From 030dd3439be68b20928bf9d70575d4ba3147aef2 Mon Sep 17 00:00:00 2001
From: JoseEspinosa <kadomu@gmail.com>
Date: Fri, 22 Mar 2024 18:18:35 +0100
Subject: [PATCH] Add error to modules that can not use conda

---
 modules/local/colabfold_batch.nf           | 5 +++++
 modules/local/mmseqs_colabfoldsearch.nf    | 5 +++++
 modules/local/multifasta_to_csv.nf         | 1 +
 modules/local/multifasta_to_singlefasta.nf | 1 +
 modules/local/run_alphafold2.nf            | 5 +++++
 modules/local/run_alphafold2_msa.nf        | 5 +++++
 modules/local/run_alphafold2_pred.nf       | 5 +++++
 modules/local/run_esmfold.nf               | 4 ++++
 8 files changed, 31 insertions(+)

diff --git a/modules/local/colabfold_batch.nf b/modules/local/colabfold_batch.nf
index 8302a189..28f26274 100644
--- a/modules/local/colabfold_batch.nf
+++ b/modules/local/colabfold_batch.nf
@@ -2,6 +2,11 @@ process COLABFOLD_BATCH {
     tag "$meta.id"
     label 'process_medium'
 
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error("Local COLABFOLD_BATCH module does not support Conda. Please use Docker / Singularity / Podman instead.")
+    }
+
     container "nf-core/proteinfold_colabfold:1.1.0"
 
     input:
diff --git a/modules/local/mmseqs_colabfoldsearch.nf b/modules/local/mmseqs_colabfoldsearch.nf
index adc45738..978a627e 100644
--- a/modules/local/mmseqs_colabfoldsearch.nf
+++ b/modules/local/mmseqs_colabfoldsearch.nf
@@ -2,6 +2,11 @@ process MMSEQS_COLABFOLDSEARCH {
     tag "$meta.id"
     label 'process_high_memory'
 
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error("Local MMSEQS_COLABFOLDSEARCH module does not support Conda. Please use Docker / Singularity / Podman instead.")
+    }
+
     container "nf-core/proteinfold_colabfold:1.1.0"
 
     input:
diff --git a/modules/local/multifasta_to_csv.nf b/modules/local/multifasta_to_csv.nf
index 2725f97d..d5d68fbf 100644
--- a/modules/local/multifasta_to_csv.nf
+++ b/modules/local/multifasta_to_csv.nf
@@ -2,6 +2,7 @@ process MULTIFASTA_TO_CSV {
     tag "$meta.id"
     label 'process_single'
 
+    conda "conda-forge::sed=4.7"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
         'nf-core/ubuntu:20.04' }"
diff --git a/modules/local/multifasta_to_singlefasta.nf b/modules/local/multifasta_to_singlefasta.nf
index 0e450b82..e9744416 100644
--- a/modules/local/multifasta_to_singlefasta.nf
+++ b/modules/local/multifasta_to_singlefasta.nf
@@ -2,6 +2,7 @@ process MULTIFASTA_TO_SINGLEFASTA {
     tag "$meta.id"
     label 'process_single'
 
+    conda "conda-forge::sed=4.7"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
         'nf-core/ubuntu:20.04' }"
diff --git a/modules/local/run_alphafold2.nf b/modules/local/run_alphafold2.nf
index 4f4c2995..5607712d 100644
--- a/modules/local/run_alphafold2.nf
+++ b/modules/local/run_alphafold2.nf
@@ -5,6 +5,11 @@ process RUN_ALPHAFOLD2 {
     tag "$meta.id"
     label 'process_medium'
 
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error("Local RUN_ALPHAFOLD2 module does not support Conda. Please use Docker / Singularity / Podman instead.")
+    }
+
     container "nf-core/proteinfold_alphafold2_standard:dev"
 
     input:
diff --git a/modules/local/run_alphafold2_msa.nf b/modules/local/run_alphafold2_msa.nf
index 01b16dfa..6c9bfcf8 100644
--- a/modules/local/run_alphafold2_msa.nf
+++ b/modules/local/run_alphafold2_msa.nf
@@ -5,6 +5,11 @@ process RUN_ALPHAFOLD2_MSA {
     tag   "$meta.id"
     label 'process_medium'
 
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error("Local RUN_ALPHAFOLD2_MSA module does not support Conda. Please use Docker / Singularity / Podman instead.")
+    }
+
     container "nf-core/proteinfold_alphafold2_msa:dev"
 
     input:
diff --git a/modules/local/run_alphafold2_pred.nf b/modules/local/run_alphafold2_pred.nf
index a0575d36..ee9983c5 100644
--- a/modules/local/run_alphafold2_pred.nf
+++ b/modules/local/run_alphafold2_pred.nf
@@ -5,6 +5,11 @@ process RUN_ALPHAFOLD2_PRED {
     tag   "$meta.id"
     label 'process_medium'
 
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error("Local RUN_ALPHAFOLD2_PRED module does not support Conda. Please use Docker / Singularity / Podman instead.")
+    }
+
     container "nf-core/proteinfold_alphafold2_split:dev"
 
     input:
diff --git a/modules/local/run_esmfold.nf b/modules/local/run_esmfold.nf
index 4d5645c3..5f7a25ce 100644
--- a/modules/local/run_esmfold.nf
+++ b/modules/local/run_esmfold.nf
@@ -2,6 +2,10 @@ process RUN_ESMFOLD {
     tag "$meta.id"
     label 'process_medium'
 
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error("Local RUN_ESMFOLD module does not support Conda. Please use Docker / Singularity / Podman instead.")
+    }
+
     container "nf-core/proteinfold_esmfold:1.1.0"
 
     input: