Merge pull request #40 from nf-core/switchtogatk

Use GATK4 to create sequence dictionary instead of Picard
nf-core · Nov 12, 2024 · 7c0e842 · 7c0e842
2 parents 608a1ec + f725863
commit 7c0e842
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Showing 17 changed files with 207 additions and 192 deletions.
diff --git a/conf/modules/gens_pon.config b/conf/modules/gens_pon.config
@@ -27,7 +27,7 @@ process {
         ]
     }
 
-    withName: '.*GENS_PON:PICARD_CREATESEQUENCEDICTIONARY' {
+    withName: '.*GENS_PON:GATK4_CREATESEQUENCEDICTIONARY' {
         ext.when = { params.dict.equals(null) }
         publishDir = [
                 mode: params.publish_dir_mode,

diff --git a/conf/modules/germlinecnvcaller_cohort.config b/conf/modules/germlinecnvcaller_cohort.config
@@ -27,7 +27,7 @@ process {
         ]
     }
 
-    withName: '.*GERMLINECNVCALLER_COHORT:PICARD_CREATESEQUENCEDICTIONARY' {
+    withName: '.*GERMLINECNVCALLER_COHORT:GATK4_CREATESEQUENCEDICTIONARY' {
         ext.when = { params.dict.equals(null) }
         publishDir = [
                 mode: params.publish_dir_mode,

diff --git a/modules.json b/modules.json
@@ -30,6 +30,11 @@
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
+                    "gatk4/createsequencedictionary": {
+                        "branch": "master",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "installed_by": ["modules"]
+                    },
                     "gatk4/createsomaticpanelofnormals": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
@@ -80,11 +85,6 @@
                         "git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d",
                         "installed_by": ["modules"]
                     },
-                    "picard/createsequencedictionary": {
-                        "branch": "master",
-                        "git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358",
-                        "installed_by": ["modules"]
-                    },
                     "samtools/faidx": {
                         "branch": "master",
                         "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",

diff --git a/.../createsequencedictionary/environment.yml → .../createsequencedictionary/environment.yml b/.../createsequencedictionary/environment.yml → .../createsequencedictionary/environment.yml
diff --git a/modules/nf-core/gatk4/createsequencedictionary/main.nf b/modules/nf-core/gatk4/createsequencedictionary/main.nf
diff --git a/modules/nf-core/gatk4/createsequencedictionary/meta.yml b/modules/nf-core/gatk4/createsequencedictionary/meta.yml
diff --git a/...eatesequencedictionary/tests/main.nf.test → ...eatesequencedictionary/tests/main.nf.test b/...eatesequencedictionary/tests/main.nf.test → ...eatesequencedictionary/tests/main.nf.test
diff --git a/modules/nf-core/gatk4/createsequencedictionary/tests/main.nf.test.snap b/modules/nf-core/gatk4/createsequencedictionary/tests/main.nf.test.snap
diff --git a/modules/nf-core/gatk4/createsequencedictionary/tests/tags.yml b/modules/nf-core/gatk4/createsequencedictionary/tests/tags.yml
diff --git a/modules/nf-core/picard/createsequencedictionary/main.nf b/modules/nf-core/picard/createsequencedictionary/main.nf
diff --git a/modules/nf-core/picard/createsequencedictionary/meta.yml b/modules/nf-core/picard/createsequencedictionary/meta.yml