Add error to modules that can not use conda

nf-core · Mar 22, 2024 · 030dd34 · 030dd34
1 parent 1bdff57
commit 030dd34
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diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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: