kfukuta/wf-transcriptomes-v202
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Merge branch 'data-aws' into 'dev'

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Move data to AWS

See merge request epi2melabs/workflows/wf-transcriptomes!81
This commit is contained in:
Sarah Griffiths 2022-11-16 18:50:02 +00:00
commit f852dde6ef
5 changed files with 72 additions and 26 deletions
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4
.gitlab-ci.yml
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@ -43,7 +43,7 @@ docker-run:
NF_IGNORE_PROCESSES: preprocess_reads,merge_transcriptomes
- if: $MATRIX_NAME == "differential_expression"
variables:
NF_BEFORE_SCRIPT: tar -xzvf test_data/differential_expression.tar.gz
NF_BEFORE_SCRIPT: wget -O differential_expression.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/differential_expression.tar.gz && tar -xzvf differential_expression.tar.gz
NF_WORKFLOW_OPTS: "--fastq differential_expression/differential_expression_fastq \
--de_analysis \
--ref_genome differential_expression/hg38_chr20.fa \
@ -52,7 +52,7 @@ docker-run:
NF_IGNORE_PROCESSES: preprocess_reads,merge_transcriptomes
- if: $MATRIX_NAME == "only_differential_expression"
variables:
NF_BEFORE_SCRIPT: tar -xzvf test_data/differential_expression.tar.gz
NF_BEFORE_SCRIPT: wget -O differential_expression.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/differential_expression.tar.gz && tar -xzvf differential_expression.tar.gz
NF_WORKFLOW_OPTS: "--fastq differential_expression/differential_expression_fastq \
--de_analysis \
--ref_genome differential_expression/hg38_chr20.fa \

2
.pre-commit-config.yaml
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@ -17,7 +17,7 @@ repos:
pass_filenames: false
additional_dependencies:
- epi2melabs
- repo: https://gitlab.com/pycqa/flake8
- repo: https://github.com/pycqa/flake8
rev: 3.7.9
hooks:
- id: flake8

2
CHANGELOG.md
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@ -7,8 +7,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
## [unreleased]
### Updated
- Removed sanitize option
- Reduce size of differential expression data.
### Added
- Demo differential expression data in repository.
- Improved DE explanation in docs
- Option to turn off transcript assembly steps with param transcript_assembly
### Fixed

45
README.md
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@ -120,15 +120,25 @@ tar -xzvf test_data.tar.gz
**Example execution of a workflow for reference-based transcript assembly and fusion detection**
```
OUTPUT=~/output;
nexflow run epi2me-labs/wf-transcriptomes --fastq ERR6053095_chr20.fastq --ref_genome chr20/hg38_chr20.fa --ref_annotation chr20/gencode.v22.annotation.chr20.gtf \
--jaffal_refBase chr20/ --jaffal_genome hg38_chr20 --jaffal_annotation genCode22" --out_dir outdir -w workspace_dir -profile conda -resume
nexflow run epi2me-labs/wf-transcriptomes \
--fastq ERR6053095_chr20.fastq \
--ref_genome chr20/hg38_chr20.fa \
--ref_annotation chr20/gencode.v22.annotation.chr20.gtf \
--jaffal_refBase chr20/ \
--jaffal_genome hg38_chr20 \
--jaffal_annotation "genCode22" \
--out_dir outdir -w workspace_dir
```
**Example workflow for denovo transcript assembly**
```
OUTPUT=~/output
nextflow run . --fastq test_data/fastq --denovo --ref_genome test_data/SIRV_150601a.fasta -profile local --out_dir ${OUTPUT} -w ${OUTPUT}/workspace \
--sample sample_id -resume
nextflow run . --fastq test_data/fastq \
--denovo \
--ref_genome test_data/SIRV_150601a.fasta \
--out_dir ${OUTPUT} \
-w ${OUTPUT}/workspace \
--sample sample_id
```
A full list of options can be seen in nextflow_schema.json. Below are some commonly used ones.
@ -223,17 +233,30 @@ barcode06,treated
```
You will also need to provide a reference genome and a reference annotation file.
Here is an example cmd to run the workflow using the test_data provided.
Here is an example cmd to run the workflow. First you will need to download the data with wget.
eg.
```
wget -O differential_expression.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/differential_expression.tar.gz && tar -xzvf differential_expression.tar.gz
OUTPUT=~/output;
nexflow run epi2me-labs/wf-transcriptomes --fastq test_data/differential_expression_fastq \
nextflow run epi2me-labs/wf-transcriptomes \
--fastq differential_expression/differential_expression_fastq \
--de_analysis \
--ref_genome test_data/hg38_chr20.fa \
--ref_annotation test_data/gencode.v22.annotation.chr20.gtf \
--direct_rna
--ref_genome differential_expression/hg38_chr20.fa \
--ref_annotation differential_expression/gencode.v22.annotation.chr20.gtf \
--direct_rna --minimap_index_opts \-k15
```
You can also run the differential expression section of the workflow on its own by providing a reference transcriptome and setting the transcriptome assembly parameter to false.
eg.
```
nextflow run epi2me-labs/wf-transcriptomes \
--fastq differential_expression/differential_expression_fastq \
--de_analysis \
--ref_genome differential_expression/hg38_chr20.fa \
--ref_annotation differential_expression/gencode.v22.annotation.chr20.gtf \
--direct_rna --minimap_index_opts \-k15 \
--ref_transcriptome differential_expression/ref_transcriptome.fasta \
--transcriptome_assembly false
```
## Workflow outputs
* an HTML report document detailing the primary findings of the workflow.

45
docs/quickstart.md
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@ -38,15 +38,25 @@ tar -xzvf test_data.tar.gz
**Example execution of a workflow for reference-based transcript assembly and fusion detection**
```
OUTPUT=~/output;
nexflow run epi2me-labs/wf-transcriptomes --fastq ERR6053095_chr20.fastq --ref_genome chr20/hg38_chr20.fa --ref_annotation chr20/gencode.v22.annotation.chr20.gtf \
--jaffal_refBase chr20/ --jaffal_genome hg38_chr20 --jaffal_annotation genCode22" --out_dir outdir -w workspace_dir -profile conda -resume
nexflow run epi2me-labs/wf-transcriptomes \
--fastq ERR6053095_chr20.fastq \
--ref_genome chr20/hg38_chr20.fa \
--ref_annotation chr20/gencode.v22.annotation.chr20.gtf \
--jaffal_refBase chr20/ \
--jaffal_genome hg38_chr20 \
--jaffal_annotation "genCode22" \
--out_dir outdir -w workspace_dir
```
**Example workflow for denovo transcript assembly**
```
OUTPUT=~/output
nextflow run . --fastq test_data/fastq --denovo --ref_genome test_data/SIRV_150601a.fasta -profile local --out_dir ${OUTPUT} -w ${OUTPUT}/workspace \
--sample sample_id -resume
nextflow run . --fastq test_data/fastq \
--denovo \
--ref_genome test_data/SIRV_150601a.fasta \
--out_dir ${OUTPUT} \
-w ${OUTPUT}/workspace \
--sample sample_id
```
A full list of options can be seen in nextflow_schema.json. Below are some commonly used ones.
@ -141,17 +151,30 @@ barcode06,treated
```
You will also need to provide a reference genome and a reference annotation file.
Here is an example cmd to run the workflow using the test_data provided.
Here is an example cmd to run the workflow. First you will need to download the data with wget.
eg.
```
wget -O differential_expression.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/differential_expression.tar.gz && tar -xzvf differential_expression.tar.gz
OUTPUT=~/output;
nexflow run epi2me-labs/wf-transcriptomes --fastq test_data/differential_expression_fastq \
nextflow run epi2me-labs/wf-transcriptomes \
--fastq differential_expression/differential_expression_fastq \
--de_analysis \
--ref_genome test_data/hg38_chr20.fa \
--ref_annotation test_data/gencode.v22.annotation.chr20.gtf \
--direct_rna
--ref_genome differential_expression/hg38_chr20.fa \
--ref_annotation differential_expression/gencode.v22.annotation.chr20.gtf \
--direct_rna --minimap_index_opts \-k15
```
You can also run the differential expression section of the workflow on its own by providing a reference transcriptome and setting the transcriptome assembly parameter to false.
eg.
```
nextflow run epi2me-labs/wf-transcriptomes \
--fastq differential_expression/differential_expression_fastq \
--de_analysis \
--ref_genome differential_expression/hg38_chr20.fa \
--ref_annotation differential_expression/gencode.v22.annotation.chr20.gtf \
--direct_rna --minimap_index_opts \-k15 \
--ref_transcriptome differential_expression/ref_transcriptome.fasta \
--transcriptome_assembly false
```
## Workflow outputs
* an HTML report document detailing the primary findings of the workflow.