From b76b952b45573d9f6685a08bf7e39deff2030b71 Mon Sep 17 00:00:00 2001
From: Anders Sune Pedersen <37172585+asp8200@users.noreply.github.com>
Date: Wed, 2 Aug 2023 12:47:19 +0200
Subject: [PATCH] Move conda-checks (first batch) (#3686)

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

* Adding conda-check in stub-section

* Adding conda-check in stub-section

* Updating certain md5sums. Ok by Emiller88. Related to https://github.com/nf-core/modules/pull/3558

* Switching from exit 1 to error-cmd and correcting error-msg
---
 modules/nf-core/bases2fastq/main.nf         |  9 ++++-----
 modules/nf-core/basicpy/main.nf             | 13 ++++++++-----
 modules/nf-core/bcl2fastq/main.nf           |  9 ++++-----
 modules/nf-core/bclconvert/main.nf          |  9 ++++-----
 modules/nf-core/cellpose/main.nf            | 12 ++++++++----
 modules/nf-core/cellranger/count/main.nf    | 13 ++++++++-----
 modules/nf-core/cellranger/mkfastq/main.nf  | 13 ++++++++-----
 modules/nf-core/cellranger/mkgtf/main.nf    |  9 ++++-----
 modules/nf-core/cellranger/mkref/main.nf    |  9 ++++-----
 modules/nf-core/cellranger/mkvdjref/main.nf |  9 ++++-----
 tests/modules/nf-core/bases2fastq/test.yml  |  6 +++---
 11 files changed, 59 insertions(+), 52 deletions(-)

diff --git a/modules/nf-core/bases2fastq/main.nf b/modules/nf-core/bases2fastq/main.nf
index c26d9aca9cf..44d83102dec 100644
--- a/modules/nf-core/bases2fastq/main.nf
+++ b/modules/nf-core/bases2fastq/main.nf
@@ -4,11 +4,6 @@ process BASES2FASTQ {
 
     container "nf-core/bases2fastq:1.1.0"
 
-    // Exit if running this module with -profile conda / -profile mamba
-    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
-        exit 1, "BASES2FASTQ module does not support Conda. Please use Docker / Singularity / Podman instead."
-    }
-
     input:
     tuple val(meta), path(run_manifest), path(run_dir)
 
@@ -26,6 +21,10 @@ process BASES2FASTQ {
     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 "BASES2FASTQ module does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def runManifest = run_manifest ? "-r ${run_manifest}" : ""
diff --git a/modules/nf-core/basicpy/main.nf b/modules/nf-core/basicpy/main.nf
index bfebe901ce8..cfcf9ac1ae8 100644
--- a/modules/nf-core/basicpy/main.nf
+++ b/modules/nf-core/basicpy/main.nf
@@ -2,11 +2,6 @@ process BASICPY {
     tag "$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, "Basicpy module does not support Conda. Please use Docker / Singularity instead."
-    }
-
     container "docker.io/yfukai/basicpy-docker-mcmicro:0.2.1"
 
     input:
@@ -20,6 +15,10 @@ process BASICPY {
     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 "Basicpy module does not support Conda. Please use Docker / Singularity instead."
+    }
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def VERSION = "1.0.1" // WARN: Version information not provided by tool on CLI. Please update this string when bumping
@@ -33,6 +32,10 @@ process BASICPY {
     """
 
     stub:
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error "Basicpy module does not support Conda. Please use Docker / Singularity instead."
+    }
     """
     touch ${prefix}.-dfp.tiff
     touch ${prefix}.-dfp.tiff
diff --git a/modules/nf-core/bcl2fastq/main.nf b/modules/nf-core/bcl2fastq/main.nf
index 8bf02ddd8aa..1797bc67c76 100644
--- a/modules/nf-core/bcl2fastq/main.nf
+++ b/modules/nf-core/bcl2fastq/main.nf
@@ -4,11 +4,6 @@ process BCL2FASTQ {
 
     container "nf-core/bcl2fastq:2.20.0.422"
 
-    // Exit if running this module with -profile conda / -profile mamba
-    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
-        exit 1, "BCL2FASTQ module does not support Conda. Please use Docker / Singularity / Podman instead."
-    }
-
     input:
     tuple val(meta), path(samplesheet), path(run_dir)
 
@@ -26,6 +21,10 @@ process BCL2FASTQ {
     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 "BCL2FASTQ module does 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/bclconvert/main.nf b/modules/nf-core/bclconvert/main.nf
index 122950dca9c..2d8b7857df6 100644
--- a/modules/nf-core/bclconvert/main.nf
+++ b/modules/nf-core/bclconvert/main.nf
@@ -4,11 +4,6 @@ process BCLCONVERT {
 
     container "nf-core/bclconvert:4.0.3"
 
-    // Exit if running this module with -profile conda / -profile mamba
-    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
-        exit 1, "BCLCONVERT module does not support Conda. Please use Docker / Singularity / Podman instead."
-    }
-
     input:
     tuple val(meta), path(samplesheet), path(run_dir)
 
@@ -26,6 +21,10 @@ process BCLCONVERT {
     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 "BCLCONVERT module does 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/cellpose/main.nf b/modules/nf-core/cellpose/main.nf
index f0f462e0ff2..a2b2206923a 100644
--- a/modules/nf-core/cellpose/main.nf
+++ b/modules/nf-core/cellpose/main.nf
@@ -2,10 +2,6 @@ process CELLPOSE {
     tag "$meta.id"
     label 'process_medium'
 
-    // Exit if running this module with -profile conda / -profile mamba
-    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
-        exit 1, "I did not manage to create a cellpose module in Conda that works in all OSes. Please use Docker / Singularity / Podman instead."}
-
     container "docker.io/biocontainers/cellpose:2.1.1_cv2"
 
     input:
@@ -20,6 +16,10 @@ process CELLPOSE {
     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 "I did not manage to create a cellpose module in Conda that works in all OSes. Please use Docker / Singularity / Podman instead."
+    }
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def model_command = model ? "--pretrained_model $model" : ""
@@ -38,6 +38,10 @@ process CELLPOSE {
     END_VERSIONS
     """
     stub:
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error "I did not manage to create a cellpose module in Conda that works in all OSes. Please use Docker / Singularity / Podman instead."
+    }
     def prefix = task.ext.prefix ?: "${meta.id}"
     def VERSION = "2.1.1" // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
diff --git a/modules/nf-core/cellranger/count/main.nf b/modules/nf-core/cellranger/count/main.nf
index 0a76cbd4169..d7a191fc721 100644
--- a/modules/nf-core/cellranger/count/main.nf
+++ b/modules/nf-core/cellranger/count/main.nf
@@ -4,11 +4,6 @@ process CELLRANGER_COUNT {
 
     container "nf-core/cellranger:7.1.0"
 
-    // Exit if running this module with -profile conda / -profile mamba
-    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
-        exit 1, "CELLRANGER_COUNT module does not support Conda. Please use Docker / Singularity / Podman instead."
-    }
-
     input:
     tuple val(meta), path(reads, stageAs: "fastq_???/*")
     path  reference
@@ -21,11 +16,19 @@ process CELLRANGER_COUNT {
     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 "CELLRANGER_COUNT module does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
     args = task.ext.args ?: ''
     prefix = task.ext.prefix ?: "${meta.id}"
     template "cellranger_count.py"
 
     stub:
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error "CELLRANGER_COUNT module does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     mkdir -p "${prefix}/outs/"
diff --git a/modules/nf-core/cellranger/mkfastq/main.nf b/modules/nf-core/cellranger/mkfastq/main.nf
index f57780afbf0..7a128edbd0b 100644
--- a/modules/nf-core/cellranger/mkfastq/main.nf
+++ b/modules/nf-core/cellranger/mkfastq/main.nf
@@ -4,11 +4,6 @@ process CELLRANGER_MKFASTQ {
 
     container "docker.io/nfcore/cellrangermkfastq:7.1.0"
 
-    // Exit if running this module with -profile conda / -profile mamba
-    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
-        exit 1, "CELLRANGER_MKFASTQ module does not support Conda. Please use Docker / Singularity / Podman instead."
-    }
-
     input:
     path bcl
     path csv
@@ -21,6 +16,10 @@ process CELLRANGER_MKFASTQ {
     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 "CELLRANGER_MKFASTQ module does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${bcl.getSimpleName()}"
     """
@@ -38,6 +37,10 @@ process CELLRANGER_MKFASTQ {
     """
 
     stub:
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error "CELLRANGER_MKFASTQ module does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
     def prefix = task.ext.prefix ?: "${bcl.getSimpleName()}"
     """
     mkdir -p "${prefix}/outs/fastq_path/"
diff --git a/modules/nf-core/cellranger/mkgtf/main.nf b/modules/nf-core/cellranger/mkgtf/main.nf
index 5411b0fdbfc..e0b0dd67e55 100644
--- a/modules/nf-core/cellranger/mkgtf/main.nf
+++ b/modules/nf-core/cellranger/mkgtf/main.nf
@@ -4,11 +4,6 @@ process CELLRANGER_MKGTF {
 
     container "nf-core/cellranger:7.1.0"
 
-    // Exit if running this module with -profile conda / -profile mamba
-    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
-        exit 1, "CELLRANGER_MKGTF module does not support Conda. Please use Docker / Singularity / Podman instead."
-    }
-
     input:
     path gtf
 
@@ -20,6 +15,10 @@ process CELLRANGER_MKGTF {
     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 "CELLRANGER_MKGTF module does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${gtf.baseName}.filtered"
     """
diff --git a/modules/nf-core/cellranger/mkref/main.nf b/modules/nf-core/cellranger/mkref/main.nf
index b4b9c547369..986891b8e48 100644
--- a/modules/nf-core/cellranger/mkref/main.nf
+++ b/modules/nf-core/cellranger/mkref/main.nf
@@ -4,11 +4,6 @@ process CELLRANGER_MKREF {
 
     container "nf-core/cellranger:7.1.0"
 
-    // Exit if running this module with -profile conda / -profile mamba
-    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
-        exit 1, "CELLRANGER_MKREF module does not support Conda. Please use Docker / Singularity / Podman instead."
-    }
-
     input:
     path fasta
     path gtf
@@ -22,6 +17,10 @@ process CELLRANGER_MKREF {
     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 "CELLRANGER_MKREF module does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
     def args = task.ext.args ?: ''
     """
     cellranger \\
diff --git a/modules/nf-core/cellranger/mkvdjref/main.nf b/modules/nf-core/cellranger/mkvdjref/main.nf
index 6d2ccc3949a..64e877f7e15 100644
--- a/modules/nf-core/cellranger/mkvdjref/main.nf
+++ b/modules/nf-core/cellranger/mkvdjref/main.nf
@@ -4,11 +4,6 @@ process CELLRANGER_MKVDJREF {
 
     container "nf-core/cellranger:7.1.0"
 
-    // Exit if running this module with -profile conda / -profile mamba
-    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
-        exit 1, "CELLRANGER_MKREF module does not support Conda. Please use Docker / Singularity / Podman instead."
-    }
-
     input:
     path fasta
     path gtf
@@ -22,6 +17,10 @@ process CELLRANGER_MKVDJREF {
     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 "CELLRANGER_MKVDJREF module does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
     def args = task.ext.args ?: ''
     """
     cellranger \\
diff --git a/tests/modules/nf-core/bases2fastq/test.yml b/tests/modules/nf-core/bases2fastq/test.yml
index 88fe9c238da..9e2aa9ac129 100644
--- a/tests/modules/nf-core/bases2fastq/test.yml
+++ b/tests/modules/nf-core/bases2fastq/test.yml
@@ -5,14 +5,14 @@
   files:
     - path: output/bases2fastq/output/Bases2Fastq-Sim_QC.html
     - path: output/bases2fastq/output/Metrics.csv
-      md5sum: 0ec6da2b82e191098283474356024abf
+      md5sum: a8094b308b5653071ac029a27733e4a6
     - path: output/bases2fastq/output/RunManifest.json
       md5sum: a07dce8ee25c2a6f9355b677c26b53e2
     - path: output/bases2fastq/output/RunStats.json
     - path: output/bases2fastq/output/UnassignedSequences.csv
       md5sum: 11c1693830ce941b8cfb8d2431a59097
     - path: output/bases2fastq/output/Samples/DefaultSample/DefaultSample_R1.fastq.gz
-      md5sum: 218abc70f61e8e8199a68f83ae836184
+      md5sum: 831c90ea31eff881e825cda691da77ae
     - path: output/bases2fastq/output/Samples/DefaultSample/DefaultSample_R2.fastq.gz
-      md5sum: b95109bfb204daa150b61239d3368ee2
+      md5sum: e6c1f7ec00910ef195ff3d427c7a9f23
     - path: output/bases2fastq/output/Samples/DefaultSample/DefaultSample_stats.json