update to call UniverSC module nf-core/modules#1706

TomKellyGenetics · Feb 27, 2023 · 3c21d5a · 3c21d5a
1 parent 120f8bb
commit 3c21d5a
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Showing 4 changed files with 26 additions and 30 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -75,23 +75,27 @@ if(params.aligner == "cellranger") {
 
 if(params.aligner == "universc") {
     process {
-        withName: UNIVERSC_MKGTF {
+        publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+        withName: CELLRANGER_MKGTF {
             publishDir = [
-                path: "${params.outdir}/${params.aligner}/mkgtf",
+                path: "${params.outdir}/cellranger/mkgtf",
                 mode: params.publish_dir_mode,
                 saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
             ]
             ext.args = "--attribute=gene_biotype:protein_coding --attribute=gene_biotype:lncRNA --attribute=gene_biotype:pseudogene"
+            container = "nfcore/universc:1.2.5.1"
         }
-        withName: UNIVERSC_MKREF {
+        withName: CELLRANGER_MKREF {
             publishDir = [
-                path: "${params.outdir}/${params.aligner}/mkref",
+                path: "${params.outdir}/cellranger/mkref",
                 mode: params.publish_dir_mode
             ]
+            container = "nfcore/universc:1.2.5.1"
         }
-        withName: UNIVERSC_LAUNCH {
+        withName: UNIVERSC {
             publishDir = [
-                path: "${params.outdir}/${params.aligner}/launch",
+                path: "${params.outdir}/universc",
                 mode: params.publish_dir_mode
             ]
         }

diff --git a/modules.json b/modules.json
@@ -17,17 +17,9 @@
                         "branch": "master",
                         "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
                     },
-                    "universc/launch": {
+                    "universc": {
                         "branch": "master",
-                        "git_sha": "acc63a2bc7a3fe83bf5733e099348c5b694c0fd7"
-                    },
-                    "universc/mkgtf": {
-                        "branch": "master",
-                        "git_sha": "acc63a2bc7a3fe83bf5733e099348c5b694c0fd7"
-                    },
-                    "universc/mkref": {
-                        "branch": "master",
-                        "git_sha": "acc63a2bc7a3fe83bf5733e099348c5b694c0fd7"
+                        "git_sha": "7a522f4ba5b97368c975b314db25929f6931648d"
                     },
                     "custom/dumpsoftwareversions": {
                         "branch": "master",

diff --git a/subworkflows/local/align_universc.nf b/subworkflows/local/align_universc.nf
@@ -1,11 +1,11 @@
 /*
- * Alignment with Cellranger
+ * Alignment with Cellranger open-source implementation called by UniverSC
  */
 
-include {UNIVERSC_MKGTF} from "../../modules/nf-core/universc/mkgtf/main.nf"
-include {UNIVERSC_MKREF} from "../../modules/nf-core/universc/mkref/main.nf"
-include {UNIVERSC_LAUNCH} from "../../modules/nf-core/universc/launch/main.nf"
-include {MTX_TO_H5AD     } from "../../modules/local/mtx_to_h5ad.nf"
+include {CELLRANGER_MKGTF} from "../../modules/nf-core/universc/mkgtf/main.nf"
+include {CELLRANGER_MKREF} from "../../modules/nf-core/universc/mkref/main.nf"
+include {UNIVERSC} from "../../modules/nf-core/universc/main.nf"
+include {MTX_TO_H5AD} from "../../modules/local/mtx_to_h5ad.nf"
 
 // Define workflow to subset and index a genome region fasta file
 workflow UNIVERSC_ALIGN {
@@ -24,24 +24,24 @@ workflow UNIVERSC_ALIGN {
 
         if (!universc_index) {
             // Filter GTF based on gene biotypes passed in params.modules
-            UNIVERSC_MKGTF( gtf )
-            ch_versions = ch_versions.mix(UNIVERSC_MKGTF.out.versions)
+            CELLRANGER_MKGTF( gtf )
+            ch_versions = ch_versions.mix(CELLRANGER_MKGTF.out.versions)
 
             // Make reference genome
-            UNIVERSC_MKREF( fasta, UNIVERSC_MKGTF.out.gtf, "cellranger_reference" )
-            ch_versions = ch_versions.mix(UNIVERSC_MKREF.out.versions)
-            universc_index = UNIVERSC_MKREF.out.reference
+            CELLRANGER_MKREF( fasta, CELLRANGER_MKGTF.out.gtf, "cellranger_reference" )
+            ch_versions = ch_versions.mix(CELLRANGER_MKREF.out.versions)
+            universc_index = CELLRANGER_MKREF.out.reference
         }
 
         // Obtain read counts
-        UNIVERSC_LAUNCH (
+        UNIVERSC (
             // TODO add technology and chemistry input parameters and set defaults
             ch_fastq.map{ meta, reads -> [meta + ["id": meta.id, "samples:", meta.id, "technology": universc_technology, "single_end:", false, "strandedness:", 'forward'], reads] },
             universc_index
         )
-        ch_versions = ch_versions.mix(UNIVERSC_LAUNCH.out.versions)
+        ch_versions = ch_versions.mix(UNIVERSC.out.versions)
 
     emit:
         ch_versions
-        universc_out  = UNIVERSC_LAUNCH.out.outs
+        universc_out  = UNIVERSC.out.outs
 }
diff --git a/workflows/scrnaseq.nf b/workflows/scrnaseq.nf
@@ -44,7 +44,7 @@ include { KALLISTO_BUSTOOLS } from '../subworkflows/local/kallisto_bustools'
 include { SCRNASEQ_ALEVIN   } from '../subworkflows/local/alevin'
 include { STARSOLO          } from '../subworkflows/local/starsolo'
 include { CELLRANGER_ALIGN  } from "../subworkflows/local/align_cellranger"
-include { UNIVERSC_ALIGN  } from "../subworkflows/local/align_universc"
+include { UNIVERSC_ALIGN    } from "../subworkflows/local/align_universc"
 include { MTX_CONVERSION    } from "../subworkflows/local/mtx_conversion"
 include { GTF_GENE_FILTER   } from '../modules/local/gtf_gene_filter'
 /*