remove enable_conda from local modules

nf-core · Dec 22, 2022 · 7e2d27f · 7e2d27f
1 parent 0ba23ed
commit 7e2d27f
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Showing 10 changed files with 10 additions and 10 deletions.
diff --git a/modules/local/cat_files.nf b/modules/local/cat_files.nf
@@ -1,7 +1,7 @@
 process CAT_FILES {
     label 'process_low'
 
-    conda (params.enable_conda ? "conda-forge:sed=4.8" : null)
+    conda "conda-forge:sed=4.8"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/cat:5.2.3--hdfd78af_1' :
         'quay.io/biocontainers/cat:5.2.3--hdfd78af_1' }"

diff --git a/modules/local/csvtk_concat.nf b/modules/local/csvtk_concat.nf
@@ -1,7 +1,7 @@
 process CSVTK_CONCAT {
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::csvtk=0.23.0" : null)
+    conda "bioconda::csvtk=0.23.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/csvtk:0.23.0--h9ee0642_0' :
         'quay.io/biocontainers/csvtk:0.23.0--h9ee0642_0' }"

diff --git a/modules/local/csvtk_split.nf b/modules/local/csvtk_split.nf
@@ -1,7 +1,7 @@
 process CSVTK_SPLIT {
     label 'process_low'
 
-    conda (params.enable_conda ? "conda-forge::sed=4.7 bioconda::csvtk=0.23.0" : null)
+    conda "conda-forge::sed=4.7 bioconda::csvtk=0.23.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/csvtk:0.23.0--h9ee0642_0' :
         'quay.io/biocontainers/csvtk:0.23.0--h9ee0642_0' }"

diff --git a/modules/local/epytope_check_requested_models.nf b/modules/local/epytope_check_requested_models.nf
@@ -1,7 +1,7 @@
 process EPYTOPE_CHECK_REQUESTED_MODELS {
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::epytope=3.1.0" : null)
+    conda "bioconda::epytope=3.1.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/epytope:3.1.0--pyh5e36f6f_0' :
         'quay.io/biocontainers/epytope:3.1.0--pyh5e36f6f_0' }"

diff --git a/modules/local/epytope_generate_peptides.nf b/modules/local/epytope_generate_peptides.nf
@@ -2,7 +2,7 @@ process EPYTOPE_GENERATE_PEPTIDES {
     label 'process_low'
     tag "${meta.sample}"
 
-    conda (params.enable_conda ? "bioconda::epytope=3.1.0" : null)
+    conda "bioconda::epytope=3.1.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/epytope:3.1.0--pyh5e36f6f_0' :
         'quay.io/biocontainers/epytope:3.1.0--pyh5e36f6f_0' }"

diff --git a/modules/local/epytope_peptide_prediction.nf b/modules/local/epytope_peptide_prediction.nf
@@ -1,7 +1,7 @@
 process EPYTOPE_PEPTIDE_PREDICTION {
     label 'process_low'
 
-    conda (params.enable_conda ? "conda-forge::coreutils=9.1 conda-forge::tcsh=6.20.00 bioconda::epytope=3.1.0 conda-forge::gawk=5.1.0 conda-forge::perl=5.32.1" : null)
+    conda "conda-forge::coreutils=9.1 conda-forge::tcsh=6.20.00 bioconda::epytope=3.1.0 conda-forge::gawk=5.1.0 conda-forge::perl=5.32.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-11bbf0d242ea96f7b9c08d5b5bc26f2cd5ac5943:3419f320edefe6077631798f50d7bd4f8dc4763f-0' :
         'quay.io/biocontainers/mulled-v2-11bbf0d242ea96f7b9c08d5b5bc26f2cd5ac5943:3419f320edefe6077631798f50d7bd4f8dc4763f-0' }"

diff --git a/modules/local/epytope_show_supported_models.nf b/modules/local/epytope_show_supported_models.nf
@@ -1,7 +1,7 @@
 process EPYTOPE_SHOW_SUPPORTED_MODELS {
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::epytope=3.1.0" : null)
+    conda "bioconda::epytope=3.1.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/epytope:3.1.0--pyh5e36f6f_0' :
         'quay.io/biocontainers/epytope:3.1.0--pyh5e36f6f_0' }"

diff --git a/modules/local/snpsift_split.nf b/modules/local/snpsift_split.nf
@@ -1,7 +1,7 @@
 process SNPSIFT_SPLIT {
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::snpsift=4.2" : null)
+    conda "bioconda::snpsift=4.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/snpsift:4.2--hdfd78af_5' :
         'quay.io/biocontainers/snpsift:4.2--hdfd78af_5' }"

diff --git a/modules/local/split_peptides.nf b/modules/local/split_peptides.nf
@@ -1,7 +1,7 @@
 process SPLIT_PEPTIDES {
     label 'process_low'
 
-    conda (params.enable_conda ? "conda-forge::python=3.8.3" : null)
+    conda "conda-forge::python=3.8.3"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/python:3.8.3' :
         'quay.io/biocontainers/python:3.8.3' }"

diff --git a/modules/local/variant_split.nf b/modules/local/variant_split.nf
@@ -1,7 +1,7 @@
 process VARIANT_SPLIT {
     label 'process_low'
 
-    conda (params.enable_conda ? "conda-forge::python=3.8.3" : null)
+    conda "conda-forge::python=3.8.3"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/python:3.8.3' :
         'quay.io/biocontainers/python:3.8.3' }"