remove params.enable_conda in favor of updated nf-core standard

mskcc · Mar 21, 2023 · 6522265 · 6522265
1 parent 8b6c016
commit 6522265
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Showing 20 changed files with 148 additions and 140 deletions.
diff --git a/modules.json b/modules.json
@@ -7,7 +7,7 @@
                 "nf-core": {
                     "arriba": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
                         "installed_by": ["modules"]
                     },
                     "cat/fastq": {
@@ -22,12 +22,12 @@
                     },
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
-                        "git_sha": "8022c68e7403eecbd8ba9c49496f69f8c49d50f0",
+                        "git_sha": "b6d4d476aee074311c89d82a69c1921bd70c8180",
                         "installed_by": ["modules"]
                     },
                     "fastp": {
                         "branch": "master",
-                        "git_sha": "1e49f31e93c56a3832833eef90a02d3cde5a3f7e",
+                        "git_sha": "20a508676f40d0fd3f911ac595af91ec845704c4",
                         "installed_by": ["modules"]
                     },
                     "gatk4/bedtointervallist": {
@@ -87,12 +87,12 @@
                     },
                     "umitools/dedup": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "git_sha": "6d9c7e43404e20a97d2f6f88548456afe78282e6",
                         "installed_by": ["modules"]
                     },
                     "umitools/extract": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "git_sha": "6d9c7e43404e20a97d2f6f88548456afe78282e6",
                         "installed_by": ["modules"]
                     }
                 }

diff --git a/modules/local/fusioncatcher/detect/main.nf b/modules/local/fusioncatcher/detect/main.nf
@@ -2,7 +2,7 @@ process FUSIONCATCHER_DETECT {
     tag "$meta.id"
     label 'process_high'
 
-    conda (params.enable_conda ? "bioconda::fusioncatcher=1.33" : null)
+    conda "bioconda::fusioncatcher=1.33"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'docker.io/clinicalgenomics/fusioncatcher:1.33' :
         'docker.io/clinicalgenomics/fusioncatcher:1.33' }"

diff --git a/modules/local/fusioncatcher/download/main.nf b/modules/local/fusioncatcher/download/main.nf
@@ -2,7 +2,7 @@ process FUSIONCATCHER_DOWNLOAD {
     tag 'fusioncatcher_download'
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::fusioncatcher=1.33" : null)
+    conda "bioconda::fusioncatcher=1.33"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'docker.io/clinicalgenomics/fusioncatcher:1.33' :
         'docker.io/clinicalgenomics/fusioncatcher:1.33' }"

diff --git a/modules/local/fusionreport/download/main.nf b/modules/local/fusionreport/download/main.nf
@@ -3,7 +3,7 @@ process FUSIONREPORT_DOWNLOAD {
     label 'process_medium'
 
     // Note: 2.7X indices incompatible with AWS iGenomes.
-    conda (params.enable_conda ? 'bioconda::star=2.7.9a' : null)
+    conda 'bioconda::star=2.7.9a'
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'cmopipeline/fusion-report:0.0.1' :
         'cmopipeline/fusion-report:0.0.1' }"

diff --git a/modules/local/fusionreport/run/main.nf b/modules/local/fusionreport/run/main.nf
@@ -3,7 +3,7 @@ process FUSIONREPORT {
     label 'process_low'
 
     // Note: 2.7X indices incompatible with AWS iGenomes.
-    conda (params.enable_conda ? 'bioconda::star=2.7.9a' : null)
+    conda 'bioconda::star=2.7.9a'
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'cmopipeline/fusion-report:0.0.1' :
         'cmopipeline/fusion-report:0.0.1' }"

diff --git a/modules/local/htseq/count/main.nf b/modules/local/htseq/count/main.nf
@@ -2,7 +2,7 @@ process HTSEQ_COUNT {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::htseq=2.0.2" : null)
+    conda "bioconda::htseq=2.0.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/htseq:2.0.2--py39h919a90d_0' :
         'quay.io/biocontainers/htseq:2.0.2--py39h919a90d_0' }"

diff --git a/modules/local/star/align/main.nf b/modules/local/star/align/main.nf
@@ -2,7 +2,7 @@ process STAR_ALIGN {
     tag "$meta.id"
     label 'process_high'
 
-    conda (params.enable_conda ? "bioconda::star=2.7.10a bioconda::samtools=1.16.1 conda-forge::gawk=5.1.0" : null)
+    conda "bioconda::star=2.7.10a bioconda::samtools=1.16.1 conda-forge::gawk=5.1.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:1df389393721fc66f3fd8778ad938ac711951107-0' :
         'quay.io/biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:1df389393721fc66f3fd8778ad938ac711951107-0' }"

diff --git a/modules/local/starfusion/build/main.nf b/modules/local/starfusion/build/main.nf
@@ -1,7 +1,7 @@
 process STARFUSION_BUILD {
     tag 'star-fusion'
 
-    conda (params.enable_conda ? "bioconda::dfam=3.3 bioconda::hmmer=3.3.2 bioconda::star-fusion=1.10.0 bioconda::trinity=date.2011_11_2 bioconda::samtools=1.9 bioconda::star=2.7.8a" : null)
+    conda "bioconda::dfam=3.3 bioconda::hmmer=3.3.2 bioconda::star-fusion=1.10.0 bioconda::trinity=date.2011_11_2 bioconda::samtools=1.9 bioconda::star=2.7.8a"
     container "docker.io/trinityctat/starfusion:1.10.1"
 
     input:

diff --git a/modules/local/starfusion/detect/main.nf b/modules/local/starfusion/detect/main.nf
@@ -2,7 +2,7 @@ process STARFUSION {
     tag "$meta.id"
     label 'process_high'
 
-    conda (params.enable_conda ? "bioconda::dfam=3.3 bioconda::hmmer=3.3.2 bioconda::star-fusion=1.10.0 bioconda::trinity=date.2011_11_2 bioconda::samtools=1.9 bioconda::star=2.7.8a" : null)
+    conda "bioconda::dfam=3.3 bioconda::hmmer=3.3.2 bioconda::star-fusion=1.10.0 bioconda::trinity=date.2011_11_2 bioconda::samtools=1.9 bioconda::star=2.7.8a" 
     container "docker.io/trinityctat/starfusion:1.10.1"
 
     input:

diff --git a/modules/local/starfusion/download/main.nf b/modules/local/starfusion/download/main.nf
@@ -1,7 +1,7 @@
 process STARFUSION_DOWNLOAD {
     tag 'star-fusion'
 
-    conda (params.enable_conda ? "bioconda::dfam=3.3 bioconda::hmmer=3.3.2 bioconda::star-fusion=1.10.0 bioconda::trinity=date.2011_11_2 bioconda::samtools=1.9 bioconda::star=2.7.8a" : null)
+    conda "bioconda::dfam=3.3 bioconda::hmmer=3.3.2 bioconda::star-fusion=1.10.0 bioconda::trinity=date.2011_11_2 bioconda::samtools=1.9 bioconda::star=2.7.8a"
     container "docker.io/trinityctat/starfusion:1.10.1"
 
     input:

diff --git a/modules/nf-core/arriba/main.nf b/modules/nf-core/arriba/main.nf
diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf
diff --git a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
diff --git a/modules/nf-core/fastp/main.nf b/modules/nf-core/fastp/main.nf
diff --git a/modules/nf-core/fastp/meta.yml b/modules/nf-core/fastp/meta.yml
diff --git a/modules/nf-core/umitools/dedup/main.nf b/modules/nf-core/umitools/dedup/main.nf
diff --git a/modules/nf-core/umitools/dedup/meta.yml b/modules/nf-core/umitools/dedup/meta.yml