Merge pull request #396 from nf-core/289-update-or-remove-universc

Remove universc subworkflow from pipeline

.github/workflows/awsfulltest.yml

@@ -19,7 +19,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        aligner: ["alevin", "kallisto", "star", "cellranger", "universc"]
+        aligner: ["alevin", "kallisto", "star", "cellranger"]
     steps:
       - uses: octokit/[email protected]
         id: check_approvals

.github/workflows/awstest.yml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        aligner: ["alevin", "kallisto", "star", "cellranger", "universc"]
+        aligner: ["alevin", "kallisto", "star", "cellranger"]
     steps:
       # Launch workflow using Seqera Platform CLI tool action
       - name: Launch workflow via Seqera Platform

.github/workflows/ci.yml

@@ -52,6 +52,11 @@ jobs:
           python-version: "3.11"
           architecture: "x64"
 
+      - uses: actions/setup-java@8df1039502a15bceb9433410b1a100fbe190c53b # v4
+        with:
+          distribution: "temurin"
+          java-version: "17"
+
       - name: Install pdiff to see diff between nf-test snapshots
         run: |
           python -m pip install --upgrade pip

CHANGELOG.md

@@ -5,6 +5,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+- Remove universc workflow from pipeline ([#289](https://github.com/nf-core/scrnaseq/issues/289))
 - Add `--save_align_intermeds` parameter that publishes BAM files to the output directory (for `starsolo`, `cellranger` and `cellranger multi`) ([#384](https://github.com/nf-core/scrnaseq/issues/384))
 - Added support for pre-built indexes in `genomes.config` file for `cellranger`, `cellranger-arc`, `simpleaf` and `simpleaf txp2gene` ([#371](https://github.com/nf-core/scrnaseq/issues/371))
 - Cleanup and fix bugs in matrix conversion code, and change to use anndataR for conversions, and cellbender for emptydrops call. ([#369](https://github.com/nf-core/scrnaseq/pull/369))

README.md

@@ -29,13 +29,12 @@ This is a community effort in building a pipeline capable to support:
 - STARSolo
 - Kallisto + BUStools
 - Cellranger
-- UniverSC
 
 ## Documentation
 
 The nf-core/scrnaseq pipeline comes with documentation about the pipeline [usage](https://nf-co.re/scrnaseq/usage), [parameters](https://nf-co.re/scrnaseq/parameters) and [output](https://nf-co.re/scrnaseq/output).
 
-![scrnaseq workflow](docs/images/scrnaseq_pipeline_v1.0_metro_clean.png)
+![scrnaseq workflow](docs/images/scrnaseq_pipeline_V3.0-metro_clean.png)
 
 ## Usage
 
@@ -63,7 +62,7 @@ nextflow run nf-core/scrnaseq \
    --genome_fasta GRCm38.p6.genome.chr19.fa \
    --gtf gencode.vM19.annotation.chr19.gtf \
    --protocol 10XV2 \
-   --aligner <alevin/kallisto/star/cellranger/universc> \
+   --aligner <alevin/kallisto/star/cellranger> \
    --outdir <OUTDIR>
 ```
 
@@ -82,7 +81,6 @@ graph TD
     A[sc RNA] -->|CellRanger| B(h5ad/seurat/mtx matrices)
     A[sc RNA] -->|kbpython| B(h5ad/seurat/mtx matrices)
     A[sc RNA] -->|STARsolo| B(h5ad/seurat/mtx matrices)
-    A[sc RNA] -->|Universc| B(h5ad/seurat/mtx matrices)
 ```
 
 Options for the respective alignment method can be found [here](https://github.com/nf-core/scrnaseq/blob/dev/docs/usage.md#aligning-options) to choose between methods.

assets/protocols.json

@@ -89,25 +89,5 @@
         "smartseq": {
             "protocol": "SMARTSEQ"
         }
-    },
-    "universc": {
-        "auto": {
-            "protocol": "10x"
-        },
-        "10XV1": {
-            "protocol": "10x-v1"
-        },
-        "10XV2": {
-            "protocol": "10x-v2"
-        },
-        "10XV3": {
-            "protocol": "10x-v3"
-        },
-        "10XV4": {
-            "protocol": "10x-v4"
-        },
-        "dropseq": {
-            "protocol": "dropseq"
-        }
     }
 }

conf/modules.config

@@ -126,36 +126,6 @@ if(params.aligner == "cellrangerarc") {
     }
 }
 
-if(params.aligner == "universc") {
-    process {
-        publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
-        withName: CELLRANGER_MKGTF {
-            publishDir = [
-                path: "${params.outdir}/cellranger/mkgtf",
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-            ]
-            ext.args = "--attribute=gene_biotype:protein_coding --attribute=gene_biotype:lncRNA --attribute=gene_biotype:pseudogene"
-            container = "nf-core/universc:1.2.5.1"
-        }
-        withName: CELLRANGER_MKREF {
-            publishDir = [
-                path: "${params.outdir}/cellranger/mkref",
-                mode: params.publish_dir_mode
-            ]
-            container = "nf-core/universc:1.2.5.1"
-        }
-        withName: UNIVERSC {
-            publishDir = [
-                path: "${params.outdir}/universc",
-                mode: params.publish_dir_mode
-            ]
-            time   = { 240.h  * task.attempt }
-        }
-    }
-}
-
 if (params.aligner == "alevin") {
     process {
         withName: GFFREAD_TXP2GENE {