Commit c910cba0 authored by MARTIN Pierre's avatar MARTIN Pierre
Browse files

Doc

parent 853f098b
......@@ -108,7 +108,7 @@ It allows you to choose the configuration profile among:
These profiles are associated to different configuration files developped [in this directory](https://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/tree/dev/conf). The `base.config` file available in this directory is the base configuration load in first which is crushed by indications of the profile you use. See [here](https://genotoul-bioinfo.pages.mia.inra.fr/use-nextflow-nfcore-course/nfcore/profiles.html) for more explanations.
### 2. Usefull options
### 2. Useful options
#### `-resume`
......@@ -237,7 +237,7 @@ No parameter available for this substep.
**WARNING 4:** the user has choice between `metaspades` or `megahit` for `--assembly` parameter. The choice can be based on CPUs and memory availability: `metaspades` needs more CPUs and memory than `megahit` but our tests showed that assembly metrics are better for `metaspades` than `megahit`.
* `--metaspades_mem [memory_value]`: memory (in G) used by `metaspades` process. Default: `440`.
* `--metaspades_mem [memory_value]`: memory (in Gb) used by `metaspades` process. Default: `440`.
#### **`03_filtering` step:**
......
......@@ -558,7 +558,7 @@ process assembly {
else if(params.assembly=='megahit')
"""
megahit -t ${task.cpus} -1 ${preprocessed_reads_R1} -2 ${preprocessed_reads_R2} -o ${params.assembly} --out-prefix "${sampleId}"
mv options.json params.txt
mv ${params.assembly}/options.json ${params.assembly}/${sampleId}.params.txt
"""
else
error "Invalid parameter: ${params.assembly}"
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment