Merge pull request #328 from christopher-mohr/fix_mirtrace_cast

Fix mirtrace cast issue
nf-core · Mar 20, 2024 · d5910ec · d5910ec
2 parents 83759fc + 684a84b
commit d5910ec
Show file tree

Hide file tree

Showing 9 changed files with 183 additions and 27 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -5,7 +5,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## v2.3.1 - XXXX-XX-XX- Gray Zinc Dalmation Patch
 
-- _tbd_
+- [[#328]](https://github.com/nf-core/smrnaseq/pull/328) - Fix [casting issue](https://github.com/nf-core/smrnaseq/issues/327) in mirtrace module
 
 ### Software dependencies
 

diff --git a/modules.json b/modules.json
@@ -47,7 +47,7 @@
                     },
                     "samtools/sort": {
                         "branch": "master",
-                        "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62",
+                        "git_sha": "4352dbdb09ec40db71e9b172b97a01dcf5622c26",
                         "installed_by": ["bam_sort_stats_samtools", "modules"]
                     },
                     "samtools/stats": {
@@ -76,7 +76,7 @@
                 "nf-core": {
                     "bam_sort_stats_samtools": {
                         "branch": "master",
-                        "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62",
+                        "git_sha": "4352dbdb09ec40db71e9b172b97a01dcf5622c26",
                         "installed_by": ["subworkflows"]
                     },
                     "bam_stats_samtools": {

diff --git a/modules/local/mirtrace.nf b/modules/local/mirtrace.nf
@@ -7,7 +7,7 @@ process MIRTRACE_RUN {
         'biocontainers/mirtrace:1.0.1--hdfd78af_1' }"
 
     input:
-    tuple val(adapter), val(ids), path(reads)
+    tuple val(adapter), val(ids), val(reads)
 
     output:
     path "mirtrace/*"  , emit: mirtrace

diff --git a/modules/nf-core/samtools/sort/main.nf b/modules/nf-core/samtools/sort/main.nf
diff --git a/modules/nf-core/samtools/sort/meta.yml b/modules/nf-core/samtools/sort/meta.yml
diff --git a/modules/nf-core/samtools/sort/tests/main.nf.test b/modules/nf-core/samtools/sort/tests/main.nf.test
diff --git a/modules/nf-core/samtools/sort/tests/main.nf.test.snap b/modules/nf-core/samtools/sort/tests/main.nf.test.snap
diff --git a/modules/nf-core/samtools/sort/tests/nextflow.config b/modules/nf-core/samtools/sort/tests/nextflow.config
diff --git a/subworkflows/nf-core/bam_sort_stats_samtools/main.nf b/subworkflows/nf-core/bam_sort_stats_samtools/main.nf
-Original file line number
+Diff line change
@@ Expand Up @@
     ## v2.3.1 - XXXX-XX-XX- Gray Zinc Dalmation Patch
-    - _tbd_
+    - [[#328]](https://github.com/nf-core/smrnaseq/pull/328) - Fix [casting issue](https://github.com/nf-core/smrnaseq/issues/327) in mirtrace module
     ### Software dependencies
@@ Expand Down @@