prevent execution with conda

nf-core · Mar 18, 2024 · 8575090 · 8575090
1 parent 77e03b1
commit 8575090
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diff --git a/modules/local/sidle_align.nf b/modules/local/sidle_align.nf
@@ -15,6 +15,10 @@ process SIDLE_ALIGN {
     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 "Sidle in QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.region}"
     def primerfw = "${meta.fw_primer}"

diff --git a/modules/local/sidle_dbextract.nf b/modules/local/sidle_dbextract.nf
@@ -17,6 +17,10 @@ process SIDLE_DBEXTRACT {
     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 "Sidle in QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.region}"
     def primerfw = "${meta.fw_primer}"

diff --git a/modules/local/sidle_dbfilt.nf b/modules/local/sidle_dbfilt.nf
@@ -16,6 +16,10 @@ process SIDLE_DBFILT {
     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 "Sidle in QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
     def args = task.ext.args ?: ''
     def args2 = task.ext.args2 ?: ''
     """

diff --git a/modules/local/sidle_dbrecon.nf b/modules/local/sidle_dbrecon.nf
@@ -18,6 +18,10 @@ process SIDLE_DBRECON {
     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 "Sidle in QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
     def args = task.ext.args ?: ''
     def db_input = ""
     // sort the input so that the regions are sorted by sequence

diff --git a/modules/local/sidle_filttax.nf b/modules/local/sidle_filttax.nf
@@ -17,6 +17,10 @@ process SIDLE_FILTTAX {
     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 "Sidle in QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
     """
     #!/usr/bin/env Rscript
 

diff --git a/modules/local/sidle_in.nf b/modules/local/sidle_in.nf
@@ -15,6 +15,10 @@ process SIDLE_IN {
     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 "Sidle in QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.region}"
     """

diff --git a/modules/local/sidle_indb.nf b/modules/local/sidle_indb.nf
@@ -16,6 +16,10 @@ process SIDLE_INDB {
     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 "Sidle in QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
     """
     export XDG_CONFIG_HOME="./xdgconfig"
     export MPLCONFIGDIR="./mplconfigdir"

diff --git a/modules/local/sidle_indbaligned.nf b/modules/local/sidle_indbaligned.nf
@@ -14,6 +14,10 @@ process SIDLE_INDBALIGNED {
     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 "Sidle in QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
     def args = task.ext.args ?: ''
     """
     export XDG_CONFIG_HOME="./xdgconfig"

diff --git a/modules/local/sidle_seqrecon.nf b/modules/local/sidle_seqrecon.nf
@@ -19,6 +19,10 @@ process SIDLE_SEQRECON {
     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 "Sidle in QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
     """
     #https://q2-sidle.readthedocs.io/en/latest/reconstruction.html#reconstructing-the-phylogenetic-tree
     #https://forum.qiime2.org/t/sidle-tutorial-missing-aligned-sequence-file/20604/4 for db_aligned_sequences

diff --git a/modules/local/sidle_tablerecon.nf b/modules/local/sidle_tablerecon.nf
@@ -21,6 +21,10 @@ process SIDLE_TABLERECON {
     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 "Sidle in QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
     def args = task.ext.args ?: ''
     def region_input = ""
     // sort the input so that the regions are sorted by sequence

diff --git a/modules/local/sidle_taxrecon.nf b/modules/local/sidle_taxrecon.nf
@@ -17,6 +17,10 @@ process SIDLE_TAXRECON {
     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 "Sidle in QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
     def args = task.ext.args ?: ''
     """
     #https://q2-sidle.readthedocs.io/en/latest/reconstruction.html#taxonomic-reconstruction

diff --git a/modules/local/sidle_treerecon.nf b/modules/local/sidle_treerecon.nf
@@ -17,6 +17,10 @@ process SIDLE_TREERECON {
     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 "Sidle in QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
     """
     # https://q2-sidle.readthedocs.io/en/latest/reconstruction.html#reconstructing-the-phylogenetic-tree
     # required: SEPP file https://forum.qiime2.org/t/sidle-tutorial-missing-aligned-sequence-file/20604/8

diff --git a/modules/local/sidle_trim.nf b/modules/local/sidle_trim.nf
@@ -16,6 +16,10 @@ process SIDLE_TRIM {
     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 "Sidle in QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.region}"
     def primerfw = "${meta.fw_primer}"