Move circeplorer reference creation to shared location

nf-core · Jan 19, 2025 · bab9e00 · bab9e00
1 parent b1930f5
commit bab9e00
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Showing 14 changed files with 299 additions and 92 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -91,6 +91,14 @@ process {
         ]
     }
 
+    withName: UCSC_GTFTOGENEPRED {
+        publishDir = [
+            path: { "${params.outdir}/references/genome/genepred" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> ( filename != 'versions.yml' && params.save_reference ) ? filename : null }
+        ]
+    }
+
     withName: SEQKIT_SPLIT {
         ext.args = "-i --by-id-prefix \"\""
         publishDir = [
@@ -157,6 +165,16 @@ process {
         ]
     }
 
+    withName: CIRCEXPLORER2_REFERENCE {
+        ext.args = "-v OFS='\\t' '{print \$12, \$1, \$2, \$3, \$4, \$5, \$6, \$7, \$8, \$9, \$10}'"
+        ext.suffix = "circexplorer2.txt"
+        publishDir = [
+            path: { "${params.outdir}/references/index" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> ( filename != 'versions.yml' && params.save_reference ) ? filename : null }
+        ]
+    }
+
     // circRNA
 
     withName: '.*:SEGEMEHL:INDEX' {

diff --git a/modules.json b/modules.json
@@ -220,6 +220,11 @@
                         "branch": "master",
                         "git_sha": "5d095e8413da1f4c72b7d07ce87f75c09482486f",
                         "installed_by": ["modules"]
+                    },
+                    "ucsc/gtftogenepred": {
+                        "branch": "master",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "installed_by": ["modules"]
                     }
                 }
             },

diff --git a/modules/local/circexplorer2/reference/main.nf b/modules/local/circexplorer2/reference/main.nf
diff --git a/modules/nf-core/ucsc/gtftogenepred/environment.yml b/modules/nf-core/ucsc/gtftogenepred/environment.yml
diff --git a/modules/nf-core/ucsc/gtftogenepred/main.nf b/modules/nf-core/ucsc/gtftogenepred/main.nf
diff --git a/modules/nf-core/ucsc/gtftogenepred/meta.yml b/modules/nf-core/ucsc/gtftogenepred/meta.yml
diff --git a/modules/nf-core/ucsc/gtftogenepred/tests/main.nf.test b/modules/nf-core/ucsc/gtftogenepred/tests/main.nf.test
diff --git a/modules/nf-core/ucsc/gtftogenepred/tests/main.nf.test.snap b/modules/nf-core/ucsc/gtftogenepred/tests/main.nf.test.snap
diff --git a/modules/nf-core/ucsc/gtftogenepred/tests/nextflow.config b/modules/nf-core/ucsc/gtftogenepred/tests/nextflow.config
diff --git a/subworkflows/local/bsj_detection.nf b/subworkflows/local/bsj_detection.nf
@@ -38,6 +38,7 @@ workflow BSJ_DETECTION {
     chromosomes
     hisat2_index
     star_index
+    circexplorer2_index
     bsj_reads
 
     main:
@@ -70,7 +71,7 @@ workflow BSJ_DETECTION {
     }
 
     if (tools_selected.contains('circexplorer2')) {
-        CIRCEXPLORER2( gtf, fasta, STAR2PASS.out.junction )
+        CIRCEXPLORER2( fasta, STAR2PASS.out.junction, circexplorer2_index )
         ch_versions                = ch_versions.mix(CIRCEXPLORER2.out.versions)
         ch_bsj_bed_per_sample_tool = ch_bsj_bed_per_sample_tool.mix(CIRCEXPLORER2.out.bed)
     }
@@ -103,7 +104,7 @@ workflow BSJ_DETECTION {
 
     if (tools_selected.contains('mapsplice')) {
         MAPSPLICE( reads, gtf, fasta, bowtie_index, chromosomes,
-            STAR2PASS.out.junction )
+            STAR2PASS.out.junction, circexplorer2_index )
         ch_versions                = ch_versions.mix(MAPSPLICE.out.versions)
         ch_bsj_bed_per_sample_tool = ch_bsj_bed_per_sample_tool.mix(MAPSPLICE.out.bed)
     }

diff --git a/subworkflows/local/detection_tools/circexplorer2.nf b/subworkflows/local/detection_tools/circexplorer2.nf
@@ -1,26 +1,24 @@
-include { CIRCEXPLORER2_REFERENCE as REFERENCE } from '../../../modules/local/circexplorer2/reference'
 include { CIRCEXPLORER2_PARSE as PARSE         } from '../../../modules/nf-core/circexplorer2/parse'
 include { CIRCEXPLORER2_ANNOTATE as ANNOTATE   } from '../../../modules/nf-core/circexplorer2/annotate'
 include { GAWK as UNIFY                        } from '../../../modules/nf-core/gawk'
 
 workflow CIRCEXPLORER2 {
     take:
-    gtf
     fasta
     star_junctions
+    circexplorer2_index
 
     main:
     ch_versions = Channel.empty()
 
-    REFERENCE( gtf )
     PARSE( star_junctions )
-    ANNOTATE( PARSE.out.junction, fasta, REFERENCE.out.txt )
-    UNIFY( ANNOTATE.out.txt
-        .map{ meta, txt -> [ meta + [tool: "circexplorer2"], txt ] }, [] )
-
-    ch_versions = ch_versions.mix(REFERENCE.out.versions)
     ch_versions = ch_versions.mix(PARSE.out.versions)
+
+    ANNOTATE( PARSE.out.junction, fasta, circexplorer2_index )
     ch_versions = ch_versions.mix(ANNOTATE.out.versions)
+
+    UNIFY( ANNOTATE.out.txt
+        .map{ meta, txt -> [ meta + [tool: "circexplorer2"], txt ] }, [] )
     ch_versions = ch_versions.mix(UNIFY.out.versions)
 
     emit:

diff --git a/subworkflows/local/detection_tools/mapsplice.nf b/subworkflows/local/detection_tools/mapsplice.nf
@@ -1,4 +1,3 @@
-include { CIRCEXPLORER2_REFERENCE as REFERENCE } from '../../../modules/local/circexplorer2/reference'
 include { MAPSPLICE_ALIGN as ALIGN             } from '../../../modules/local/mapsplice/align'
 include { CIRCEXPLORER2_PARSE as PARSE         } from '../../../modules/nf-core/circexplorer2/parse'
 include { CIRCEXPLORER2_ANNOTATE as ANNOTATE   } from '../../../modules/nf-core/circexplorer2/annotate'
@@ -12,18 +11,17 @@ workflow MAPSPLICE {
     bowtie_index
     chromosomes
     star_junctions
+    circexplorer2_index
 
     main:
     ch_versions = Channel.empty()
 
-    REFERENCE( gtf )
     ALIGN( reads, bowtie_index, chromosomes, gtf )
     PARSE( ALIGN.out.raw_fusions )
-    ANNOTATE( PARSE.out.junction, fasta, REFERENCE.out.txt )
+    ANNOTATE( PARSE.out.junction, fasta, circexplorer2_index )
     UNIFY( ANNOTATE.out.txt.map{ meta, txt ->
         [ meta + [tool: "mapsplice"], txt ] }, [] )
 
-    ch_versions = ch_versions.mix(REFERENCE.out.versions)
     ch_versions = ch_versions.mix(ALIGN.out.versions)
     ch_versions = ch_versions.mix(PARSE.out.versions)
     ch_versions = ch_versions.mix(ANNOTATE.out.versions)