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Update README #36

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205 changes: 142 additions & 63 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -7,32 +7,36 @@ to obtain consensus sequences, HA and NA subtypes, clade calls, and amino acid m

## Analyses

- Read trimming & QC: `fastp`
- Primer removal with `cutadapt`
- FASTQ quality reporting with `FastQC`
- Aggregate the reports with `multiqc`
- Sequence analysis with `FluViewer`
- Read trimming & QC: [fastp](https://github.com/OpenGene/fastp)
- Primer removal with [cutadapt](https://github.com/marcelm/cutadapt)
- FASTQ quality reporting with [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
- Aggregate the reports with [MultiQC](https://multiqc.info/)
- Sequence analysis with [BCCDC-PHL/FluViewer](https://github.com/BCCDC-PHL/FluViewer)
- Extract HPAI motif (applies to H5 sequences only)
- Clade calls for H1, H3 and H5 influenza using Nextclade (H1 and H3, custom Nextclade for H5 used at BCCDC-PHL)
- Clade calls for H1, H3 and H5 influenza using [Nextclade](https://github.com/nextstrain/nextclade)
- Amino acid SNP calls against a specified reference
- Genotype calls using GenoFLU against curated database
- Genotype calls using GenoFLU against curated database

```mermaid
flowchart TD
fastq(FASTQ Input) --> fastq_trimmed{Read Trimming: fastp}
fastq_trimmed --> primer_trimmed{Remove Primers: cutadapt}
fastq_trimmed --> MultiQC{MultiQC}
primer_trimmed --> FASTQC{FASTQC}
FASTQC --> MultiQC
primer_trimmed --> MultiQC --> MultiQC_report[MultiQC Report]
primer_trimmed --> FluViewer{FluViewer}
FluViewer --> HPAI{HPAI script} --> HPAI_result[HPAI Results]
FluViewer --> Segcov[Segment Coverage Plots]
FluViewer --> Consensus[Consensus Sequence]
Consensus --> SNPCaller{SNP Calling: snp-calling.py} --> SNPCalls[AA SNP Outputs]
Consensus --> CladeCaller{Clade Calling: Nextclade} --> CladeCalls[Clade Call Outputs]
FluViewer --> VCF[Variant Call Outputs]
Consensus --> GenoFLU[GenoFLU Genotype Calling]
fastq_input[FASTQ Input] --> fastp(fastp)
fastp -- trimmed_reads --> cutadapt(cutadapt)
cutadapt -- qc_stats --> multiqc(multiqc)
cutadapt -- primer_trimmed_reads --> fastqc(fastqc)
fastqc -- qc_stats --> multiqc
multiqc --> multiqc_report[MultiQC Report]
cutadapt -- primer_trimmed_reads --> normalize_reads(normalize_reads)
normalize_reads -- normalized_reads --> fluviewer(fluviewer)
fluviewer_db[FluViewer DB] --> fluviewer
fluviewer -- ha_consensus --> clade_calling(clade_calling)
clade_calling --> clade_calls[clade-calls]
fluviewer -- consensus_main --> snp_caling(snp_calling)
snp_calling --> snp_calls[snp-calls]
fluviewer -- consensus_main --> genoflu(genoflu)
fluviewer --> segment_coverage_plots[Segment Coverage Plots]
fluviewer --> consensus_sequence[Consensus Sequence]
fluviewer --> variants[Variants VCF]
genoflu --> genoflu_tsv[GenoFLU tsv]
```


Expand All @@ -54,8 +58,8 @@ Short read Illumina sequences, files ending in '.fastq.gz', '.fq.gz', '.fastq',
For a full list of optional arguments, see: https://github.com/BCCDC-PHL/FluViewer

| Argument | Description | Default Value |
|----------------------------|--------------------------------------------------------------------------------------------------|----------------:|
| `--target_depth` | Depth to normalize coverage to, where sufficient depth is available in inputs. | 200 |
|-----------------------|--------------------------------------------------------------------------------------------------|----------------:|
| `--target_depth` | Depth to normalize coverage to, where sufficient depth is available in inputs. | 200 |
| `--min_depth` | Minimum read depth for base calling. | 20 |
| `--min_q` | Minimum PHRED score for base quality and mapping quality. | 20 |
| `--min_cov` | Minimum coverage of database reference sequence by contig, percentage. | 25 |
Expand All @@ -64,7 +68,7 @@ For a full list of optional arguments, see: https://github.com/BCCDC-PHL/FluView
**Example command:**
```
nextflow run BCCDC-PHL/fluviewer-nf \
-r v0.2.2 \
-r v0.3.0 \
-profile conda \
--cache ~/.conda/envs \
--fastq_input /path/to/your_fastqs \
Expand All @@ -77,23 +81,83 @@ nextflow run BCCDC-PHL/fluviewer-nf \
Outputs are written to the directory specified with the `--outdir` parameter. Below that are individual folders for each sample, containing the results of FluViewer, SNP calling, and clade calling.

```
|-Run number
|-----FluViewer_version_output
|----sample_number
| |-----FluViewer outputs
| |-----SNP Call outputs
| |-----Clade Call outputs
| |-----GenoFLU outputs
|----sample_number
| |-----FluViewer outputs
| |-----SNP Call outputs
| |-----Clade Call outputs
| |-----GenoFLU outputs
| ...
|----Provenance_files
|----sample_number_multiqc_report.html
|----sample_number_report.html
|----sample_number_timeline.html
<outdir>
├── <run_name>_fluviewer-nf_multiqc_report.html
├── <run_name>_fluviewer-nf_nextflow_report.html
├── <run_name>_fluviewer-nf_nextflow_timeline.html
└── <sample-id>
├── <sample-id>.fastp.html
├── <sample-id>.fastp.json
├── <sample-id>_<date-time>_provenance.yml
├── <sample-id>_HA_consensus.fa
├── <sample-id>_HPAI.tsv
├── <sample-id>_NA_consensus.fa
├── <sample-id>_alignment.bam
├── <sample-id>_alignment.bam.bai
├── <sample-id>_consensus_seqs.fa
├── <sample-id>_contigs_blast.tsv
├── <sample-id>_depth_of_cov.png
├── <sample-id>_fluviewer_provenance.yml
├── <sample-id>_genoflu.tsv
├── <sample-id>_mapping_refs.fa
├── <sample-id>_report.tsv
├── <sample-id>_variants.vcf
├── clade-calls
│ ├── <sample-id>_nextclade.aligned.fasta.gz
│ ├── <sample-id>_nextclade.csv
│ ├── <sample-id>_nextclade.json
│ ├── <sample-id>_nextclade.ndjson
│ ├── <sample-id>_nextclade.tsv
│ ├── <sample-id>_nextclade_HA1.translation.fasta.gz
│ ├── <sample-id>_nextclade_HA2.translation.fasta.gz
│ └── <sample-id>_nextclade_SigPep.translation.fasta.gz
├── fluviewer_logs
│ ├── 01_assemble_contigs
│ │ ├── spades_stderr.txt
│ │ └── spades_stdout.txt
│ ├── 02_blast_contigs
│ │ ├── blastn_contigs_stderr.txt
│ │ └── blastn_contigs_stdout.txt
│ ├── 03_scaffolding
│ │ ├── blastn_scaffolds_stderr.txt
│ │ └── blastn_scaffolds_stdout.txt
│ ├── 04_read_mapping
│ │ ├── bwa_index_stderr.txt
│ │ ├── bwa_index_stdout.txt
│ │ ├── bwa_mem_stderr.txt
│ │ ├── bwa_mem_stdout.txt
│ │ ├── samtools_index_stderr.txt
│ │ ├── samtools_index_stdout.txt
│ │ ├── samtools_view_stderr.txt
│ │ └── samtools_view_stdout.txt
│ ├── 05_variant_calling
│ │ ├── freebayes_stderr.txt
│ │ └── freebayes_stdout.txt
│ ├── 06_consensus_calling
│ │ ├── bcftools_consensus_stderr.txt
│ │ ├── bcftools_consensus_stdout.txt
│ │ ├── bcftools_index_stderr.txt
│ │ ├── bcftools_index_stdout.txt
│ │ ├── bcftools_view_stderr.txt
│ │ └── bcftools_view_stdout.txt
│ ├── 07_summary_reporting
│ │ ├── samtools_depth_stderr.txt
│ │ ├── samtools_depth_stdout.txt
│ │ ├── samtools_idxstats_stderr.txt
│ │ └── samtools_idxstats_stdout.txt
│ ├── fluviewer.log
│ ├── makeblastdb_contigs_stderr.txt
│ └── makeblastdb_contigs_stdout.txt
└── snp-calls
├── <sample-id>_HA_mutations.tsv
├── <sample-id>_M_mutations.tsv
├── <sample-id>_NA_mutations.tsv
├── <sample-id>_NP_mutations.tsv
├── <sample-id>_NS_mutations.tsv
├── <sample-id>_PA_mutations.tsv
├── <sample-id>_PB1_mutations.tsv
├── <sample-id>_PB2_mutations.tsv
└── pairwise
```

Output for each sample includes:
Expand Down Expand Up @@ -121,35 +185,50 @@ Output for each run includes:
For each pipeline invocation, each sample will produce a `provenance.yml` file with the following contents. Note the below is a contrived example.

```yml
- pipeline_name: BCCDC-PHL/FluViewer-nf
pipeline_version: 0.2.2
timestamp_analysis_start: 2023-11-21T05:43:25.541743
- input_filename: {Sample}_R1.fastq.gz
input_path: /home/{USER{}}/Flu/test_data/test_production_run/{Sample}_R1.fastq.gz
sha256: 47380e49f10374660a2061d3571efe5339401484e646c2b47896fa701dbcf0a8
- input_filename: {Sample}_R2.fastq.gz
input_path: /home/{USER}/Flu/test_data/test_production_run/{Sample}.fastq.gz
sha256: 39c95fd26af111ee9a6caeb840a7aced444b657550efea3ab7f74add0b30f69d
- pipeline_name: BCCDC-PHL/fluviewer-nf
pipeline_version: 0.3.0
nextflow_session_id: 59fdd919-fc28-4af5-99e0-60355b11807c
nextflow_run_name: hopeful_bhaskara
timestamp_analysis_start: 2024-07-15T16:30:11.150887-07:00
- input_filename: sample-01_R1.fastq.gz
file_type: fastq_input
sha256: 2c1d5b310a5ca11cc2b1665c094a064fc3aa597e06f392985dac639bd2ab4d81
- input_filename: sample-01_R2.fastq.gz
file_type: fastq_input
sha256: 73745eed4badc3594cdd8554e90c75ae4b9b4599ca255064415ded433e598749
- process_name: fastp
tools:
- tool_name: fastp
tool_version: 0.23.1
tool_version: 0.23.2
- process_name: cutadapt
tools:
- tool_name: cutadapt
tool_version: 4.1
tool_version: 4.4
- process_name: normalize_depth
tools:
- tool_name: bbnorm
tool_version: 39.01
- process_name: fluviewer
tools:
- tool_name: FluViewer
tool_version: FluViewer v0.0.2
- tool_name: fluviewer
tool_version: 0.1.11-6
databases:
- database_name: FluViewer_db.fa
database_path: /path/to/FluViewer_db.fa
database_sha256: c9ba1af0a637671d86a14aceac3cbfde309ae9a5bd613d75c87ba2ff390b4c48
process_name: nextclade
tools:
- tool_name: nextclade
tool_version: 3.8.1
subcommand: run
- process_name: snp_caling
tools:
- tool_name: blastx
tool_version: 2.15.0+
databases:
- database_name: FluViewer_db_full_20220915.fasta
database_path: /home/{USER}/Flu/ref/FluViewer_db_full_20220915.fasta
database_sha256: 55b33afa21ad44ed1e6db896cf420fae6b1524c0ad205775a1ce9dd11595905d

- process_name: nextclade
tool_name: nextclade
tool_version: 2.9.1
Dataset location: /scratch/{USER}/flu/nextclade_datasets/nextclade_flu_h5nx_ha/
Dataset version: "tag": "2023-04-02T12:00:00Z"
- database_name: blastx_subtype_db.fasta
- process_name: genoflu
tools:
- tool_name: genoflu
tool_version: 1.03
```
2 changes: 1 addition & 1 deletion modules/fluviewer.nf
Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@ process normalize_depth {
printf -- "- process_name: normalize_depth\\n" >> ${sample_id}_normalize_depth_provenance.yml
printf -- " tools:\\n" >> ${sample_id}_normalize_depth_provenance.yml
printf -- " - tool_name: bbnorm\\n" >> ${sample_id}_normalize_depth_provenance.yml
printf -- " tool_version: \$(bbnorm.sh --version)\\n" >> ${sample_id}_normalize_depth_provenance.yml
printf -- " tool_version: \$(bbnorm.sh --version 2>&1 | head -n 2 | tail -n 1 | cut -d ' ' -f 3)\\n" >> ${sample_id}_normalize_depth_provenance.yml

bbnorm.sh \
-Xmx${max_memory_gb}g \
Expand Down