Update readme

README.md

@@ -23,7 +23,7 @@ nextflow pull edinburgh-genome-foundry/Sequeduct -r v0.3.1
 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:0.3.1
+docker pull ghcr.io/edinburgh-genome-foundry/sequeduct:v0.3.1
 ```
 
 Alternatively, build the image locally from the cloned repo:
@@ -57,20 +57,22 @@ nextflow run edinburgh-genome-foundry/Sequeduct -r v0.3.1 -entry review --refere
  -profile docker
 # De novo assembly
 nextflow run edinburgh-genome-foundry/Sequeduct -r v0.3.1 -entry assembly --fastq_dir='fastq_pass' \
- --results_csv='assembly_sheet.csv' \
+ --assembly_sheet='assembly_sheet.csv' \
  -profile docker 
 ```
 
 The above commands each output a directory within a created `results` directory. Similarly, Nextflow creates and uses a directory named `work`, so ensure that your project directory doesn't have a directory with the same name. 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 Review pipeline utilises the output files of the Analysis pipeline, but otherwise the pipelines are independent. Please find example sheets in the `examples` directory.
 
 A more detailed example and demonstration data are available at the [Sequeduct demo](https://github.com/Edinburgh-Genome-Foundry/Sequeduct_demo) site.
 
-Use `-with-docker sequeduct_local` to use a locally built Docker image (instead of `-profile docker`).
+Use `-with-docker sequeduct_local` (where sequeduct_local is the tag you specified during build) to use a locally built Docker image (instead of `-profile docker`).
 
 ### Details
 
 For simplicity, the names in the sample sheet are used for finding the reference Genbank files, therefore sample names must match filenames with a ".gb" extension.
 
+If you have the FASTQ files in gzip compressed format (`.gz`), then you must uncompress them (e.g. run `gunzip --recursive *` in the FASTQ folder).
+
 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`).