From a68f0895644afee2d40a33b78a1c3ee3c31c8db9 Mon Sep 17 00:00:00 2001 From: JeanMainguy Date: Tue, 12 Mar 2024 17:34:14 +0100 Subject: [PATCH] homogenise genomes list file by adding a s to the file: genomes.fasta.list --- docs/user/PangenomeAnalyses/pangenomeWorkflow.md | 6 +++--- docs/user/QuickUsage/quickWorkflow.md | 6 +++--- docs/user/RGP/rgpPrediction.md | 4 ++-- 3 files changed, 8 insertions(+), 8 deletions(-) diff --git a/docs/user/PangenomeAnalyses/pangenomeWorkflow.md b/docs/user/PangenomeAnalyses/pangenomeWorkflow.md index 44865c45..5793229c 100644 --- a/docs/user/PangenomeAnalyses/pangenomeWorkflow.md +++ b/docs/user/PangenomeAnalyses/pangenomeWorkflow.md @@ -45,12 +45,12 @@ 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), @@ -58,7 +58,7 @@ if you wish to use different gene clustering methods than those provided by PPan 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). diff --git a/docs/user/QuickUsage/quickWorkflow.md b/docs/user/QuickUsage/quickWorkflow.md index 5890751b..472593ae 100644 --- a/docs/user/QuickUsage/quickWorkflow.md +++ b/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: diff --git a/docs/user/RGP/rgpPrediction.md b/docs/user/RGP/rgpPrediction.md index cd16dd7b..08aa704b 100644 --- a/docs/user/RGP/rgpPrediction.md +++ b/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.