Merge pull request #157 from nf-core/151-error-no-genomic-sequence-av…

…ailable-check-g-option-error-in-gffread-command-for-task-nfcore_circrnacircrnaquantificationtranscriptome-error Remove GTF regions on unknown chromosomes
nf-core · Jul 15, 2024 · 009e891 · 009e891
2 parents 4a2d30f + 73bf5e4
commit 009e891
Show file tree

Hide file tree

Showing 11 changed files with 506 additions and 10 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -70,6 +70,10 @@ process {
         ]
     }
 
+    withName: GTFFILTER {
+        ext.suffix = "filtered.gtf"
+    }
+
     withName: SEQKIT_SPLIT {
         ext.args = "-i --by-id-prefix \"\""
         publishDir = [

diff --git a/modules.json b/modules.json
@@ -80,6 +80,11 @@
                         "git_sha": "de45447d060b8c8b98575bc637a4a575fd0638e1",
                         "installed_by": ["modules"]
                     },
+                    "custom/gtffilter": {
+                        "branch": "master",
+                        "git_sha": "a0aee18374b7f072aa0f89f4d66f5a3a9f8176d2",
+                        "installed_by": ["modules"]
+                    },
                     "custom/tx2gene": {
                         "branch": "master",
                         "git_sha": "ec155021a9104441bf6a9bae3b55d1b5b0bfdb3a",

diff --git a/modules/nf-core/custom/gtffilter/environment.yml b/modules/nf-core/custom/gtffilter/environment.yml
diff --git a/modules/nf-core/custom/gtffilter/main.nf b/modules/nf-core/custom/gtffilter/main.nf
diff --git a/modules/nf-core/custom/gtffilter/meta.yml b/modules/nf-core/custom/gtffilter/meta.yml
diff --git a/modules/nf-core/custom/gtffilter/templates/gtffilter.py b/modules/nf-core/custom/gtffilter/templates/gtffilter.py
diff --git a/modules/nf-core/custom/gtffilter/tests/main.nf.test b/modules/nf-core/custom/gtffilter/tests/main.nf.test