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orthofinder: remove mv line #12899

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orthofinder: remove mv line #12899

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f92d4f5
Remove 'mv' line from orthofinder
FernandoDuarteF Sep 2, 2026
6aa7cf9
Merge branch 'nf-core:master' into update_orthofinder
FernandoDuarteF Sep 7, 2026
621b562
Merge branch 'master' into update_orthofinder
FernandoDuarteF Sep 7, 2026
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42 changes: 18 additions & 24 deletions modules/nf-core/orthofinder/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -12,8 +12,8 @@ process ORTHOFINDER {
tuple val(meta2), path(prior_run)

output:
tuple val(meta), path("$prefix") , emit: orthofinder
tuple val(meta), path("$prefix/WorkingDirectory") , emit: working
tuple val(meta), path("$results_dir") , emit: orthofinder
tuple val(meta), path("$results_dir/WorkingDirectory") , emit: working
tuple val("${task.process}"), val('orthofinder'), eval("NO_COLOR=1 orthofinder --version | cut -d 'v' -f2 | perl -pe 's/\\e\\[[0-9;]*m//g'"), emit: versions_orthofinder, topic: versions


Expand All @@ -25,6 +25,7 @@ process ORTHOFINDER {
def args = task.ext.args ?: ''
prefix = task.ext.prefix ?: "${meta.id}"
def include_command = prior_run ? "-b $prior_run" : ''
results_dir = prior_run ? "${prior_run}/OrthoFinder/Results_${prefix}" : "input/OrthoFinder/Results_${prefix}"

"""
orthofinder \\
Expand All @@ -34,33 +35,26 @@ process ORTHOFINDER {
-n $prefix \\
$include_command \\
$args

if [ -e input/OrthoFinder/Results_$prefix ]; then
mv input/OrthoFinder/Results_$prefix $prefix
fi

if [ -e ${prior_run}/OrthoFinder/Results_$prefix ]; then
mv ${prior_run}/OrthoFinder/Results_$prefix $prefix
fi
"""

stub:
prefix = task.ext.prefix ?: "${meta.id}"
results_dir = prior_run ? "${prior_run}/OrthoFinder/Results_${prefix}" : "input/OrthoFinder/Results_${prefix}"

"""
mkdir -p $prefix/Comparative_Genomics_Statistics
mkdir $prefix/Gene_Duplication_Events
mkdir $prefix/Gene_Trees
mkdir $prefix/Orthogroup_Sequences
mkdir $prefix/Orthogroups
mkdir $prefix/Orthologues
mkdir $prefix/Phylogenetic_Hierarchical_Orthogroups
mkdir $prefix/Phylogenetically_Misplaced_Genes
mkdir $prefix/Putative_Xenologs
mkdir $prefix/Resolved_Gene_Trees
mkdir $prefix/Single_Copy_Orthologue_Sequences
mkdir $prefix/Species_Tree
mkdir $prefix/WorkingDirectory
touch $prefix/Log.txt
mkdir -p $results_dir/Comparative_Genomics_Statistics
mkdir $results_dir/Gene_Duplication_Events
mkdir $results_dir/Gene_Trees
mkdir $results_dir/Orthogroup_Sequences
mkdir $results_dir/Orthogroups
mkdir $results_dir/Orthologues
mkdir $results_dir/Phylogenetic_Hierarchical_Orthogroups
mkdir $results_dir/Phylogenetically_Misplaced_Genes
mkdir $results_dir/Putative_Xenologs
mkdir $results_dir/Resolved_Gene_Trees
mkdir $results_dir/Single_Copy_Orthologue_Sequences
mkdir $results_dir/Species_Tree
mkdir $results_dir/WorkingDirectory
touch $results_dir/Log.txt
"""
}
4 changes: 2 additions & 2 deletions modules/nf-core/orthofinder/meta.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -46,7 +46,7 @@ output:
description: |
Groovy Map containing sample information
e.g. `[ id:'sample1' ]`
- $prefix:
- $results_dir:
type: directory
description: OrthoFinder output directory
working:
Expand All @@ -55,7 +55,7 @@ output:
description: |
Groovy Map containing sample information
e.g. `[ id:'sample1' ]`
- $prefix/WorkingDirectory:
- $results_dir/WorkingDirectory:
type: directory
description: OrthoFinder WorkingDirectory (used for the resume function)
versions_orthofinder:
Expand Down