Doc

docs/usage.md

@@ -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:**
 

main.nf

@@ -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}"