From 3bd057bfdfb64578636ff3ae7f7cb8eeab3c0cb6 Mon Sep 17 00:00:00 2001
From: Erik Fasterius <erik.fasterius@outlook.com>
Date: Mon, 15 Jan 2024 12:44:16 +0100
Subject: [PATCH] Change Space Ranger count module publishDir (#4675)

* Emit `outs/` directory without sample ID prefix

Emit the `outs/` directory instead of `${meta.id}/outs/`. This allows
pipelines utilising this module to configure the publish directory in
their respective `modules.config` instead of having the sample ID
hard-coded to be included.

This is useful when one would like the output to be something like
`${meta.id}/spaceranger/outs` (i.e. adding optional paths between
`${meta.id}` and `outs/`), as that type of path adheres to the
`results/{SOFTWARE/CONTEXT}/` output pattern commonly used elsewhere in
nf-core.

* Harmonise Space Ranger naming throughout module

* Update test paths

* Update licence formatting

* Add empty `dependencies:` environment entry

* Revert "Add empty `dependencies:` environment entry"

This reverts commit e67a233592a57eaeeaf449bd003d32125f7ff0f5.

* Remove Conda environment files

Remove the Conda `environment.yml` files, which are not needed as the
module cannot use Conda.
---
 modules/nf-core/spaceranger/count/main.nf  | 8 ++++----
 modules/nf-core/spaceranger/count/meta.yml | 8 ++++----
 modules/nf-core/spaceranger/mkgtf/meta.yml | 2 +-
 modules/nf-core/spaceranger/mkref/meta.yml | 4 ++--
 4 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/modules/nf-core/spaceranger/count/main.nf b/modules/nf-core/spaceranger/count/main.nf
index c0f10e591f9..cac83e0e33e 100644
--- a/modules/nf-core/spaceranger/count/main.nf
+++ b/modules/nf-core/spaceranger/count/main.nf
@@ -10,7 +10,7 @@ process SPACERANGER_COUNT {
     path(probeset)
 
     output:
-    tuple val(meta), path("**/outs/**"), emit: outs
+    tuple val(meta), path("outs/**"), emit: outs
     path "versions.yml", emit: versions
 
     when:
@@ -46,6 +46,7 @@ process SPACERANGER_COUNT {
         $alignment \\
         $slidefile \\
         $args
+    mv ${prefix}/outs outs
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -58,10 +59,9 @@ process SPACERANGER_COUNT {
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
         error "SPACERANGER_COUNT module does not support Conda. Please use Docker / Singularity / Podman instead."
     }
-    def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    mkdir -p "${prefix}/outs/"
-    touch ${prefix}/outs/fake_file.txt
+    mkdir -p outs/
+    touch outs/fake_file.txt
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/spaceranger/count/meta.yml b/modules/nf-core/spaceranger/count/meta.yml
index 123c96c2687..167ac8c8851 100644
--- a/modules/nf-core/spaceranger/count/meta.yml
+++ b/modules/nf-core/spaceranger/count/meta.yml
@@ -1,7 +1,7 @@
 ---
 # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json
 name: "spaceranger_count"
-description: Module to use the 10x Spaceranger pipeline to proces 10x spatial transcriptomics data
+description: Module to use the 10x Space Ranger pipeline to process 10x spatial transcriptomics data
 keywords:
   - align
   - count
@@ -70,7 +70,7 @@ input:
       pattern: "*.json"
   - reference:
       type: directory
-      description: Folder containing all the reference indices needed by Spaceranger
+      description: Folder containing all the reference indices needed by Space Ranger
   - probeset:
       type: file
       description: OPTIONAL - Probe set specification.
@@ -83,8 +83,8 @@ output:
         e.g. [ id:'test', single_end:false ]
   - outs:
       type: file
-      description: Files containing the outputs of Cell Ranger, see official 10X Genomics documentation for a complete list
-      pattern: "${meta.id}/outs/*"
+      description: Files containing the outputs of Space Ranger, see official 10X Genomics documentation for a complete list
+      pattern: "outs/*"
   - versions:
       type: file
       description: File containing software versions
diff --git a/modules/nf-core/spaceranger/mkgtf/meta.yml b/modules/nf-core/spaceranger/mkgtf/meta.yml
index 8bdc7a313ea..125b12622ba 100644
--- a/modules/nf-core/spaceranger/mkgtf/meta.yml
+++ b/modules/nf-core/spaceranger/mkgtf/meta.yml
@@ -1,7 +1,7 @@
 ---
 # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json
 name: "spaceranger_mkgtf"
-description: Module to build a filtered GTF needed by the 10x Genomics Cell Ranger tool. Uses the cellranger mkgtf command.
+description: Module to build a filtered GTF needed by the 10x Genomics Space Ranger tool. Uses the spaceranger mkgtf command.
 keywords:
   - reference
   - mkref
diff --git a/modules/nf-core/spaceranger/mkref/meta.yml b/modules/nf-core/spaceranger/mkref/meta.yml
index ed2e3ddd2ef..453a3e56cc6 100644
--- a/modules/nf-core/spaceranger/mkref/meta.yml
+++ b/modules/nf-core/spaceranger/mkref/meta.yml
@@ -1,7 +1,7 @@
 ---
 # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json
 name: "spaceranger_mkref"
-description: Module to build the reference needed by the 10x Genomics Spaceranger tool. Uses the spaceranger mkref command.
+description: Module to build the reference needed by the 10x Genomics Space Ranger tool. Uses the spaceranger mkref command.
 keywords:
   - reference
   - mkref
@@ -37,7 +37,7 @@ input:
 output:
   - reference:
       type: directory
-      description: Folder containing all the reference indices needed by Cell Ranger
+      description: Folder containing all the reference indices needed by Space Ranger
   - versions:
       type: file
       description: File containing software version