From b9172e8c26a3db5009f7872654c44587e254f094 Mon Sep 17 00:00:00 2001
From: Anders Sune Pedersen <37172585+asp8200@users.noreply.github.com>
Date: Thu, 3 Aug 2023 11:09:37 +0200
Subject: [PATCH] Move conda-checks (third batch) (#3692)

Moving conda-check and replacing exit 1 with error-cmd
---
 modules/nf-core/sentieon/applyvarcal/main.nf |  9 ++++-----
 modules/nf-core/sentieon/bwaindex/main.nf    | 13 ++++++++-----
 modules/nf-core/sentieon/bwamem/main.nf      |  9 ++++-----
 modules/nf-core/sentieon/dedup/main.nf       |  9 ++++-----
 modules/nf-core/sentieon/gvcftyper/main.nf   |  9 ++++-----
 modules/nf-core/sentieon/haplotyper/main.nf  |  9 ++++-----
 modules/nf-core/sentieon/varcal/main.nf      |  9 ++++-----
 7 files changed, 32 insertions(+), 35 deletions(-)

diff --git a/modules/nf-core/sentieon/applyvarcal/main.nf b/modules/nf-core/sentieon/applyvarcal/main.nf
index 41630740a74..1dc3883dedb 100644
--- a/modules/nf-core/sentieon/applyvarcal/main.nf
+++ b/modules/nf-core/sentieon/applyvarcal/main.nf
@@ -5,11 +5,6 @@ process SENTIEON_APPLYVARCAL {
 
     secret 'SENTIEON_LICENSE_BASE64'
 
-    // Exit if running this module with -profile conda / -profile mamba
-    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
-        exit 1, "Sentieon modules does not support Conda. Please use Docker / Singularity / Podman instead."
-    }
-
     container 'nf-core/sentieon:202112.06'
 
     input:
@@ -26,6 +21,10 @@ process SENTIEON_APPLYVARCAL {
     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 "Sentieon modules do not support Conda. Please use Docker / Singularity / Podman instead."
+    }
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def sentieon_auth_mech_base64 = task.ext.sentieon_auth_mech_base64 ?: ''
diff --git a/modules/nf-core/sentieon/bwaindex/main.nf b/modules/nf-core/sentieon/bwaindex/main.nf
index 9ddd68f65c6..a1ebee644fd 100644
--- a/modules/nf-core/sentieon/bwaindex/main.nf
+++ b/modules/nf-core/sentieon/bwaindex/main.nf
@@ -3,11 +3,6 @@ process SENTIEON_BWAINDEX {
     label 'process_high'
     label 'sentieon'
 
-    // Exit if running this module with -profile conda / -profile mamba
-    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
-        exit 1, "Sentieon modules does not support Conda. Please use Docker / Singularity / Podman instead."
-    }
-
     container 'nf-core/sentieon:202112.06'
 
     input:
@@ -21,6 +16,10 @@ process SENTIEON_BWAINDEX {
     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 "Sentieon modules do not support Conda. Please use Docker / Singularity / Podman instead."
+    }
     def args = task.ext.args ?: ''
     """
     mkdir bwa
@@ -39,6 +38,10 @@ process SENTIEON_BWAINDEX {
     """
 
     stub:
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error "Sentieon modules do not support Conda. Please use Docker / Singularity / Podman instead."
+    }
     """
     mkdir bwa
 
diff --git a/modules/nf-core/sentieon/bwamem/main.nf b/modules/nf-core/sentieon/bwamem/main.nf
index fa31b336654..aeca2825609 100644
--- a/modules/nf-core/sentieon/bwamem/main.nf
+++ b/modules/nf-core/sentieon/bwamem/main.nf
@@ -5,11 +5,6 @@ process SENTIEON_BWAMEM {
 
     secret 'SENTIEON_LICENSE_BASE64'
 
-    // Exit if running this module with -profile conda / -profile mamba
-    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
-        exit 1, "Sentieon modules does not support Conda. Please use Docker / Singularity / Podman instead."
-    }
-
     container 'nf-core/sentieon:202112.06'
 
     input:
@@ -26,6 +21,10 @@ process SENTIEON_BWAMEM {
     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 "Sentieon modules do not support Conda. Please use Docker / Singularity / Podman instead."
+    }
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def sentieon_auth_mech_base64 = task.ext.sentieon_auth_mech_base64 ?: ''
diff --git a/modules/nf-core/sentieon/dedup/main.nf b/modules/nf-core/sentieon/dedup/main.nf
index 7f6d1ce7360..faa14fe011f 100644
--- a/modules/nf-core/sentieon/dedup/main.nf
+++ b/modules/nf-core/sentieon/dedup/main.nf
@@ -5,11 +5,6 @@ process SENTIEON_DEDUP {
 
     secret 'SENTIEON_LICENSE_BASE64'
 
-    // Exit if running this module with -profile conda / -profile mamba
-    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
-        exit 1, "Sentieon modules does not support Conda. Please use Docker / Singularity / Podman instead."
-    }
-
     container 'nf-core/sentieon:202112.06'
 
     input:
@@ -31,6 +26,10 @@ process SENTIEON_DEDUP {
     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 "Sentieon modules do not support Conda. Please use Docker / Singularity / Podman instead."
+    }
     def args = task.ext.args ?: ''
     def args2 = task.ext.args2 ?: ''
     def args3 = task.ext.args3 ?: ''
diff --git a/modules/nf-core/sentieon/gvcftyper/main.nf b/modules/nf-core/sentieon/gvcftyper/main.nf
index 5f50e47c0b4..a8ece7ba930 100644
--- a/modules/nf-core/sentieon/gvcftyper/main.nf
+++ b/modules/nf-core/sentieon/gvcftyper/main.nf
@@ -5,11 +5,6 @@ process SENTIEON_GVCFTYPER {
 
     secret 'SENTIEON_LICENSE_BASE64'
 
-    // Exit if running this module with -profile conda / -profile mamba
-    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
-        exit 1, "Sentieon modules does not support Conda. Please use Docker / Singularity / Podman instead."
-    }
-
     container 'nf-core/sentieon:202112.06'
 
     input:
@@ -28,6 +23,10 @@ process SENTIEON_GVCFTYPER {
     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 "Sentieon modules do not support Conda. Please use Docker / Singularity / Podman instead."
+    }
     def prefix = task.ext.prefix ?: "${meta.id}"
     def sentieon_auth_mech_base64 = task.ext.sentieon_auth_mech_base64 ?: ''
     def sentieon_auth_data_base64 = task.ext.sentieon_auth_data_base64 ?: ''
diff --git a/modules/nf-core/sentieon/haplotyper/main.nf b/modules/nf-core/sentieon/haplotyper/main.nf
index f913526a1c2..f83a1371221 100644
--- a/modules/nf-core/sentieon/haplotyper/main.nf
+++ b/modules/nf-core/sentieon/haplotyper/main.nf
@@ -5,11 +5,6 @@ process SENTIEON_HAPLOTYPER {
 
     secret 'SENTIEON_LICENSE_BASE64'
 
-    // Exit if running this module with -profile conda / -profile mamba
-    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
-        exit 1, "Sentieon modules does not support Conda. Please use Docker / Singularity / Podman instead."
-    }
-
     container 'nf-core/sentieon:202112.06'
 
     input:
@@ -32,6 +27,10 @@ process SENTIEON_HAPLOTYPER {
     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 "Sentieon modules do not support Conda. Please use Docker / Singularity / Podman instead."
+    }
     def args = task.ext.args ?: ''    // options for the driver
     def args2 = task.ext.args2 ?: ''  // options for the vcf generation
     def args3 = task.ext.args3 ?: ''  // options for the gvcf generation
diff --git a/modules/nf-core/sentieon/varcal/main.nf b/modules/nf-core/sentieon/varcal/main.nf
index 8a001587421..81820e03284 100644
--- a/modules/nf-core/sentieon/varcal/main.nf
+++ b/modules/nf-core/sentieon/varcal/main.nf
@@ -5,11 +5,6 @@ process SENTIEON_VARCAL {
 
     secret 'SENTIEON_LICENSE_BASE64'
 
-    // Exit if running this module with -profile conda / -profile mamba
-    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
-        exit 1, "Sentieon modules does not support Conda. Please use Docker / Singularity / Podman instead."
-    }
-
     container 'nf-core/sentieon:202112.06'
 
     input:
@@ -31,6 +26,10 @@ process SENTIEON_VARCAL {
     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 "Sentieon modules do not support Conda. Please use Docker / Singularity / Podman instead."
+    }
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def reference_command = fasta ? "--reference $fasta " : ''