Merge branch 'rel-3.2'

Author: alpae

.gitignore

@@ -6,3 +6,4 @@ archive
 .git
 .gitignore
 __pycache__
+*.orig

FastOMA.nf

@@ -2,7 +2,7 @@ import groovy.json.JsonBuilder;
 
 // NXF_WRAPPER_STAGE_FILE_THRESHOLD='50000'
 
-params.input_folder = "testdata/in_folder"
+params.input_folder = "${projectDir}/testdata/in_folder"
 params.output_folder = "out_folder/"
 params.proteome_folder = params.input_folder + "/proteome"
 params.hogmap_in = params.input_folder + "/hogmap_in"

FastOMA/__init__.py

@@ -1,3 +1,3 @@
 
 __packagename__ = "FastOMA"
-__version__ = "0.3.1"
+__version__ = "0.3.2"

README.md

@@ -88,7 +88,7 @@ There are four ways to run/install FastOMA detailed below:
 The FastOMA workflow can be run directly without any installation using nextflow's ability to fetch a workflow from github. A specific version can be selected by specifying the `-r` option to nextflow to select a specific version of FastOMA:
 
 ```bash
-nextflow run desimozlab/FastOMA -r v0.3.1 -profile conda  --input_folder testdata/in_folder
+nextflow run desimozlab/FastOMA -r v0.3.1 -profile conda 
 ```
 
 This will fetch version v0.3.1 from github and run the FastOMA workflow using the conda profile. See section [How to run fastOMA](#how-to-run-fastoma). 
@@ -184,7 +184,7 @@ nextflow run FastOMA.nf -profile docker \
     --output_folder myresult/
 ```
 This will use the container that is tagged with the current commit id. Similarly, one could also use 
-`--container_version "0.2.0"` to use the container with version `dessimozlab/fastoma:0.2.0` from dockerhub. Check the latest version on the [DockerHub](https://hub.docker.com/r/dessimozlab/fastoma/tags).
+`--container_version "0.3.1"` to use the container with version `dessimozlab/fastoma:0.3.1` from dockerhub. Check the latest version on the [DockerHub](https://hub.docker.com/r/dessimozlab/fastoma/tags).
 
 ### Singularity
 Since Docker needs administrator privileges (root access), [Singluarity](https://apptainer.org/index.html) (a.k.a Apptainer) is a good alternative. This can be installed using [Conda](https://anaconda.org/conda-forge/singularity) with `conda install conda-forge::singularity`. However, in most of the academic HPC cluster, singluarity is already installed and can be called with `module load`.

nextflow.config

@@ -8,12 +8,12 @@ manifest {
   nextflowVersion = ">=22.10.4"
   defaultBranch = "main"
   doi = "10.1101/2024.01.29.577392"
-  version = "0.3.1"
+  version = "0.3.2"
 }
 
 params {
   container_name = "dessimozlab/fastoma"
-  container_version = "0.3.1"
+  container_version = "0.3.2"
   omamer_db = "https://omabrowser.org/All/LUCA.h5"
   debug_enabled = false
   help = false
@@ -63,8 +63,9 @@ profiles {
   }
 
   conda {
-    process.conda = "environment-conda.yml"
+    process.conda = "${projectDir}/environment-conda.yml"
     conda.enabled = true
+    conda.createTimeout = '3 h'
   }
 
   slurm_singularity {
@@ -80,12 +81,13 @@ profiles {
 
   slurm_conda {
     process {
-      conda = "environment-conda.yml"
+      conda = "${projectDir}/environment-conda.yml"
       executor = "slurm"
       time = 4.h
       memory = 20.GB
     }
     conda.enabled = true
+    conda.createTimeout = '3 h'
   }
 }