Merge pull request #452 from nschcolnicov/standardize_bowtie

Removed untar, updated bowtie_channel
nf-core · Oct 1, 2024 · 2016dac · 2016dac
2 parents f1768c5 + b79dccb
commit 2016dac
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -41,6 +41,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [[#443]](https://github.com/nf-core/smrnaseq/pull/443) - Migrate [mirna and genome_quant bowtie to nf-core](https://github.com/nf-core/smrnaseq/issues/436) - Replace local processes with `BOWTIE_ALIGN`.
 - [[#447]](https://github.com/nf-core/smrnaseq/pull/447) - Fix [Minor fixes and general pipeline cleanup](https://github.com/nf-core/smrnaseq/issues/400) - Update variable and processes names, update channel comments, remove unused modules and params.
 - [[#448]](https://github.com/nf-core/smrnaseq/pull/448) - Migrate local mirdeep to [nf-core mirdeep2 modules and subworkflow](https://github.com/nf-core/smrnaseq/issues/443) and generate [test profile for mirdeep2](https://github.com/nf-core/smrnaseq/issues/399).
+- [[#452]](https://github.com/nf-core/smrnaseq/pull/452) - Fix [Fix ch_bowtie_index channel structure](https://github.com/nf-core/smrnaseq/issues/451) and replace untarfiles with untar [replace untarfiles with untar](https://github.com/nf-core/smrnaseq/issues/449).
 
 ## v2.3.1 - 2024-04-18 - Gray Zinc Dalmation Patch
 

diff --git a/conf/modules.config b/conf/modules.config
@@ -42,7 +42,7 @@ process {
         ]
     }
 
-    withName: 'UNTAR' {
+    withName: '.*:PREPARE_GENOME:UNTAR_BOWTIE_INDEX' {
         publishDir = [
             mode: params.publish_dir_mode,
             enabled: params.save_intermediates,

diff --git a/modules.json b/modules.json
@@ -157,7 +157,7 @@
                         "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
                         "installed_by": ["fastq_fastqc_umitools_fastp", "modules"]
                     },
-                    "untarfiles": {
+                    "untar": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]

diff --git a/modules/nf-core/untarfiles/environment.yml → modules/nf-core/untar/environment.yml b/modules/nf-core/untarfiles/environment.yml → modules/nf-core/untar/environment.yml
diff --git a/modules/nf-core/untar/main.nf b/modules/nf-core/untar/main.nf
diff --git a/modules/nf-core/untarfiles/meta.yml → modules/nf-core/untar/meta.yml b/modules/nf-core/untarfiles/meta.yml → modules/nf-core/untar/meta.yml
diff --git a/modules/nf-core/untar/tests/main.nf.test b/modules/nf-core/untar/tests/main.nf.test