Move conda-checks (second batch) (nf-core#3690)

Moving conda-check and replacing exit 1 with error-cmd Ignoring linting errors due to GHCR - will be fixed later.
asp8200 · Aug 3, 2023 · ed67f2f · ed67f2f
1 parent b9172e8
commit ed67f2f
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Showing 5 changed files with 28 additions and 25 deletions.
diff --git a/modules/nf-core/cellranger/multi/main.nf b/modules/nf-core/cellranger/multi/main.nf
@@ -4,11 +4,6 @@ process CELLRANGER_MULTI {
 
     container "nf-core/cellranger:7.1.0"
 
-    // Exit if running this module with -profile conda / -profile mamba
-    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
-        exit 1, "CELLRANGER_MULTI module does not support Conda. Please use Docker / Singularity / Podman instead."
-    }
-
     input:
     val meta
     tuple val(meta_gex)        , path (gex_fastqs   , stageAs: "fastqs/gex/*")
@@ -38,6 +33,10 @@ process CELLRANGER_MULTI {
     task.ext.when == null || task.ext.when
 
     script:
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error "CELLRANGER_MULTI module does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
     def args   = task.ext.args   ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
 

diff --git a/modules/nf-core/cellranger/vdj/main.nf b/modules/nf-core/cellranger/vdj/main.nf
@@ -4,11 +4,6 @@ process CELLRANGER_VDJ {
 
     container "nf-core/cellranger:7.1.0"
 
-    // Exit if running this module with -profile conda / -profile mamba
-    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
-        exit 1, "CELLRANGER_VDJ module does not support Conda. Please use Docker / Singularity / Podman instead."
-    }
-
     input:
     tuple val(meta), path(reads)
     path  reference
@@ -21,6 +16,10 @@ process CELLRANGER_VDJ {
     task.ext.when == null || task.ext.when
 
     script:
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error "CELLRANGER_VDJ module does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def reference_name = reference.name
@@ -41,6 +40,10 @@ process CELLRANGER_VDJ {
     """
 
     stub:
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error "CELLRANGER_VDJ module does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     mkdir -p "${meta.id}/outs/"

diff --git a/modules/nf-core/deepvariant/main.nf b/modules/nf-core/deepvariant/main.nf
@@ -4,11 +4,6 @@ process DEEPVARIANT {
 
     container "nf-core/deepvariant:1.5.0"
 
-    // Exit if running this module with -profile conda / -profile mamba
-    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
-        exit 1, "DEEPVARIANT module does not support Conda. Please use Docker / Singularity / Podman instead."
-    }
-
     input:
     tuple val(meta), path(input), path(index), path(intervals)
     tuple val(meta2), path(fasta)
@@ -26,6 +21,10 @@ process DEEPVARIANT {
     task.ext.when == null || task.ext.when
 
     script:
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error "DEEPVARIANT module does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
     def args = task.ext.args ?: ''
     prefix = task.ext.prefix ?: "${meta.id}"
     def regions = intervals ? "--regions=${intervals}" : ""
@@ -48,6 +47,10 @@ process DEEPVARIANT {
     """
 
     stub:
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error "DEEPVARIANT module does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
     prefix = task.ext.prefix ?: "${meta.id}"
     """
     touch ${prefix}.vcf.gz

diff --git a/modules/nf-core/fastk/fastk/main.nf b/modules/nf-core/fastk/fastk/main.nf
@@ -5,11 +5,6 @@ process FASTK_FASTK {
     // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     container 'ghcr.io/nbisweden/fastk_genescopefk_merquryfk:1.2'
 
-    // Exit if running this module with -profile conda / -profile mamba
-    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
-        exit 1, "FASTK_FASTK module does not support Conda. Please use Docker / Singularity / Podman instead."
-    }
-
     input:
     tuple val(meta), path(reads)
 
@@ -23,6 +18,10 @@ process FASTK_FASTK {
     task.ext.when == null || task.ext.when
 
     script:
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error "FASTK_FASTK module does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def FASTK_VERSION = 'f18a4e6d2207539f7b84461daebc54530a9559b0' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.

diff --git a/modules/nf-core/fastk/histex/main.nf b/modules/nf-core/fastk/histex/main.nf
@@ -5,11 +5,6 @@ process FASTK_HISTEX {
     // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     container 'ghcr.io/nbisweden/fastk_genescopefk_merquryfk:1.2'
 
-    // Exit if running this module with -profile conda / -profile mamba
-    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
-        exit 1, "FASTK_HISTEX module does not support Conda. Please use Docker / Singularity / Podman instead."
-    }
-
     input:
     tuple val(meta), path(histogram)
 
@@ -21,6 +16,10 @@ process FASTK_HISTEX {
     task.ext.when == null || task.ext.when
 
     script:
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error "FASTK_HISTEX module does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def FASTK_VERSION = 'f18a4e6d2207539f7b84461daebc54530a9559b0' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.