN_FASTQC_FASTP])
+ v12([RUN_MULTIQC_FASTP])
+ v8(( ))
+ end
+ v0 --> v4
+ v1 --> v2
+ v3 --> v4
+ v4 --> v7
+ v4 --> v6
+ v4 --> v5
+ v4 --> v8
+ v7 --> v8
+ v11 --> v12
+ v8 --> v12
+ v12 --> v13
+
+
+
+
+
+```
+
3. **Alignment and indexing**
- The third workflow runs [`STAR`](https://github.com/alexdobin/STAR) on the adapter-trimmed fastq files followed by [`SAMtools`](https://sourceforge.net/projects/samtools/files/samtools/) indexing
- To run this workflow alone use: `nextflow run main.nf -params-file params.json -profile iris -entry STAR_FASTQ`
+```html
+
+
+
+
+
+
+flowchart TB
+ subgraph " "
+ v0["Channel.fromFilePairs"]
+ v1["Channel.fromPath"]
+ v3["adapterFASTA"]
+ v11["filename"]
+ end
+ subgraph " "
+ v2["adapter_ch"]
+ v5[" "]
+ v6[" "]
+ v13[" "]
+ end
+ subgraph FASTP_FASTQ
+ v4([RUN_FASTP])
+ v7([RUN_FASTQC_FASTP])
+ v12([RUN_MULTIQC_FASTP])
+ v8(( ))
+ end
+ v0 --> v4
+ v1 --> v2
+ v3 --> v4
+ v4 --> v7
+ v4 --> v6
+ v4 --> v5
+ v4 --> v8
+ v7 --> v8
+ v11 --> v12
+ v8 --> v12
+ v12 --> v13
+
+
+
+
+
+```
+
4. **Post-alignment QC**
- The fourth workflow runs QC on the resulting BAM files ([`SAMtools`](https://sourceforge.net/projects/samtools/files/samtools/) `flagstat` and various [`RSeQC`](http://rseqc.sourceforge.net/) modules), followed by [`MultiQC`](http://multiqc.info/) on those results
- To run this workflow alone use: `nextflow run main.nf -params-file params.json -profile iris -entry QC_BAM`
+```html
+
+
+
+
+
+
+flowchart TB
+ subgraph " "
+ v0["Channel.fromFilePairs"]
+ v2["Channel.fromPath"]
+ v13["Channel.fromPath"]
+ v14["Channel.fromPath"]
+ v22["filename"]
+ end
+ subgraph " "
+ v1["fastq_ch"]
+ v9[" "]
+ v10[" "]
+ v11[" "]
+ v24[" "]
+ end
+ subgraph QC_BAM
+ subgraph BAM_QC
+ v4([GET_BED])
+ v5([SAMTOOLS_FLAGSTAT])
+ v6([RSEQC_BAMSTAT])
+ v7([RSEQC_INFEREXP])
+ v8([RSEQC_READDUPLICATION])
+ v12([RSEQC_READDISTRIBUTION])
+ v3(( ))
+ end
+ v23([RUN_MULTIQC_STAR])
+ v15(( ))
+ end
+ v0 --> v1
+ v2 --> v3
+ v4 --> v7
+ v4 --> v12
+ v3 --> v5
+ v5 --> v15
+ v3 --> v6
+ v6 --> v15
+ v3 --> v7
+ v7 --> v15
+ v3 --> v8
+ v8 --> v11
+ v8 --> v10
+ v8 --> v9
+ v8 --> v15
+ v3 --> v12
+ v12 --> v15
+ v13 --> v15
+ v14 --> v15
+ v22 --> v23
+ v15 --> v23
+ v23 --> v24
+
+
+
+
+
+```
+
## Environment
Currently, this workflow assumes that a `conda` environment has been created with all necessary packages (TODO: add yml file).
@@ -37,7 +245,6 @@ Generate own `params.json` file using the following parameters:
"condaEnv" : "TODO",
"genomeDir" : "TODO",
"adapterFASTA" : "TODO",
- "linkBED" : "TODO",
"fileBED" : "TODO"
}
```
@@ -52,8 +259,7 @@ Below is a description of what each variable should contain. If variable is opti
| condaEnv | No | Path to conda environment to use |
| genomeDir | No | Path to STAR genome directory to use for alignment |
| adapterFASTA | Yes | FASTA file containing adapters to trim with FASTP |
-| linkBED | Yes | Link to bed file to use; only necessary with some RSeqQC modules |
-| fileBED | Yes | Bed file name to use; only necessary with some RSeqQC modules |
+| fileBED | Yes | Path to bed file to use; only necessary with some RSeqQC modules |
## Output directory/file structure
@@ -97,7 +303,6 @@ TODO: Add `bam_multiqc_report` and any quantification (`RSEM`/`featureCounts`) o
│ │ ├── _R1_fastqc.zip
│ │ ├── _R2_fastqc.html
│ │ └── _R2_fastqc.zip
-├── .bed
├── multiqc
│ ├── fastp_multiqc_report
│ │ ├── multiqc_data