Bulk change conda syntax for all modules (#2654)

* Add pinned conda channels * Remove error raise for modules that dont support conda * Add missing conda recipe * Remove error raise for modules that dont support conda * Bulk change conda syntax across all modules * Bump NF version to >=22.10.1
nf-core · Dec 13, 2022 · c8e35eb · c8e35eb
1 parent 9c25368
commit c8e35eb
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diff --git a/modules/nf-core/abacas/main.nf b/modules/nf-core/abacas/main.nf
@@ -2,7 +2,7 @@ process ABACAS {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::abacas=1.3.1" : null)
+    conda "bioconda::abacas=1.3.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/abacas:1.3.1--pl526_0' :
         'quay.io/biocontainers/abacas:1.3.1--pl526_0' }"

diff --git a/modules/nf-core/abricate/run/main.nf b/modules/nf-core/abricate/run/main.nf
@@ -2,7 +2,7 @@ process ABRICATE_RUN {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::abricate=1.0.1" : null)
+    conda "bioconda::abricate=1.0.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/abricate%3A1.0.1--ha8f3691_1':
         'quay.io/biocontainers/abricate:1.0.1--ha8f3691_1' }"

diff --git a/modules/nf-core/abricate/summary/main.nf b/modules/nf-core/abricate/summary/main.nf
@@ -2,7 +2,7 @@ process ABRICATE_SUMMARY {
     tag "$meta.id"
     label 'process_single'
 
-    conda (params.enable_conda ? "bioconda::abricate=1.0.1" : null)
+    conda "bioconda::abricate=1.0.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/abricate%3A1.0.1--ha8f3691_1':
         'quay.io/biocontainers/abricate:1.0.1--ha8f3691_1' }"

diff --git a/modules/nf-core/adapterremoval/main.nf b/modules/nf-core/adapterremoval/main.nf
@@ -2,7 +2,7 @@ process ADAPTERREMOVAL {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::adapterremoval=2.3.2" : null)
+    conda "bioconda::adapterremoval=2.3.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/adapterremoval:2.3.2--hb7ba0dd_0' :
         'quay.io/biocontainers/adapterremoval:2.3.2--hb7ba0dd_0' }"

diff --git a/modules/nf-core/adapterremovalfixprefix/main.nf b/modules/nf-core/adapterremovalfixprefix/main.nf
@@ -3,7 +3,7 @@ process ADAPTERREMOVALFIXPREFIX {
     label 'process_single'
 
     // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
-    conda (params.enable_conda ? "bioconda::adapterremovalfixprefix=0.0.5" : null)
+    conda "bioconda::adapterremovalfixprefix=0.0.5"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/adapterremovalfixprefix:0.0.5--hdfd78af_2':
         'quay.io/biocontainers/adapterremovalfixprefix:0.0.5--hdfd78af_2' }"

diff --git a/modules/nf-core/agat/convertspgff2gtf/main.nf b/modules/nf-core/agat/convertspgff2gtf/main.nf
@@ -2,7 +2,7 @@ process AGAT_CONVERTSPGFF2GTF {
     tag "$meta.id"
     label 'process_single'
 
-    conda (params.enable_conda ? "bioconda::agat=1.0.0" : null)
+    conda "bioconda::agat=1.0.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/agat:1.0.0--pl5321hdfd78af_0' :
         'quay.io/biocontainers/agat:1.0.0--pl5321hdfd78af_0' }"

diff --git a/modules/nf-core/agat/convertspgxf2gxf/main.nf b/modules/nf-core/agat/convertspgxf2gxf/main.nf
@@ -2,7 +2,7 @@ process AGAT_CONVERTSPGXF2GXF {
     tag "$meta.id"
     label 'process_single'
 
-    conda (params.enable_conda ? "bioconda::agat=1.0.0" : null)
+    conda "bioconda::agat=1.0.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/agat:1.0.0--pl5321hdfd78af_0' :
         'quay.io/biocontainers/agat:1.0.0--pl5321hdfd78af_0' }"

diff --git a/modules/nf-core/agat/spstatistics/main.nf b/modules/nf-core/agat/spstatistics/main.nf
@@ -2,7 +2,7 @@ process AGAT_SPSTATISTICS {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::agat=1.0.0" : null)
+    conda "bioconda::agat=1.0.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/agat:1.0.0--pl5321hdfd78af_0' :
         'quay.io/biocontainers/agat:1.0.0--pl5321hdfd78af_0' }"

diff --git a/modules/nf-core/agat/sqstatbasic/main.nf b/modules/nf-core/agat/sqstatbasic/main.nf
@@ -2,7 +2,7 @@ process AGAT_SQSTATBASIC {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::agat=1.0.0" : null)
+    conda "bioconda::agat=1.0.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/agat:1.0.0--pl5321hdfd78af_0' :
         'quay.io/biocontainers/agat:1.0.0--pl5321hdfd78af_0' }"

diff --git a/modules/nf-core/agrvate/main.nf b/modules/nf-core/agrvate/main.nf
@@ -2,7 +2,7 @@ process AGRVATE {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::agrvate=1.0.2" : null)
+    conda "bioconda::agrvate=1.0.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/agrvate:1.0.2--hdfd78af_0' :
         'quay.io/biocontainers/agrvate:1.0.2--hdfd78af_0' }"

diff --git a/modules/nf-core/allelecounter/main.nf b/modules/nf-core/allelecounter/main.nf
@@ -2,7 +2,7 @@ process ALLELECOUNTER {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? 'bioconda::cancerit-allelecount=4.3.0' : null)
+    conda "bioconda::cancerit-allelecount=4.3.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/cancerit-allelecount:4.3.0--h41abebc_0' :
         'quay.io/biocontainers/cancerit-allelecount:4.3.0--h41abebc_0' }"

diff --git a/modules/nf-core/ampcombi/main.nf b/modules/nf-core/ampcombi/main.nf
@@ -2,7 +2,7 @@ process AMPCOMBI {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::ampcombi=0.1.7" : null)
+    conda "bioconda::ampcombi=0.1.7"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ampcombi:0.1.7--pyhdfd78af_0':
         'quay.io/biocontainers/ampcombi:0.1.7--pyhdfd78af_0' }"

diff --git a/modules/nf-core/ampir/main.nf b/modules/nf-core/ampir/main.nf
@@ -2,7 +2,7 @@ process AMPIR {
     tag "$meta.id"
     label 'process_single'
 
-    conda (params.enable_conda ? "conda-forge::r-ampir=1.1.0" : null)
+    conda "conda-forge::r-ampir=1.1.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/r-ampir:1.1.0':
         'quay.io/biocontainers/r-ampir:1.1.0' }"

diff --git a/modules/nf-core/amplify/predict/main.nf b/modules/nf-core/amplify/predict/main.nf
@@ -3,7 +3,7 @@ process AMPLIFY_PREDICT {
     label 'process_single'
 
     // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
-    conda (params.enable_conda ? "bioconda::amplify=1.0.3" : null)
+    conda "bioconda::amplify=1.0.3"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/amplify:1.0.3--py36hdfd78af_0':
         'quay.io/biocontainers/amplify:1.0.3--py36hdfd78af_0' }"

diff --git a/modules/nf-core/amps/main.nf b/modules/nf-core/amps/main.nf
@@ -1,7 +1,7 @@
 process AMPS {
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::hops=0.35" : null)
+    conda "bioconda::hops=0.35"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/hops:0.35--hdfd78af_1' :
         'quay.io/biocontainers/hops:0.35--hdfd78af_1' }"

diff --git a/modules/nf-core/amrfinderplus/run/main.nf b/modules/nf-core/amrfinderplus/run/main.nf
@@ -2,7 +2,7 @@ process AMRFINDERPLUS_RUN {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::ncbi-amrfinderplus=3.10.42" : null)
+    conda "bioconda::ncbi-amrfinderplus=3.10.42"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ncbi-amrfinderplus:3.10.42--h6e70893_0':
         'quay.io/biocontainers/ncbi-amrfinderplus:3.10.42--h6e70893_0' }"

diff --git a/modules/nf-core/amrfinderplus/update/main.nf b/modules/nf-core/amrfinderplus/update/main.nf
@@ -2,7 +2,7 @@ process AMRFINDERPLUS_UPDATE {
     tag "update"
     label 'process_single'
 
-    conda (params.enable_conda ? "bioconda::ncbi-amrfinderplus=3.10.42" : null)
+    conda "bioconda::ncbi-amrfinderplus=3.10.42"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ncbi-amrfinderplus:3.10.42--h6e70893_0':
         'quay.io/biocontainers/ncbi-amrfinderplus:3.10.42--h6e70893_0' }"

diff --git a/modules/nf-core/angsd/docounts/main.nf b/modules/nf-core/angsd/docounts/main.nf
@@ -2,7 +2,7 @@ process ANGSD_DOCOUNTS {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::angsd=0.939" : null)
+    conda "bioconda::angsd=0.939"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/angsd:0.939--h468462d_0':
         'quay.io/biocontainers/angsd:0.939--h468462d_0' }"

diff --git a/modules/nf-core/antismash/antismashlite/main.nf b/modules/nf-core/antismash/antismashlite/main.nf
@@ -2,7 +2,7 @@ process ANTISMASH_ANTISMASHLITE {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::antismash-lite=6.0.1" : null)
+    conda "bioconda::antismash-lite=6.0.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/antismash-lite:6.0.1--pyhdfd78af_1' :
         'quay.io/biocontainers/antismash-lite:6.0.1--pyhdfd78af_1' }"

diff --git a/modules/nf-core/antismash/antismashlitedownloaddatabases/main.nf b/modules/nf-core/antismash/antismashlitedownloaddatabases/main.nf
@@ -1,7 +1,7 @@
 process ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES {
     label 'process_single'
 
-    conda (params.enable_conda ? "bioconda::antismash-lite=6.0.1" : null)
+    conda "bioconda::antismash-lite=6.0.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/antismash-lite:6.0.1--pyhdfd78af_1' :
         'quay.io/biocontainers/antismash-lite:6.0.1--pyhdfd78af_1' }"

diff --git a/modules/nf-core/arcashla/extract/main.nf b/modules/nf-core/arcashla/extract/main.nf
@@ -2,7 +2,7 @@ process ARCASHLA_EXTRACT {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::arcas-hla=0.5.0" : null)
+    conda "bioconda::arcas-hla=0.5.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/arcas-hla:0.5.0--hdfd78af_0':
         'quay.io/biocontainers/arcas-hla:0.5.0--hdfd78af_0' }"

diff --git a/modules/nf-core/aria2/main.nf b/modules/nf-core/aria2/main.nf
@@ -3,7 +3,7 @@ process ARIA2 {
     tag "$source_url"
     label 'process_single'
 
-    conda (params.enable_conda ? "conda-forge::aria2=1.36.0" : null)
+    conda "conda-forge::aria2=1.36.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/aria2:1.36.0' :
         'quay.io/biocontainers/aria2:1.36.0' }"

diff --git a/modules/nf-core/ariba/getref/main.nf b/modules/nf-core/ariba/getref/main.nf
@@ -2,7 +2,7 @@ process ARIBA_GETREF {
     tag "$db_name"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::ariba=2.14.6" : null)
+    conda "bioconda::ariba=2.14.6"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ariba:2.14.6--py39h67e14b5_3':
         'quay.io/biocontainers/ariba:2.14.6--py39h67e14b5_3' }"

diff --git a/modules/nf-core/ariba/run/main.nf b/modules/nf-core/ariba/run/main.nf
@@ -2,7 +2,7 @@ process ARIBA_RUN {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::ariba=2.14.6" : null)
+    conda "bioconda::ariba=2.14.6"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ariba:2.14.6--py39h67e14b5_3':
         'quay.io/biocontainers/ariba:2.14.6--py39h67e14b5_3' }"

diff --git a/modules/nf-core/arriba/main.nf b/modules/nf-core/arriba/main.nf
@@ -2,7 +2,7 @@ process ARRIBA {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::arriba=2.3.0" : null)
+    conda "bioconda::arriba=2.3.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/arriba:2.3.0--haa8aa89_0' :
         'quay.io/biocontainers/arriba:2.3.0--haa8aa89_0' }"

diff --git a/modules/nf-core/artic/guppyplex/main.nf b/modules/nf-core/artic/guppyplex/main.nf
@@ -2,7 +2,7 @@ process ARTIC_GUPPYPLEX {
     tag "$meta.id"
     label 'process_high'
 
-    conda (params.enable_conda ? "bioconda::artic=1.2.3" : null)
+    conda "bioconda::artic=1.2.3"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/artic:1.2.3--pyhdfd78af_0' :
         'quay.io/biocontainers/artic:1.2.3--pyhdfd78af_0' }"

diff --git a/modules/nf-core/artic/minion/main.nf b/modules/nf-core/artic/minion/main.nf
@@ -2,7 +2,7 @@ process ARTIC_MINION {
     tag "$meta.id"
     label 'process_high'
 
-    conda (params.enable_conda ? "bioconda::artic=1.2.3" : null)
+    conda "bioconda::artic=1.2.3"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/artic:1.2.3--pyhdfd78af_0' :
         'quay.io/biocontainers/artic:1.2.3--pyhdfd78af_0' }"

diff --git a/modules/nf-core/ascat/main.nf b/modules/nf-core/ascat/main.nf
@@ -2,7 +2,7 @@ process ASCAT {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::ascat=3.0.0 bioconda::cancerit-allelecount=4.3.0" : null)
+    conda "bioconda::ascat=3.0.0 bioconda::cancerit-allelecount=4.3.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-c278c7398beb73294d78639a864352abef2931ce:dfe5aaa885de434adb2b490b68972c5840c6d761-0':
         'quay.io/biocontainers/mulled-v2-c278c7398beb73294d78639a864352abef2931ce:dfe5aaa885de434adb2b490b68972c5840c6d761-0' }"

diff --git a/modules/nf-core/assemblyscan/main.nf b/modules/nf-core/assemblyscan/main.nf
@@ -2,7 +2,7 @@ process ASSEMBLYSCAN {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::assembly-scan=0.4.1" : null)
+    conda "bioconda::assembly-scan=0.4.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/assembly-scan:0.4.1--pyhdfd78af_0' :
         'quay.io/biocontainers/assembly-scan:0.4.1--pyhdfd78af_0' }"

diff --git a/modules/nf-core/ataqv/ataqv/main.nf b/modules/nf-core/ataqv/ataqv/main.nf
@@ -2,7 +2,7 @@ process ATAQV_ATAQV {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::ataqv=1.3.0" : null)
+    conda "bioconda::ataqv=1.3.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ataqv:1.3.0--py39hccc85d7_2' :
         'quay.io/biocontainers/ataqv:1.3.0--py39hccc85d7_2' }"

diff --git a/modules/nf-core/ataqv/mkarv/main.nf b/modules/nf-core/ataqv/mkarv/main.nf
@@ -1,7 +1,7 @@
 process ATAQV_MKARV {
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::ataqv=1.3.0" : null)
+    conda "bioconda::ataqv=1.3.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ataqv:1.3.0--py39hccc85d7_2':
         'quay.io/biocontainers/ataqv:1.3.0--py39hccc85d7_2' }"

diff --git a/modules/nf-core/atlas/call/main.nf b/modules/nf-core/atlas/call/main.nf
@@ -2,7 +2,7 @@ process ATLAS_CALL {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::atlas=0.9.9" : null)
+    conda "bioconda::atlas=0.9.9"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/atlas:0.9.9--h082e891_0':
         'quay.io/biocontainers/atlas:0.9.9--h082e891_0' }"

diff --git a/modules/nf-core/atlas/pmd/main.nf b/modules/nf-core/atlas/pmd/main.nf
@@ -2,7 +2,7 @@ process ATLAS_PMD {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::atlas=0.9.9" : null)
+    conda "bioconda::atlas=0.9.9"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/atlas:0.9.9--h082e891_0':
         'quay.io/biocontainers/atlas:0.9.9--h082e891_0' }"

diff --git a/modules/nf-core/atlas/recal/main.nf b/modules/nf-core/atlas/recal/main.nf
@@ -2,7 +2,7 @@ process ATLAS_RECAL {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::atlas=0.9.9" : null)
+    conda "bioconda::atlas=0.9.9"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/atlas:0.9.9--h082e891_0':
         'quay.io/biocontainers/atlas:0.9.9--h082e891_0' }"

diff --git a/modules/nf-core/atlas/splitmerge/main.nf b/modules/nf-core/atlas/splitmerge/main.nf
@@ -2,7 +2,7 @@ process ATLAS_SPLITMERGE {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::atlas=0.9.9" : null)
+    conda "bioconda::atlas=0.9.9"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/atlas:0.9.9--h082e891_0':
         'quay.io/biocontainers/atlas:0.9.9--h082e891_0' }"

diff --git a/modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/main.nf b/modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/main.nf
@@ -2,7 +2,7 @@ process ATLASGENEANNOTATIONMANIPULATION_GTF2FEATUREANNOTATION {
     tag "${meta.id}"
     label 'process_single'
 
-    conda (params.enable_conda ? "bioconda::atlas-gene-annotation-manipulation=1.1.0" : null)
+    conda "bioconda::atlas-gene-annotation-manipulation=1.1.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/atlas-gene-annotation-manipulation%3A1.1.0--hdfd78af_0':
         'quay.io/biocontainers/atlas-gene-annotation-manipulation:1.1.0--hdfd78af_0' }"

diff --git a/modules/nf-core/bakta/bakta/main.nf b/modules/nf-core/bakta/bakta/main.nf
@@ -2,7 +2,7 @@ process BAKTA_BAKTA {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::bakta=1.6.0" : null)
+    conda "bioconda::bakta=1.6.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/bakta:1.6.0--pyhdfd78af_0' :
         'quay.io/biocontainers/bakta:1.6.0--pyhdfd78af_0' }"

diff --git a/modules/nf-core/bakta/baktadbdownload/main.nf b/modules/nf-core/bakta/baktadbdownload/main.nf
@@ -1,7 +1,7 @@
 process BAKTA_BAKTADBDOWNLOAD {
     label 'process_single'
 
-    conda (params.enable_conda ? "bioconda::bakta=1.6.0" : null)
+    conda "bioconda::bakta=1.6.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/bakta:1.6.0--pyhdfd78af_0' :
         'quay.io/biocontainers/bakta:1.6.0--pyhdfd78af_0' }"

diff --git a/modules/nf-core/bamaligncleaner/main.nf b/modules/nf-core/bamaligncleaner/main.nf
@@ -2,7 +2,7 @@ process BAMALIGNCLEANER {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::bamaligncleaner=0.2.1" : null)
+    conda "bioconda::bamaligncleaner=0.2.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/bamaligncleaner:0.2.1--pyhdfd78af_0' :
         'quay.io/biocontainers/bamaligncleaner:0.2.1--pyhdfd78af_0' }"

diff --git a/modules/nf-core/bamcmp/main.nf b/modules/nf-core/bamcmp/main.nf
@@ -2,7 +2,7 @@ process BAMCMP {
     label 'process_low'
 
     // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
-    conda (params.enable_conda ? "bioconda::bamcmp=2.2" : null)
+    conda "bioconda::bamcmp=2.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/bamcmp:2.2--h05f6578_0' :
         'quay.io/biocontainers/bamcmp:2.2--h05f6578_0' }"

diff --git a/modules/nf-core/bamtools/convert/main.nf b/modules/nf-core/bamtools/convert/main.nf
@@ -2,7 +2,7 @@ process BAMTOOLS_CONVERT {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::bamtools=2.5.1" : null)
+    conda "bioconda::bamtools=2.5.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/bamtools:2.5.1--h9a82719_9' :
         'quay.io/biocontainers/bamtools:2.5.1--h9a82719_9' }"

diff --git a/modules/nf-core/bamtools/split/main.nf b/modules/nf-core/bamtools/split/main.nf
@@ -2,7 +2,7 @@ process BAMTOOLS_SPLIT {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::bamtools=2.5.2" : null)
+    conda "bioconda::bamtools=2.5.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/bamtools:2.5.2--hd03093a_0' :
         'quay.io/biocontainers/bamtools:2.5.2--hd03093a_0' }"

diff --git a/modules/nf-core/bamtools/stats/main.nf b/modules/nf-core/bamtools/stats/main.nf
@@ -2,7 +2,7 @@ process BAMTOOLS_STATS {
     tag "$meta.id"
     label 'process_single'
 
-    conda (params.enable_conda ? "bioconda::bamtools=2.5.1" : null)
+    conda "bioconda::bamtools=2.5.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/bamtools:2.5.1--h9a82719_9' :
         'quay.io/biocontainers/bamtools:2.5.1--h9a82719_9' }"