Update readme

README.md

@@ -14,56 +14,64 @@ Sequencing analysis pipeline (aqueduct) for validating plasmids and DNA assembly
 
 Install [Nextflow](https://www.nextflow.io/) and [Docker](https://www.docker.com/).
 
-Set up [credentials in the SCM configuration file](https://www.nextflow.io/docs/latest/sharing.html#github-credentials), then pull the Nextflow image:
+Pull the Nextflow pipeline:
 
 ```bash
 nextflow pull edinburgh-genome-foundry/Sequeduct -r v0.2.2
 ```
 
-Pull the Docker image that contains the required software:
+Pull the Docker image that contains the required software (requires access to EGF's container repo):
 
 ```bash
 docker pull ghcr.io/edinburgh-genome-foundry/sequeduct:latest
 ```
 
+Alternatively, build the image locally from the cloned repo:
+
+```bash
+docker build . -f containers/Dockerfile --tag sequeduct_local
+```
+
 ### Run
 
 Create a directory for your project and copy (or link) the FASTQ directories from your Nanopore run (e.g. into `fastq`). Specify this together with a sample sheet in your commands:
 
 ```bash
 # Preview
-nextflow run edinburgh-genome-foundry/Sequeduct -r v0.2.2 -entry preview --fastq_dir='fastq' --reference_dir='genbank' \
+nextflow run edinburgh-genome-foundry/Sequeduct -r v0.2.2 -entry preview --fastq_dir='fastq' \
+ --reference_dir='genbank' \
  --sample_sheet='sample_sheet.csv' \
  -profile docker
 # Analysis
-nextflow run edinburgh-genome-foundry/Sequeduct -r v0.2.2 -entry analysis --fastq_dir='fastq' --reference_dir='genbank' \
+nextflow run edinburgh-genome-foundry/Sequeduct -r v0.2.2 -entry analysis --fastq_dir='fastq' \
+ --reference_dir='genbank' \
  --sample_sheet='sample_sheet.csv' \
  --projectname='EGF project' \
  -profile docker
 # Review
 nextflow run edinburgh-genome-foundry/Sequeduct -r v0.2.2 -entry review --reference_dir='genbank' \
- --results_csv='results_finalised.csv' \
+ --results_csv='results_sheet.csv' \
  --projectname='EGF project review' \
  --all_parts='parts_fasta/part_sequences.fasta' \
  --assembly_plan='assembly_plan.csv' \
  -profile docker
+# De novo assembly
+nextflow run edinburgh-genome-foundry/Sequeduct -r v0.2.2 -entry assembly --fastq_dir='fastq' \
+ --results_csv='results_sheet.csv' \
+ --projectname='EGF assembly' \
+ -profile docker 
 ```
 
-The above three commands each output a directory within `results`. Similarly, Nextflow creates and uses a directory named `work`, so ensure that your project directory doesn't have one. Specify revision of the project with `-r` (a git branch or tag), and choose a configuration profile (with `-profile`). Profiles are specified in the Nextflow config files.
+The above commands each output a directory within `results`. Similarly, Nextflow creates and uses a directory named `work`, so ensure that your project directory doesn't have one. Specify revision of the project with `-r` (a git branch or tag), and choose a configuration profile (with `-profile`). Profiles are specified in the Nextflow config files.
+
+Use `-with-docker sequeduct_local` to use a locally built Docker image (instead of `-profile docker`).
 
 ### Details
 
 Note that canu v2.2 requires minimum 100 reads, otherwise it returns an error. A [fix has been posted](https://github.com/marbl/canu/issues/2035), but it's not released yet.
 
 For convenience, a script is included to collect plot files from the result directories (`bin/collect_plots.py`).
 
-## Build the image locally
-
-```bash
-git clone [email protected]:Edinburgh-Genome-Foundry/Ediacara.git
-docker build . -f containers/Dockerfile --tag sequeduct_local
-```
-
 ## Copyright
 
 Copyright 2021 Edinburgh Genome Foundry

results_sheet.csv

@@ -0,0 +1,3 @@
+Barcode,Sample,Result,Review_consensus,Review_de_novo,Length
+barcode01,EGF1_2,WARNING,1,1,8
+barcode02,EGF1_3,WARNING,1,1,11