homogenise genomes list file by adding a s to the file: genomes.fasta…

….list

docs/user/PangenomeAnalyses/pangenomeWorkflow.md

@@ -45,20 +45,20 @@ To use this command, you need to provide a tab-separated list of either annotati
 
 You can use the workflow with annotation files as such: 
 ```
-ppanggolin workflow --anno genome.gbff.list
+ppanggolin workflow --anno genomes.gbff.list
 ```
 
 For fasta files, you have to change for: 
 ```
-ppanggolin workflow --fasta genome.fasta.list
+ppanggolin workflow --fasta genomes.fasta.list
 ```
 
 Moreover, as detailed [in the section about providing your gene families](./pangenomeAnalyses.md#read-clustering), 
 if you wish to use different gene clustering methods than those provided by PPanGGOLiN,
 it is also possible to provide your own clustering results with the workflow command as such:
 
 ```
-ppanggolin workflow --anno genome.gbff.list --clusters clusters.tsv
+ppanggolin workflow --anno genomes.gbff.list --clusters clusters.tsv
 ```
 
 All the workflow parameters are obtained from the commands explained below, except for the `--no_flat_files` option, which solely pertains to it. This option prevents the automatic generation of the output files listed and described [in the pangenome output section](./pangenomeAnalyses.md#pangenome-outputs).

docs/user/QuickUsage/quickWorkflow.md

@@ -63,12 +63,12 @@ The minimal subcommand only need your own annotations files (using `.gff` or `.g
 as long as they include the genomic dna sequences, such as the ones provided by Prokka or Bakta.
 
 ```bash
-ppanggolin all --anno genome.gbff.list
+ppanggolin all --anno genomes.gbff.list
 ```
 
 It uses parameters that we found to be generally the best when working with species pangenomes.
 
-The file **genome.gbff.list** is a tab-separated file with the following organisation :
+The file **genomes.gbff.list** is a tab-separated file with the following organisation :
 
 1. The first column contains a unique genome name
 2. The second column the path to the associated annotation file
@@ -80,7 +80,7 @@ An example with 50 _Chlamydia trachomatis_ genomes can be found in the [testingD
 You can also give PPanGGOLiN `.fasta` files, such as:
 
 ```
-ppanggolin all --fasta genome.fasta.list
+ppanggolin all --fasta genomes.fasta.list
 ```
 
 Again you must use a tab-separated file but this time with the following organisation:

docs/user/RGP/rgpPrediction.md

@@ -59,12 +59,12 @@ graph LR
 
 You can use the `panrgp` with annotation (gff3 or gbff) files with `--anno` option, as such: 
 ```bash
-ppanggolin panrgp --anno genome.gbff.list
+ppanggolin panrgp --anno genomes.gbff.list
 ```
 
 For fasta files, you need to use the alternative `--fasta` option, as such:
 ```bash
-ppanggolin panrgp --fasta genome.fasta.list
+ppanggolin panrgp --fasta genomes.fasta.list
 ```
 
 Just like [workflow](../PangenomeAnalyses/pangenomeAnalyses.md#workflow), this command will deal with the [annotation](../PangenomeAnalyses/pangenomeAnalyses.md#annotation), [clustering](../PangenomeAnalyses/pangenomeAnalyses.md#compute-pangenome-gene-families), [graph](../PangenomeAnalyses/pangenomeAnalyses.md#graph) and [partition](../PangenomeAnalyses/pangenomeAnalyses.md#partition) commands by itself.