Move conda check to script section

CHANGELOG.md

@@ -12,6 +12,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### `Fixed`
 
 - [#655](https://github.com/nf-core/ampliseq/pull/655) - Added `NUMBA_CACHE_DIR` to fix downstream analysis with QIIME2 that failed on some systems
+- [#656](https://github.com/nf-core/ampliseq/pull/656) - Moved conda-check to script-section and replaced `exit 1` with `error()`
 
 ### `Dependencies`
 

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="./xdgconfig"
     export MPLCONFIGDIR="./mplconfigdir"

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="./xdgconfig"
     export MPLCONFIGDIR="./mplconfigdir"

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="./xdgconfig"
     export MPLCONFIGDIR="./mplconfigdir"

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}": ""
     """

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="./xdgconfig"
     export MPLCONFIGDIR="./mplconfigdir"

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="./xdgconfig"

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="./xdgconfig"
     export MPLCONFIGDIR="./mplconfigdir"

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="./xdgconfig"
     export MPLCONFIGDIR="./mplconfigdir"

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="./xdgconfig"
     export MPLCONFIGDIR="./mplconfigdir"

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

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="./xdgconfig"
     export MPLCONFIGDIR="./mplconfigdir"

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="./xdgconfig"
     export MPLCONFIGDIR="./mplconfigdir"

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="./xdgconfig"
     export MPLCONFIGDIR="./mplconfigdir"

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="./xdgconfig"
     export MPLCONFIGDIR="./mplconfigdir"

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="./xdgconfig"
     export MPLCONFIGDIR="./mplconfigdir"

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}"
     """

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="./xdgconfig"
     export MPLCONFIGDIR="./mplconfigdir"