From 2326b7ef4ab9c5cc01924eeb00f94ee2cc820f79 Mon Sep 17 00:00:00 2001
From: daniel <d4straub@gmail.com>
Date: Tue, 7 Nov 2023 14:44:57 +0100
Subject: [PATCH] move conda check to script section

---
 CHANGELOG.md                               | 2 ++
 modules/local/qiime2_alphararefaction.nf   | 9 ++++-----
 modules/local/qiime2_ancom_asv.nf          | 9 ++++-----
 modules/local/qiime2_ancom_tax.nf          | 9 ++++-----
 modules/local/qiime2_barplot.nf            | 9 ++++-----
 modules/local/qiime2_classify.nf           | 9 ++++-----
 modules/local/qiime2_diversity_adonis.nf   | 9 ++++-----
 modules/local/qiime2_diversity_alpha.nf    | 9 ++++-----
 modules/local/qiime2_diversity_beta.nf     | 9 ++++-----
 modules/local/qiime2_diversity_betaord.nf  | 9 ++++-----
 modules/local/qiime2_diversity_core.nf     | 9 ++++-----
 modules/local/qiime2_export_absolute.nf    | 9 ++++-----
 modules/local/qiime2_export_relasv.nf      | 9 ++++-----
 modules/local/qiime2_export_reltax.nf      | 9 ++++-----
 modules/local/qiime2_extract.nf            | 9 ++++-----
 modules/local/qiime2_featuretable_group.nf | 9 ++++-----
 modules/local/qiime2_filtersamples.nf      | 9 ++++-----
 modules/local/qiime2_filtertaxa.nf         | 9 ++++-----
 modules/local/qiime2_inasv.nf              | 9 ++++-----
 modules/local/qiime2_inseq.nf              | 9 ++++-----
 modules/local/qiime2_intax.nf              | 9 ++++-----
 modules/local/qiime2_intree.nf             | 9 ++++-----
 modules/local/qiime2_train.nf              | 9 ++++-----
 modules/local/qiime2_tree.nf               | 9 ++++-----
 24 files changed, 94 insertions(+), 115 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index ddb0e72c..c9381a95 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -11,6 +11,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Fixed`
 
+- [#656](https://github.com/nf-core/ampliseq/pull/656) - Moved conda-check to script-section and replaced `exit 1` with `error()`
+
 ### `Dependencies`
 
 ### `Removed`
diff --git a/modules/local/qiime2_alphararefaction.nf b/modules/local/qiime2_alphararefaction.nf
index 273749ba..44319b94 100644
--- a/modules/local/qiime2_alphararefaction.nf
+++ b/modules/local/qiime2_alphararefaction.nf
@@ -3,11 +3,6 @@ process QIIME2_ALPHARAREFACTION {
 
     container "qiime2/core:2023.7"
 
-    // Exit if running this module with -profile conda / -profile mamba
-    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
-        exit 1, "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead."
-    }
-
     input:
     path(metadata)
     path(table)
@@ -22,6 +17,10 @@ process QIIME2_ALPHARAREFACTION {
     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 "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
     """
     export XDG_CONFIG_HOME="\${PWD}/HOME"
 
diff --git a/modules/local/qiime2_ancom_asv.nf b/modules/local/qiime2_ancom_asv.nf
index 52c599c4..54ccd6c4 100644
--- a/modules/local/qiime2_ancom_asv.nf
+++ b/modules/local/qiime2_ancom_asv.nf
@@ -7,11 +7,6 @@ process QIIME2_ANCOM_ASV {
 
     container "qiime2/core:2023.7"
 
-    // Exit if running this module with -profile conda / -profile mamba
-    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
-        exit 1, "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead."
-    }
-
     input:
     tuple path(metadata), path(table)
 
@@ -23,6 +18,10 @@ process QIIME2_ANCOM_ASV {
     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 "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
     """
     export XDG_CONFIG_HOME="\${PWD}/HOME"
 
diff --git a/modules/local/qiime2_ancom_tax.nf b/modules/local/qiime2_ancom_tax.nf
index 3c065bb3..91567c0e 100644
--- a/modules/local/qiime2_ancom_tax.nf
+++ b/modules/local/qiime2_ancom_tax.nf
@@ -5,11 +5,6 @@ process QIIME2_ANCOM_TAX {
 
     container "qiime2/core:2023.7"
 
-    // Exit if running this module with -profile conda / -profile mamba
-    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
-        exit 1, "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead."
-    }
-
     input:
     tuple path(metadata), path(table), path(taxonomy) ,val(taxlevel)
 
@@ -21,6 +16,10 @@ process QIIME2_ANCOM_TAX {
     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 "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
     """
     export XDG_CONFIG_HOME="\${PWD}/HOME"
     mkdir ancom
diff --git a/modules/local/qiime2_barplot.nf b/modules/local/qiime2_barplot.nf
index a06100d4..d66ef4ee 100644
--- a/modules/local/qiime2_barplot.nf
+++ b/modules/local/qiime2_barplot.nf
@@ -3,11 +3,6 @@ process QIIME2_BARPLOT {
 
     container "qiime2/core:2023.7"
 
-    // Exit if running this module with -profile conda / -profile mamba
-    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
-        exit 1, "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead."
-    }
-
     input:
     path(metadata)
     path(table)
@@ -22,6 +17,10 @@ process QIIME2_BARPLOT {
     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 "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
     suffix = setting ? "_${table.baseName}" : ""
     def metadata_cmd = metadata ? "--m-metadata-file ${metadata}": ""
     """
diff --git a/modules/local/qiime2_classify.nf b/modules/local/qiime2_classify.nf
index 96910c9a..d7cf1929 100644
--- a/modules/local/qiime2_classify.nf
+++ b/modules/local/qiime2_classify.nf
@@ -4,11 +4,6 @@ process QIIME2_CLASSIFY {
 
     container "qiime2/core:2023.7"
 
-    // Exit if running this module with -profile conda / -profile mamba
-    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
-        exit 1, "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead."
-    }
-
     input:
     path(trained_classifier)
     path(repseq)
@@ -22,6 +17,10 @@ process QIIME2_CLASSIFY {
     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 "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
     """
     export XDG_CONFIG_HOME="\${PWD}/HOME"
 
diff --git a/modules/local/qiime2_diversity_adonis.nf b/modules/local/qiime2_diversity_adonis.nf
index 6b81f00e..24b7afe8 100644
--- a/modules/local/qiime2_diversity_adonis.nf
+++ b/modules/local/qiime2_diversity_adonis.nf
@@ -4,11 +4,6 @@ process QIIME2_DIVERSITY_ADONIS {
 
     container "qiime2/core:2023.7"
 
-    // Exit if running this module with -profile conda / -profile mamba
-    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
-        exit 1, "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead."
-    }
-
     input:
     tuple path(metadata), path(core), val(formula)
 
@@ -20,6 +15,10 @@ process QIIME2_DIVERSITY_ADONIS {
     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 "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
     def args = task.ext.args ?: ''
     """
     export XDG_CONFIG_HOME="\${PWD}/HOME"
diff --git a/modules/local/qiime2_diversity_alpha.nf b/modules/local/qiime2_diversity_alpha.nf
index baebc03e..237c9664 100644
--- a/modules/local/qiime2_diversity_alpha.nf
+++ b/modules/local/qiime2_diversity_alpha.nf
@@ -4,11 +4,6 @@ process QIIME2_DIVERSITY_ALPHA {
 
     container "qiime2/core:2023.7"
 
-    // Exit if running this module with -profile conda / -profile mamba
-    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
-        exit 1, "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead."
-    }
-
     input:
     tuple path(metadata), path(core)
 
@@ -20,6 +15,10 @@ process QIIME2_DIVERSITY_ALPHA {
     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 "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
     """
     export XDG_CONFIG_HOME="\${PWD}/HOME"
 
diff --git a/modules/local/qiime2_diversity_beta.nf b/modules/local/qiime2_diversity_beta.nf
index 44df25f9..dbc6cd18 100644
--- a/modules/local/qiime2_diversity_beta.nf
+++ b/modules/local/qiime2_diversity_beta.nf
@@ -4,11 +4,6 @@ process QIIME2_DIVERSITY_BETA {
 
     container "qiime2/core:2023.7"
 
-    // Exit if running this module with -profile conda / -profile mamba
-    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
-        exit 1, "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead."
-    }
-
     input:
     tuple path(metadata), path(core), val(category)
 
@@ -20,6 +15,10 @@ process QIIME2_DIVERSITY_BETA {
     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 "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
     """
     export XDG_CONFIG_HOME="\${PWD}/HOME"
 
diff --git a/modules/local/qiime2_diversity_betaord.nf b/modules/local/qiime2_diversity_betaord.nf
index b29bd99e..3c199740 100644
--- a/modules/local/qiime2_diversity_betaord.nf
+++ b/modules/local/qiime2_diversity_betaord.nf
@@ -4,11 +4,6 @@ process QIIME2_DIVERSITY_BETAORD {
 
     container "qiime2/core:2023.7"
 
-    // Exit if running this module with -profile conda / -profile mamba
-    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
-        exit 1, "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead."
-    }
-
     input:
     tuple path(metadata), path(core)
 
@@ -20,6 +15,10 @@ process QIIME2_DIVERSITY_BETAORD {
     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 "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
     """
     export XDG_CONFIG_HOME="\${PWD}/HOME"
     mkdir beta_diversity
diff --git a/modules/local/qiime2_diversity_core.nf b/modules/local/qiime2_diversity_core.nf
index 22235dfb..c1866ead 100644
--- a/modules/local/qiime2_diversity_core.nf
+++ b/modules/local/qiime2_diversity_core.nf
@@ -3,11 +3,6 @@ process QIIME2_DIVERSITY_CORE {
 
     container "qiime2/core:2023.7"
 
-    // Exit if running this module with -profile conda / -profile mamba
-    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
-        exit 1, "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead."
-    }
-
     input:
     path(metadata)
     path(table)
@@ -26,6 +21,10 @@ process QIIME2_DIVERSITY_CORE {
     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 "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
     """
     # FIX: detecting a viable GPU on your system, but the GPU is unavailable for compute, causing UniFrac to fail.
     # COMMENT: might be fixed in version after QIIME2 2023.5
diff --git a/modules/local/qiime2_export_absolute.nf b/modules/local/qiime2_export_absolute.nf
index 57c03a5e..75fe7f09 100644
--- a/modules/local/qiime2_export_absolute.nf
+++ b/modules/local/qiime2_export_absolute.nf
@@ -3,11 +3,6 @@ process QIIME2_EXPORT_ABSOLUTE {
 
     container "qiime2/core:2023.7"
 
-    // Exit if running this module with -profile conda / -profile mamba
-    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
-        exit 1, "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead."
-    }
-
     input:
     path(table)
     path(repseq)
@@ -28,6 +23,10 @@ process QIIME2_EXPORT_ABSOLUTE {
     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 "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
     """
     export XDG_CONFIG_HOME="\${PWD}/HOME"
 
diff --git a/modules/local/qiime2_export_relasv.nf b/modules/local/qiime2_export_relasv.nf
index 58e05b58..c9e0b139 100644
--- a/modules/local/qiime2_export_relasv.nf
+++ b/modules/local/qiime2_export_relasv.nf
@@ -3,11 +3,6 @@ process QIIME2_EXPORT_RELASV {
 
     container "qiime2/core:2023.7"
 
-    // Exit if running this module with -profile conda / -profile mamba
-    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
-        exit 1, "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead."
-    }
-
     input:
     path(table)
 
@@ -19,6 +14,10 @@ process QIIME2_EXPORT_RELASV {
     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 "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
     """
     export XDG_CONFIG_HOME="\${PWD}/HOME"
 
diff --git a/modules/local/qiime2_export_reltax.nf b/modules/local/qiime2_export_reltax.nf
index c5b93d7c..f8849ed3 100644
--- a/modules/local/qiime2_export_reltax.nf
+++ b/modules/local/qiime2_export_reltax.nf
@@ -3,11 +3,6 @@ process QIIME2_EXPORT_RELTAX {
 
     container "qiime2/core:2023.7"
 
-    // Exit if running this module with -profile conda / -profile mamba
-    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
-        exit 1, "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead."
-    }
-
     input:
     path(table)
     path(taxonomy)
@@ -22,6 +17,10 @@ process QIIME2_EXPORT_RELTAX {
     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 "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
     """
     export XDG_CONFIG_HOME="\${PWD}/HOME"
 
diff --git a/modules/local/qiime2_extract.nf b/modules/local/qiime2_extract.nf
index 6889befb..3ba5a99c 100644
--- a/modules/local/qiime2_extract.nf
+++ b/modules/local/qiime2_extract.nf
@@ -5,11 +5,6 @@ process QIIME2_EXTRACT {
 
     container "qiime2/core:2023.7"
 
-    // Exit if running this module with -profile conda / -profile mamba
-    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
-        exit 1, "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead."
-    }
-
     input:
     tuple val(meta), path(database)
 
@@ -21,6 +16,10 @@ process QIIME2_EXTRACT {
     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 "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
     """
     export XDG_CONFIG_HOME="\${PWD}/HOME"
 
diff --git a/modules/local/qiime2_featuretable_group.nf b/modules/local/qiime2_featuretable_group.nf
index d47ee14f..11f74f94 100644
--- a/modules/local/qiime2_featuretable_group.nf
+++ b/modules/local/qiime2_featuretable_group.nf
@@ -4,11 +4,6 @@ process QIIME2_FEATURETABLE_GROUP {
 
     container "qiime2/core:2023.7"
 
-    // Exit if running this module with -profile conda / -profile mamba
-    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
-        exit 1, "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead."
-    }
-
     input:
     tuple path(table), path(metadata), val(category)
 
@@ -20,6 +15,10 @@ process QIIME2_FEATURETABLE_GROUP {
     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 "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
     """
     export XDG_CONFIG_HOME="\${PWD}/HOME"
 
diff --git a/modules/local/qiime2_filtersamples.nf b/modules/local/qiime2_filtersamples.nf
index 7f64e7e2..c4bad400 100644
--- a/modules/local/qiime2_filtersamples.nf
+++ b/modules/local/qiime2_filtersamples.nf
@@ -4,11 +4,6 @@ process QIIME2_FILTERSAMPLES {
 
     container "qiime2/core:2023.7"
 
-    // Exit if running this module with -profile conda / -profile mamba
-    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
-        exit 1, "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead."
-    }
-
     input:
     tuple path(metadata), path(table), val(filter)
 
@@ -20,6 +15,10 @@ process QIIME2_FILTERSAMPLES {
     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 "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
     def args = task.ext.args ?: "--p-where \'${filter}<>\"\"\'"
     def prefix = task.ext.prefix ?: "${filter}"
     """
diff --git a/modules/local/qiime2_filtertaxa.nf b/modules/local/qiime2_filtertaxa.nf
index 39cbb82c..4ffb0fa9 100644
--- a/modules/local/qiime2_filtertaxa.nf
+++ b/modules/local/qiime2_filtertaxa.nf
@@ -4,11 +4,6 @@ process QIIME2_FILTERTAXA {
 
     container "qiime2/core:2023.7"
 
-    // Exit if running this module with -profile conda / -profile mamba
-    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
-        exit 1, "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead."
-    }
-
     input:
     path(table)
     path(repseq)
@@ -27,6 +22,10 @@ process QIIME2_FILTERTAXA {
     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 "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
     """
     export XDG_CONFIG_HOME="\${PWD}/HOME"
 
diff --git a/modules/local/qiime2_inasv.nf b/modules/local/qiime2_inasv.nf
index d4848ba7..28a44821 100644
--- a/modules/local/qiime2_inasv.nf
+++ b/modules/local/qiime2_inasv.nf
@@ -4,11 +4,6 @@ process QIIME2_INASV {
 
     container "qiime2/core:2023.7"
 
-    // Exit if running this module with -profile conda / -profile mamba
-    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
-        exit 1, "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead."
-    }
-
     input:
     path(asv)
 
@@ -20,6 +15,10 @@ process QIIME2_INASV {
     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 "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
     """
     # remove first line if needed
     sed '/^# Constructed from biom file/d' "$asv" > biom-table.txt
diff --git a/modules/local/qiime2_inseq.nf b/modules/local/qiime2_inseq.nf
index 7c7c2007..fbb3eecb 100644
--- a/modules/local/qiime2_inseq.nf
+++ b/modules/local/qiime2_inseq.nf
@@ -4,11 +4,6 @@ process QIIME2_INSEQ {
 
     container "qiime2/core:2023.7"
 
-    // Exit if running this module with -profile conda / -profile mamba
-    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
-        exit 1, "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead."
-    }
-
     input:
     path(seq)
 
@@ -20,6 +15,10 @@ process QIIME2_INSEQ {
     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 "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
     """
     qiime tools import \\
         --input-path "$seq" \\
diff --git a/modules/local/qiime2_intax.nf b/modules/local/qiime2_intax.nf
index b9c3b039..42715945 100644
--- a/modules/local/qiime2_intax.nf
+++ b/modules/local/qiime2_intax.nf
@@ -4,11 +4,6 @@ process QIIME2_INTAX {
 
     container "qiime2/core:2023.7"
 
-    // Exit if running this module with -profile conda / -profile mamba
-    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
-        exit 1, "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead."
-    }
-
     input:
     path(tax) //ASV_tax_species.tsv
     val(script)
@@ -21,6 +16,10 @@ process QIIME2_INTAX {
     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 "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
     def script_cmd = script ? "$script $tax" : "cp $tax tax.tsv"
     """
     $script_cmd
diff --git a/modules/local/qiime2_intree.nf b/modules/local/qiime2_intree.nf
index a7a3ff3b..3e13879c 100644
--- a/modules/local/qiime2_intree.nf
+++ b/modules/local/qiime2_intree.nf
@@ -4,11 +4,6 @@ process QIIME2_INTREE {
 
     container "qiime2/core:2023.7"
 
-    // Exit if running this module with -profile conda / -profile mamba
-    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
-        exit 1, "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead."
-    }
-
     input:
     tuple val(meta), path(tree)
 
@@ -20,6 +15,10 @@ process QIIME2_INTREE {
     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 "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
     """
     qiime tools import \\
         --type 'Phylogeny[Rooted]' \\
diff --git a/modules/local/qiime2_train.nf b/modules/local/qiime2_train.nf
index 4c4d69b2..d07945c8 100644
--- a/modules/local/qiime2_train.nf
+++ b/modules/local/qiime2_train.nf
@@ -5,11 +5,6 @@ process QIIME2_TRAIN {
 
     container "qiime2/core:2023.7"
 
-    // Exit if running this module with -profile conda / -profile mamba
-    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
-        exit 1, "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead."
-    }
-
     input:
     tuple val(meta), path(qza)
 
@@ -21,6 +16,10 @@ process QIIME2_TRAIN {
     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 "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
     """
     export XDG_CONFIG_HOME="\${PWD}/HOME"
 
diff --git a/modules/local/qiime2_tree.nf b/modules/local/qiime2_tree.nf
index 6e7a89fe..89f30f60 100644
--- a/modules/local/qiime2_tree.nf
+++ b/modules/local/qiime2_tree.nf
@@ -3,11 +3,6 @@ process QIIME2_TREE {
 
     container "qiime2/core:2023.7"
 
-    // Exit if running this module with -profile conda / -profile mamba
-    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
-        exit 1, "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead."
-    }
-
     input:
     path(repseq)
 
@@ -20,6 +15,10 @@ process QIIME2_TREE {
     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 "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
     """
     export XDG_CONFIG_HOME="\${PWD}/HOME"