replaced local star/align module with updated nf-core star/align module

mskcc · May 17, 2023 · 0429642 · 0429642
1 parent 99dbd82
commit 0429642
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Showing 5 changed files with 48 additions and 13 deletions.
diff --git a/modules.json b/modules.json
@@ -80,6 +80,11 @@
                         "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
                         "installed_by": ["modules"]
                     },
+                    "star/align": {
+                        "branch": "master",
+                        "git_sha": "57d75dbac06812c59798a48585032f6e50bb1914",
+                        "installed_by": ["modules"]
+                    },
                     "star/genomegenerate": {
                         "branch": "master",
                         "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",

diff --git a/modules/local/star/align/main.nf → modules/nf-core/star/align/main.nf b/modules/local/star/align/main.nf → modules/nf-core/star/align/main.nf
diff --git a/modules/local/star/align/meta.yml → modules/nf-core/star/align/meta.yml b/modules/local/star/align/meta.yml → modules/nf-core/star/align/meta.yml
diff --git a/subworkflows/local/align_reads.nf b/subworkflows/local/align_reads.nf
@@ -1,4 +1,4 @@
-include { STAR_ALIGN       } from '../../modules/local/star/align/main'
+include { STAR_ALIGN       } from '../../modules/nf-core/star/align/main'
 include { UMITOOLS_DEDUP   } from '../../modules/nf-core/umitools/dedup/main'
 include {
     SAMTOOLS_INDEX;
@@ -19,7 +19,10 @@ workflow ALIGN_READS {
     STAR_ALIGN(
         reads,
         star_index,
-        gtf
+        gtf,
+        false,
+        [],
+        []
     )
     ch_versions = ch_versions.mix(STAR_ALIGN.out.versions.first())
 

diff --git a/subworkflows/local/fusion.nf b/subworkflows/local/fusion.nf
@@ -1,6 +1,6 @@
-include { STAR_ALIGN as STAR_FOR_ARRIBA     } from '../../modules/local/star/align/main'
+include { STAR_ALIGN as STAR_FOR_ARRIBA     } from '../../modules/nf-core/star/align/main'
 include { ARRIBA                            } from '../../modules/nf-core/arriba/main'
-include { STAR_ALIGN as STAR_FOR_STARFUSION } from '../../modules/local/star/align/main'
+include { STAR_ALIGN as STAR_FOR_STARFUSION } from '../../modules/nf-core/star/align/main'
 include { STARFUSION                        } from '../../modules/local/starfusion/detect/main'
 include { FUSIONCATCHER_DETECT              } from '../../modules/local/fusioncatcher/detect/main'
 include { FUSIONREPORT                      } from '../../modules/local/fusionreport/run/main'
@@ -24,7 +24,10 @@ workflow FUSION {
     STAR_FOR_ARRIBA(
         reads,
         star_index,
-        gtf
+        gtf,
+        false,
+        [],
+        []
     )
     ch_versions = ch_versions.mix(STAR_FOR_ARRIBA.out.versions.first())
 
@@ -44,7 +47,10 @@ workflow FUSION {
         reads,
         // use the star index in the starfusion reference to ensure compatibility
         starfusion_ref.map{ file( it + "/ref_genome.fa.star.idx")},
-        gtf
+        gtf,
+        false,
+        [],
+        []
     )
     ch_versions = ch_versions.mix(STAR_FOR_STARFUSION.out.versions.first())