Merge pull request #284 from genomic-medicine-sweden/remove_enable_conda

updates modules to remove enable_conda
nf-core · Feb 16, 2023 · 7a0d47a · 7a0d47a
2 parents ba19f8a + 8955858
commit 7a0d47a
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Showing 78 changed files with 163 additions and 150 deletions.
diff --git a/modules.json b/modules.json
diff --git a/modules/local/add_most_severe_consequence.nf b/modules/local/add_most_severe_consequence.nf
@@ -2,7 +2,7 @@ process ADD_MOST_SEVERE_CSQ {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "conda-forge::python=3.9.5" : null)
+    conda "conda-forge::python=3.9.5"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/python:3.9--1' :
         'quay.io/biocontainers/python:3.9--1' }"

diff --git a/modules/local/add_most_severe_pli.nf b/modules/local/add_most_severe_pli.nf
@@ -2,7 +2,7 @@ process ADD_MOST_SEVERE_PLI {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "conda-forge::python=3.9.5" : null)
+    conda "conda-forge::python=3.9.5"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/python:3.9--1' :
         'quay.io/biocontainers/python:3.9--1' }"

diff --git a/modules/local/change_name.nf b/modules/local/change_name.nf
@@ -3,7 +3,7 @@ process CHANGE_NAME {
     label 'process_low'
     label 'process_single'
 
-    conda (params.enable_conda ? "conda-forge::python=3.9.5" : null)
+    conda "conda-forge::python=3.9.5"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/python:3.9--1' :
         'quay.io/biocontainers/python:3.9--1' }"

diff --git a/modules/local/check_input_vcf.nf b/modules/local/check_input_vcf.nf
@@ -2,7 +2,7 @@ process CHECK_INPUT_VCF {
     tag "check_vcf"
     label 'process_single'
 
-    conda (params.enable_conda ? "conda-forge::python=3.9.5" : null)
+    conda "conda-forge::python=3.9.5"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/python:3.9--1' :
         'quay.io/biocontainers/python:3.9--1' }"

diff --git a/modules/local/create_bed_from_fai.nf b/modules/local/create_bed_from_fai.nf
@@ -2,7 +2,7 @@ process BUILD_BED {
     tag "$meta.id"
     label 'process_single'
 
-    conda (params.enable_conda ? "anaconda::gawk=5.1.0" : null)
+    conda "anaconda::gawk=5.1.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/gawk:5.1.0' :
         'quay.io/biocontainers/gawk:5.1.0' }"

diff --git a/modules/local/create_pedfile.nf b/modules/local/create_pedfile.nf
@@ -2,7 +2,7 @@ process MAKE_PED {
     tag "make_ped"
     label 'process_single'
 
-    conda (params.enable_conda ? "conda-forge::python=3.9.5" : null)
+    conda "conda-forge::python=3.9.5"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/python:3.9--1' :
         'quay.io/biocontainers/python:3.9--1' }"

diff --git a/modules/local/ensemblvep/main.nf b/modules/local/ensemblvep/main.nf
@@ -2,8 +2,9 @@ process ENSEMBLVEP {
     tag "$meta.id"
     label 'process_medium'
 
-    if (params.enable_conda) {
-        exit 1, "Conda environments cannot be used with vep at the moment. Please use Docker or Singularity containers."
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        exit 1, "Local VEP module does not support Conda. Please use Docker / Singularity / Podman instead."
     }
 
     container "ensemblorg/ensembl-vep:release_107.0"

diff --git a/modules/local/filter_vep.nf b/modules/local/filter_vep.nf
@@ -2,8 +2,9 @@ process FILTER_VEP {
     tag "$meta.id"
     label 'process_low'
 
-    if (params.enable_conda) {
-        exit 1, "Conda environments cannot be used with vep at the moment. Please use Docker or Singularity containers."
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        exit 1, "Local VEP module does not support Conda. Please use Docker / Singularity / Podman instead."
     }
     container "ensemblorg/ensembl-vep:release_107.0"
 

diff --git a/modules/local/gatk4/collectreadcounts/main.nf b/modules/local/gatk4/collectreadcounts/main.nf
@@ -2,7 +2,7 @@ process GATK4_COLLECTREADCOUNTS {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
+    conda "bioconda::gatk4=4.2.4.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
         'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"

diff --git a/modules/local/gatk4/denoisereadcounts/main.nf b/modules/local/gatk4/denoisereadcounts/main.nf
@@ -2,7 +2,7 @@ process GATK4_DENOISEREADCOUNTS {
     tag "$meta.id"
     label 'process_high'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
+    conda "bioconda::gatk4=4.2.4.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
         'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"

diff --git a/modules/local/get_chrom_sizes.nf b/modules/local/get_chrom_sizes.nf
@@ -2,7 +2,7 @@ process GET_CHROM_SIZES {
     tag "$fai"
     label 'process_single'
 
-    conda (params.enable_conda ? "conda-forge::coreutils=8.31" : null)
+    conda "conda-forge::coreutils=8.31"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/gnu-wget:1.18--0' :
         'quay.io/biocontainers/gnu-wget:1.18--0' }"

diff --git a/modules/nf-core/bcftools/concat/main.nf b/modules/nf-core/bcftools/concat/main.nf
diff --git a/modules/nf-core/bcftools/concat/meta.yml b/modules/nf-core/bcftools/concat/meta.yml
diff --git a/modules/nf-core/bcftools/merge/main.nf b/modules/nf-core/bcftools/merge/main.nf
diff --git a/modules/nf-core/bcftools/norm/main.nf b/modules/nf-core/bcftools/norm/main.nf
diff --git a/modules/nf-core/bcftools/roh/main.nf b/modules/nf-core/bcftools/roh/main.nf
diff --git a/modules/nf-core/bcftools/view/main.nf b/modules/nf-core/bcftools/view/main.nf
diff --git a/modules/nf-core/bwa/index/main.nf b/modules/nf-core/bwa/index/main.nf
diff --git a/modules/nf-core/bwamem2/index/main.nf b/modules/nf-core/bwamem2/index/main.nf
diff --git a/modules/nf-core/bwamem2/index/meta.yml b/modules/nf-core/bwamem2/index/meta.yml
diff --git a/modules/nf-core/bwamem2/mem/main.nf b/modules/nf-core/bwamem2/mem/main.nf
diff --git a/modules/nf-core/cat/cat/main.nf b/modules/nf-core/cat/cat/main.nf
diff --git a/modules/nf-core/cnvpytor/callcnvs/main.nf b/modules/nf-core/cnvpytor/callcnvs/main.nf
diff --git a/modules/nf-core/cnvpytor/histogram/main.nf b/modules/nf-core/cnvpytor/histogram/main.nf
diff --git a/modules/nf-core/cnvpytor/importreaddepth/main.nf b/modules/nf-core/cnvpytor/importreaddepth/main.nf
diff --git a/modules/nf-core/cnvpytor/partition/main.nf b/modules/nf-core/cnvpytor/partition/main.nf
diff --git a/modules/nf-core/cnvpytor/view/main.nf b/modules/nf-core/cnvpytor/view/main.nf
diff --git a/modules/nf-core/deepvariant/main.nf b/modules/nf-core/deepvariant/main.nf
diff --git a/modules/nf-core/expansionhunter/main.nf b/modules/nf-core/expansionhunter/main.nf
diff --git a/modules/nf-core/gatk4/bedtointervallist/main.nf b/modules/nf-core/gatk4/bedtointervallist/main.nf
diff --git a/modules/nf-core/gatk4/createsequencedictionary/main.nf b/modules/nf-core/gatk4/createsequencedictionary/main.nf
diff --git a/modules/nf-core/gatk4/filtermutectcalls/main.nf b/modules/nf-core/gatk4/filtermutectcalls/main.nf
diff --git a/modules/nf-core/gatk4/intervallisttools/main.nf b/modules/nf-core/gatk4/intervallisttools/main.nf
diff --git a/modules/nf-core/gatk4/mergebamalignment/main.nf b/modules/nf-core/gatk4/mergebamalignment/main.nf
diff --git a/modules/nf-core/gatk4/mergevcfs/main.nf b/modules/nf-core/gatk4/mergevcfs/main.nf
diff --git a/modules/nf-core/gatk4/mutect2/main.nf b/modules/nf-core/gatk4/mutect2/main.nf
diff --git a/modules/nf-core/gatk4/printreads/main.nf b/modules/nf-core/gatk4/printreads/main.nf
diff --git a/modules/nf-core/gatk4/revertsam/main.nf b/modules/nf-core/gatk4/revertsam/main.nf
diff --git a/modules/nf-core/gatk4/samtofastq/main.nf b/modules/nf-core/gatk4/samtofastq/main.nf
diff --git a/modules/nf-core/gatk4/selectvariants/main.nf b/modules/nf-core/gatk4/selectvariants/main.nf
diff --git a/modules/nf-core/gatk4/splitintervals/main.nf b/modules/nf-core/gatk4/splitintervals/main.nf
diff --git a/modules/nf-core/gatk4/variantfiltration/main.nf b/modules/nf-core/gatk4/variantfiltration/main.nf