From ebb27711cd5f4de921244bfa81c676504072d31c Mon Sep 17 00:00:00 2001
From: Anders Sune Pedersen <37172585+asp8200@users.noreply.github.com>
Date: Thu, 10 Aug 2023 18:17:24 +0200
Subject: [PATCH] Move conda-checks (sixth batch) (#3713)

* Moving conda-check and replacing exit 1 with error-cmd

* Disabling conda-based pytests for parabricks modules
---
 .github/workflows/test.yml                   |  4 ++++
 modules/nf-core/merquryfk/ploidyplot/main.nf |  9 ++++-----
 modules/nf-core/mosdepth/main.nf             |  4 ++--
 modules/nf-core/parabricks/applybqsr/main.nf |  9 ++++-----
 modules/nf-core/parabricks/fq2bam/main.nf    | 13 ++++++++-----
 modules/nf-core/scimap/mcmicro/main.nf       |  9 ++++-----
 6 files changed, 26 insertions(+), 22 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 9614aecf774..c10eb0a62e1 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -202,6 +202,10 @@ jobs:
             tags: merquryfk/ploidyplot
           - profile: "conda"
             tags: mitohifi/findmitoreference
+          - profile: "conda"
+            tags: parabricks/applybqsr
+          - profile: "conda"
+            tags: parabricks/fq2bam
           - profile: "conda"
             tags: scimap/mcmicro
           - profile: "conda"
diff --git a/modules/nf-core/merquryfk/ploidyplot/main.nf b/modules/nf-core/merquryfk/ploidyplot/main.nf
index 7103dda364b..f408292ed2c 100644
--- a/modules/nf-core/merquryfk/ploidyplot/main.nf
+++ b/modules/nf-core/merquryfk/ploidyplot/main.nf
@@ -5,11 +5,6 @@ process MERQURYFK_PLOIDYPLOT {
     // 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, "MERQURYFK_PLOIDYPLOT module does not support Conda. Please use Docker / Singularity / Podman instead."
-    }
-
     input:
     tuple val(meta), path(fastk_hist), path(fastk_ktab)
 
@@ -26,6 +21,10 @@ process MERQURYFK_PLOIDYPLOT {
     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 "MERQURYFK_PLOIDYPLOT 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/mosdepth/main.nf b/modules/nf-core/mosdepth/main.nf
index c17e4e658ee..74db3a274b3 100644
--- a/modules/nf-core/mosdepth/main.nf
+++ b/modules/nf-core/mosdepth/main.nf
@@ -35,10 +35,10 @@ process MOSDEPTH {
     def reference = fasta ? "--fasta ${fasta}" : ""
     def interval = bed ? "--by ${bed}" : ""
     if (bed && args.contains("--by")) {
-        exit 1, "'--by' can only be specified once when running mosdepth! Either remove input BED file definition or remove '--by' from 'ext.args' definition"
+        error "'--by' can only be specified once when running mosdepth! Either remove input BED file definition or remove '--by' from 'ext.args' definition"
     }
     if (!bed && args.contains("--thresholds")) {
-        exit 1, "'--thresholds' can only be specified in conjunction with '--by'"
+        error "'--thresholds' can only be specified in conjunction with '--by'"
     }
 
     """
diff --git a/modules/nf-core/parabricks/applybqsr/main.nf b/modules/nf-core/parabricks/applybqsr/main.nf
index 3ebf5926b6a..48696bc1bed 100644
--- a/modules/nf-core/parabricks/applybqsr/main.nf
+++ b/modules/nf-core/parabricks/applybqsr/main.nf
@@ -2,11 +2,6 @@ process PARABRICKS_APPLYBQSR {
     tag "$meta.id"
     label 'process_high'
 
-    // Exit if running this module with -profile conda / -profile mamba
-    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
-        exit 1, "Parabricks module does not support Conda. Please use Docker / Singularity / Podman instead."
-    }
-
     container "nvcr.io/nvidia/clara/clara-parabricks:4.0.1-1"
 
     input:
@@ -22,6 +17,10 @@ process PARABRICKS_APPLYBQSR {
     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 "Parabricks module does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def interval_command = intervals ? intervals.collect{"--interval-file $it"}.join(' ') : ""
diff --git a/modules/nf-core/parabricks/fq2bam/main.nf b/modules/nf-core/parabricks/fq2bam/main.nf
index c63e3b4e292..01a7ba1f87d 100644
--- a/modules/nf-core/parabricks/fq2bam/main.nf
+++ b/modules/nf-core/parabricks/fq2bam/main.nf
@@ -2,11 +2,6 @@ process PARABRICKS_FQ2BAM {
     tag "$meta.id"
     label 'process_high'
 
-    // Exit if running this module with -profile conda / -profile mamba
-    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
-        exit 1, "Parabricks module does not support Conda. Please use Docker / Singularity / Podman instead."
-    }
-
     container "nvcr.io/nvidia/clara/clara-parabricks:4.0.1-1"
 
     input:
@@ -27,6 +22,10 @@ process PARABRICKS_FQ2BAM {
     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 "Parabricks module does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def in_fq_command = meta.single_end ? "--in-se-fq $reads" : "--in-fq $reads"
@@ -65,6 +64,10 @@ process PARABRICKS_FQ2BAM {
     """
 
     stub:
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error "Parabricks module does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def in_fq_command = meta.single_end ? "--in-se-fq $reads" : "--in-fq $reads"
diff --git a/modules/nf-core/scimap/mcmicro/main.nf b/modules/nf-core/scimap/mcmicro/main.nf
index e344deda083..c8ff4cec03f 100644
--- a/modules/nf-core/scimap/mcmicro/main.nf
+++ b/modules/nf-core/scimap/mcmicro/main.nf
@@ -2,11 +2,6 @@ process SCIMAP_MCMICRO {
     tag "$meta.id"
     label 'process_single'
 
-    // Exit if running this module with -profile conda / -profile mamba
-    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
-        exit 1, "Scimap module does not support Conda. Please use Docker / Singularity / Podman instead."
-    }
-
     container "docker.io/labsyspharm/scimap:0.22.0"
 
     input:
@@ -21,6 +16,10 @@ process SCIMAP_MCMICRO {
     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 "Scimap module does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def VERSION='0.22.0' // WARN: Version information not provided by tool on CLI. Please update this string when bumping