Merge branch 'dev'

Author: alpae

Dockerfile

@@ -19,6 +19,7 @@ RUN pip install --upgrade hatch pip
 COPY pyproject.toml .
 RUN python -m venv /app \
     && hatch dep show requirements --all > requirements.txt \
+    && /app/bin/pip install wheel setuptools \
     && /app/bin/pip install -r requirements.txt
 
 COPY . .

FastOMA.nf

@@ -446,6 +446,7 @@ process extract_pairwise_ortholog_relations {
 process fastoma_report {
   publishDir params.output_folder, mode: 'copy'
   input:
+    path notebook
     path orthoxml
     path proteome_folder
     path species_tree_checked
@@ -461,7 +462,7 @@ process fastoma_report {
         >&2 echo "Ensure you have installed fastoma with the 'report' feature\n (e.g. pip install fastoma[report])"
         exit 1
     fi
-    papermill ${workflow.projectDir}/FastOMA/fastoma_notebook_stat.ipynb \
+    papermill $notebook \
               report.ipynb \
               -p output_folder "./" \
               -p proteome_folder "$proteome_folder"
@@ -479,6 +480,7 @@ workflow {
     hogmap_in = Channel.fromPath(params.hogmap_in, type:'dir')
 
     omamerdb = Channel.fromPath(params.omamer_db)
+    notebook = Channel.fromPath("$workflow.projectDir/FastOMA/fastoma_notebook_stat.ipynb", type: "file", checkIfExists: true).first()
     (species_tree_checked, ready_input_check) = check_input(proteome_folder, hogmap_in, species_tree, omamerdb, splice_folder)
     omamer_input_channel = proteomes.combine(omamerdb).combine(hogmap_in).combine(ready_input_check)
     hogmap = omamer_run(omamer_input_channel)
@@ -498,7 +500,7 @@ workflow {
         FALSE: n>25
     }
     extract_pairwise_ortholog_relations(orthoxml_file, c.TRUE)
-    fastoma_report(orthoxml_file, proteome_folder, species_tree_checked)
+    fastoma_report(notebook, orthoxml_file, proteome_folder, species_tree_checked)
 }
 
 workflow.onComplete {

nextflow.config

@@ -6,11 +6,14 @@ manifest {
   homePage = "https://omabrowser.org"
   mainScript = "FastOMA.nf"
   nextflowVersion = ">=22.10.4"
+  defaultBranch = "main"
+  doi = "10.1101/2024.01.29.577392"
+  version = "0.3.1dev"
 }
 
 params {
   container_name = "dessimozlab/fastoma"
-  container_version = "main"
+  container_version = "dev"
   omamer_db = "https://omabrowser.org/All/LUCA.h5"
   debug_enabled = false
   help = false

pyproject.toml

@@ -20,6 +20,7 @@ dependencies = [
     "lxml >=4.6,<6",
     "omamer ~=2.0",
     "pyham ~=1.1",
+    "numpy <2",   # temporary fix as pytables does not yet work with numpy 2.0
     "pyparsing",
     "networkx",
 ]