From 41d40f4e023e79cb6d8e2df2db80db98c0f9f793 Mon Sep 17 00:00:00 2001 From: sina Date: Thu, 30 Nov 2023 15:41:28 +0100 Subject: [PATCH] update --- README.md | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/README.md b/README.md index 99828af..40afa1c 100644 --- a/README.md +++ b/README.md @@ -52,11 +52,11 @@ The details of output are described [below](https://github.com/DessimozLab/FastO # How to run FastOMA In summary, you need to 1) install FastOMA and its prerequisites (below), and 2) put the input files in the folder `in_folder` -and 3) run FastOMA using the nextflow recipe `FastOMA_light.nf`. +and 3) run FastOMA using the nextflow recipe `FastOMA.nf`. ``` -nextflow run FastOMA_light.nf -profile docker --input_folder /path/to/in_folder --output_folder /path/to/out_folder +nextflow run FastOMA.nf -profile docker --input_folder /path/to/in_folder --output_folder /path/to/out_folder ``` -The script `FastOMA_light.nf` is tailored for a few species. To run FastOMA with hundreds of species, please use `FastOMA.nf`. +The script `FastOMA.nf` is tailored for a few species. To run FastOMA with hundreds of species, please use `FastOMA.nf`. ## More details on how to run We provide for every commit of the repository a docker image for FastOMA on dockerhub. You can specify the container as @@ -154,9 +154,9 @@ $ tree ../testdata/in_folder Finally, run the package using nextflow as below: ``` # cd FastOMA/testdata -nextflow ../FastOMA_light.nf --input_folder in_folder --output_folder out_folder -with-report +nextflow ../FastOMA.nf --input_folder in_folder --output_folder out_folder -with-report ``` -The script `FastOMA_light.nf` is tailored for a few species. In real case scenario, please use `FastOMA.nf`. +The script `FastOMA.nf` is tailored for a few species. In real case scenario, please use `FastOMA.nf`. The only difference between these two scripts is the amount of CPU and memory assigned to each job. @@ -329,6 +329,7 @@ These are initial gene families that are used in `infer_subhogs` step, which cou ## Change log +- Update v0.1.5: docker, add help, clean nextflow - Update v0.1.4: new gene families with linclust if mmseqs is installed, using quoted protein name to handle species chars, check input first - Update v0.1.3: merge rootHOGs and handle singleton using omamer multi-hits - Update v0.1.2: improve rootHOG inference, splice, OMAmerv2 with multi-hits