From b59f668d53fe48e477def7d0e392b39b4d4b9202 Mon Sep 17 00:00:00 2001
From: Cristina Araiz <caraiz@C1MS72A2H3QK.crg.es>
Date: Thu, 18 Jul 2024 15:54:12 +0200
Subject: [PATCH] update propr/grea with nf-core modules install

---
 modules/nf-core/propr/grea/main.nf          | 4 ++--
 modules/nf-core/propr/grea/templates/grea.R | 6 +++---
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/modules/nf-core/propr/grea/main.nf b/modules/nf-core/propr/grea/main.nf
index 66cf3c05..d2e1ee6d 100644
--- a/modules/nf-core/propr/grea/main.nf
+++ b/modules/nf-core/propr/grea/main.nf
@@ -1,11 +1,11 @@
 process PROPR_GREA {
     tag "$meta.id"
-    label 'process_high'
+    label 'process_single'
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/r-propr:5.0.4':
-        'quay.io/biocontainers/r-propr:5.0.4' }"
+        'biocontainers/r-propr:5.0.4' }"
 
     input:
     tuple val(meta), path(adj)
diff --git a/modules/nf-core/propr/grea/templates/grea.R b/modules/nf-core/propr/grea/templates/grea.R
index 6e1c6a00..2d568b70 100644
--- a/modules/nf-core/propr/grea/templates/grea.R
+++ b/modules/nf-core/propr/grea/templates/grea.R
@@ -122,8 +122,8 @@ add_missing <- function(adjacency_matrix, knowledge_matrix){
 opt <- list(
     adj              = '$adj',
     gmt              = '$gmt',
-    prefix           = ifelse('$task.ext.prefix' == 'null', '$meta.pathway_name',  '$task.ext.prefix'),
-    permutation      = 10,
+    prefix           = ifelse('$task.ext.prefix' == 'null', '$meta.id',  '$task.ext.prefix'),
+    permutation      = 100,
     fixseed          = TRUE,
     ncores           = as.integer('$task.cpus')
 )
@@ -214,7 +214,7 @@ write.table(
     G,
     file      = paste0(opt\$prefix, '.go.tsv'),
     col.names = TRUE,
-    row.names = TRUE, # False
+    row.names = TRUE,
     sep       = '\\t',
     quote     = FALSE