Move conda-checks (sixth batch) (nf-core#3713)

* Moving conda-check and replacing exit 1 with error-cmd * Disabling conda-based pytests for parabricks modules
asp8200 · Aug 10, 2023 · ebb2771 · ebb2771
1 parent b28e4dd
commit ebb2771
Show file tree

Hide file tree

Showing 6 changed files with 26 additions and 22 deletions.
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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