Merge pull request #677 from JoseEspinosa/bump_stringtie_version

Bump stringtie version to 2.1.7
nf-core · Jul 23, 2021 · b003444 · b003444
2 parents 6fa0454 + 2e1e206
commit b003444
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Showing 3 changed files with 7 additions and 5 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -19,6 +19,7 @@ Note, since the pipeline is now using Nextflow DSL2, each process will be run wi
 |-------------|-------------|-------------|
 | `umi_tools` | 1.1.1       | 1.1.2       |
 | `samtools`  | 1.10        | 1.12        |
+| `stringtie` | 2.1.4       | 2.1.7       |
 
 > **NB:** Dependency has been __updated__ if both old and new version information is present.
 > **NB:** Dependency has been __added__ if just the new version information is present.

diff --git a/modules.json b/modules.json
@@ -91,7 +91,7 @@
                 "git_sha": "e937c7950af70930d1f34bb961403d9d2aa81c7d"
             },
             "stringtie/stringtie": {
-                "git_sha": "e937c7950af70930d1f34bb961403d9d2aa81c7d"
+                "git_sha": "217303f5c1a92effb8a97c29294ee9f2e19f697e"
             },
             "subread/featurecounts": {
                 "git_sha": "e937c7950af70930d1f34bb961403d9d2aa81c7d"

diff --git a/modules/nf-core/modules/stringtie/stringtie/main.nf b/modules/nf-core/modules/stringtie/stringtie/main.nf
@@ -11,11 +11,11 @@ process STRINGTIE {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::stringtie=2.1.4" : null)
+    conda (params.enable_conda ? "bioconda::stringtie=2.1.7" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/stringtie:2.1.4--h7e0af3c_0"
+        container "https://depot.galaxyproject.org/singularity/stringtie:2.1.7--h978d192_0"
     } else {
-        container "quay.io/biocontainers/stringtie:2.1.4--h7e0af3c_0"
+        container "quay.io/biocontainers/stringtie:2.1.7--h978d192_0"
     }
 
     input:
@@ -48,8 +48,9 @@ process STRINGTIE {
         -A ${prefix}.gene.abundance.txt \\
         -C ${prefix}.coverage.gtf \\
         -b ${prefix}.ballgown \\
+        -p $task.cpus \\
         $options.args
 
-    stringtie --version > ${software}.version.txt
+    echo \$(stringtie --version 2>&1) > ${software}.version.txt
     """
 }