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Merge branch 'CW-2700_demo_not_working' into 'dev'

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Resolve CW-2700 "Demo not working"

Closes CW-2700

See merge request epi2melabs/workflows/wf-transcriptomes!127
This commit is contained in:
Neil Horner 2023-09-06 08:59:17 +00:00
commit 36d37a8d5f
2 changed files with 22 additions and 20 deletions
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21
README.md
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@ -140,9 +140,9 @@ nextflow run epi2me-labs/wf-transcriptomes \
**Example workflow for denovo transcript assembly** **Example workflow for denovo transcript assembly**
``` ```
OUTPUT=~/output OUTPUT=~/output
nextflow run . --fastq test_data/fastq \ nextflow run epi2me-labs/wf-transcriptomes \
--denovo \ --fastq test_data/fastq \
--ref_genome test_data/SIRV_150601a.fasta \ --transcriptome_source denovo \
--out_dir ${OUTPUT} \ --out_dir ${OUTPUT} \
-w ${OUTPUT}/workspace \ -w ${OUTPUT}/workspace \
--sample sample_id --sample sample_id
@ -235,14 +235,15 @@ Here is an example cmd to run the workflow. First you will need to download the
eg. 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 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;
nextflow run epi2me-labs/wf-transcriptomes \ nextflow run epi2me-labs/wf-transcriptomes \
--fastq differential_expression/differential_expression_fastq \ --fastq differential_expression/differential_expression_fastq \
--transcriptome-source precomputed \
--de_analysis \ --de_analysis \
--ref_genome differential_expression/hg38_chr20.fa \ --ref_genome differential_expression/hg38_chr20.fa \
--ref_annotation differential_expression/gencode.v22.annotation.chr20.gtf \ --ref_annotation differential_expression/gencode.v22.annotation.chr20.gff \
--direct_rna --minimap2_index_opts \ --direct_rna --minimap2_index_opts '-k 15' \
-k15 --ref_transcriptome differential_expression/ref_transcriptome.fasta \
--sample_sheet test_data/sample_sheet.csv
``` ```
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. 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. eg.
@ -252,9 +253,9 @@ nextflow run epi2me-labs/wf-transcriptomes \
--de_analysis \ --de_analysis \
--ref_genome differential_expression/hg38_chr20.fa \ --ref_genome differential_expression/hg38_chr20.fa \
--ref_annotation differential_expression/gencode.v22.annotation.chr20.gtf \ --ref_annotation differential_expression/gencode.v22.annotation.chr20.gtf \
--direct_rna --minimap2_index_opts \ --direct_rna --minimap2_index_opts '-k 15' \
-k15 \ --ref_transcriptome differential_expression/ref_transcriptome.fasta \
--ref_transcriptome differential_expression/ref_transcriptome.fasta --sample_sheet test_data/sample_sheet.csv
``` ```
## Workflow outputs ## Workflow outputs

21
docs/quickstart.md
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@ -50,9 +50,9 @@ nextflow run epi2me-labs/wf-transcriptomes \
**Example workflow for denovo transcript assembly** **Example workflow for denovo transcript assembly**
``` ```
OUTPUT=~/output OUTPUT=~/output
nextflow run . --fastq test_data/fastq \ nextflow run epi2me-labs/wf-transcriptomes \
--denovo \ --fastq test_data/fastq \
--ref_genome test_data/SIRV_150601a.fasta \ --transcriptome_source denovo \
--out_dir ${OUTPUT} \ --out_dir ${OUTPUT} \
-w ${OUTPUT}/workspace \ -w ${OUTPUT}/workspace \
--sample sample_id --sample sample_id
@ -145,14 +145,15 @@ Here is an example cmd to run the workflow. First you will need to download the
eg. 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 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;
nextflow run epi2me-labs/wf-transcriptomes \ nextflow run epi2me-labs/wf-transcriptomes \
--fastq differential_expression/differential_expression_fastq \ --fastq differential_expression/differential_expression_fastq \
--transcriptome-source precomputed \
--de_analysis \ --de_analysis \
--ref_genome differential_expression/hg38_chr20.fa \ --ref_genome differential_expression/hg38_chr20.fa \
--ref_annotation differential_expression/gencode.v22.annotation.chr20.gtf \ --ref_annotation differential_expression/gencode.v22.annotation.chr20.gff \
--direct_rna --minimap2_index_opts \ --direct_rna --minimap2_index_opts '-k 15' \
-k15 --ref_transcriptome differential_expression/ref_transcriptome.fasta \
--sample_sheet test_data/sample_sheet.csv
``` ```
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. 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. eg.
@ -162,9 +163,9 @@ nextflow run epi2me-labs/wf-transcriptomes \
--de_analysis \ --de_analysis \
--ref_genome differential_expression/hg38_chr20.fa \ --ref_genome differential_expression/hg38_chr20.fa \
--ref_annotation differential_expression/gencode.v22.annotation.chr20.gtf \ --ref_annotation differential_expression/gencode.v22.annotation.chr20.gtf \
--direct_rna --minimap2_index_opts \ --direct_rna --minimap2_index_opts '-k 15' \
-k15 \ --ref_transcriptome differential_expression/ref_transcriptome.fasta \
--ref_transcriptome differential_expression/ref_transcriptome.fasta --sample_sheet test_data/sample_sheet.csv
``` ```
## Workflow outputs ## Workflow outputs