Update UNIVERSC module

modules/nf-core/universc/main.nf

@@ -7,52 +7,32 @@ process UNIVERSC {
         exit 1, "UNIVERSC module does not support Conda. Please use Docker / Singularity / Podman instead."
     }
     container "docker.io/nfcore/universc:1.2.5.1"
-    if (workflow.containerEngine == 'docker'){
-        containerOptions = "--privileged"
-    }
-    if ( workflow.containerEngine == 'podman'){
-        containerOptions = "--runtime crun --userns=keep-id --systemd=always"
-    }
-    if (workflow.containerEngine == 'singularity'){
-        containerOptions = "-B /var/tmp --writable-tmpfs"
-        params.singularity_autoMounts = true
-    }
 
     input:
     tuple val(meta), path(reads)
     path  reference
 
 
     output:
-    tuple val(meta), path("sample-${meta.id}/outs/*"), emit: outs
+    tuple val(meta), path("${meta.id}/outs/*"), emit: outs
     path "versions.yml"                              , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args ?: ''
-    def sample_arg = meta.samples.unique().join(",")
-    def reference_name = reference.name
-    def input_reads = meta.single_end ? "--file $reads" : "-R1 ${reads[0]} -R2 ${reads[1]}"
+    def args           = task.ext.args ?: ''
+    def sample_arg     = meta.samples.unique().join(",")
+    def input_reads    = meta.single_end ? "--file $reads" : "-R1 ${reads[0]} -R2 ${reads[1]}"
     """
     universc \\
-        --id 'sample-${meta.id}' \\
+        --id '${meta.id}' \\
         ${input_reads} \\
-        --technology '${meta.technology}' \\
-        --chemistry '${meta.chemistry}' \\
-        --reference ${reference_name} \\
-        --description ${sample_arg} \\
+        --reference ${reference} \\
+        $args
         --jobmode "local" \\
         --localcores ${task.cpus} \\
-        --localmem ${task.memory.toGiga()} \\
-        --per-cell-data \\
-        $args 1> _log 2> _err
-
-    # save log files
-    echo !! > sample-${meta.id}/outs/_invocation
-    cp _log sample-${meta.id}/outs/_log
-    cp _err sample-${meta.id}/outs/_err
+        --localmem ${task.memory.toGiga()}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -61,7 +41,6 @@ process UNIVERSC {
     END_VERSIONS
     """
 
-
     stub:
     """
     mkdir -p "sample-${meta.id}/outs/"

tests/modules/nf-core/universc/nextflow.config

@@ -3,7 +3,14 @@ process {
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
 
     withName: UNIVERSC {
-        ext.args = ''
+        ext.args = {
+            [
+                meta.technology ? "--technology '${meta.technology}'" : "",
+                meta.chemistry  ? "--chemistry '${meta.chemistry}'"   : "",
+                meta.samples    ? "--description ${meta.samples.unique().join(',')}" : "",
+                "--per-cell-data"
+            ].join(' ').strip()
+        }
         container = "docker.io/nfcore/universc:1.2.5.1"
     }
 

tests/modules/nf-core/universc/test.yml

@@ -3,66 +3,25 @@
   tags:
     - universc
   files:
-    - path: output/cellranger/genome.filtered.gtf
-      md5sum: 9dc1a510bbe4438cfc2a74423bf2b2bd
-    - path: output/cellranger/homo_sapiens_chr22_reference/fasta/genome.fa
-      md5sum: f315020d899597c1b57e5fe9f60f4c3e
-    - path: output/cellranger/homo_sapiens_chr22_reference/fasta/genome.fa.fai
-      md5sum: 3520cd30e1b100e55f578db9c855f685
-    - path: output/cellranger/homo_sapiens_chr22_reference/genes/genes.gtf
-      md5sum: c37539d5bdae419bae799165d3f80c53
-    - path: output/cellranger/homo_sapiens_chr22_reference/reference.json
-      md5sum: 1f7bf05454cc908bf70cd232ae70b02d
-    - path: output/cellranger/homo_sapiens_chr22_reference/star/Genome
-      md5sum: 22102926fadf5890e905ca71b2da3f35
-    - path: output/cellranger/homo_sapiens_chr22_reference/star/SA
-      md5sum: bcf3e1a855783105150b46c905465333
-    - path: output/cellranger/homo_sapiens_chr22_reference/star/SAindex
-      md5sum: b93fb07d342e6c32a00ebc4311c0ad38
-    - path: output/cellranger/homo_sapiens_chr22_reference/star/chrLength.txt
-      md5sum: c81f40f27e72606d7d07097c1d56a5b5
-    - path: output/cellranger/homo_sapiens_chr22_reference/star/chrName.txt
-      md5sum: 5ae68a67b70976ee95342a7451cb5af1
-    - path: output/cellranger/homo_sapiens_chr22_reference/star/chrNameLength.txt
-      md5sum: b190587cae0531f3cf25552d8aa674db
-    - path: output/cellranger/homo_sapiens_chr22_reference/star/chrStart.txt
-      md5sum: bc73df776dd3d5bb9cfcbcba60880519
-    - path: output/cellranger/homo_sapiens_chr22_reference/star/exonGeTrInfo.tab
-      md5sum: d04497f69d6ef889efd4d34fe63edcc4
-    - path: output/cellranger/homo_sapiens_chr22_reference/star/exonInfo.tab
-      md5sum: 0d560290fab688b7268d88d5494bf9fe
-    - path: output/cellranger/homo_sapiens_chr22_reference/star/geneInfo.tab
-      md5sum: a20c70b081f5d83649c48ebbd951cb77
-    - path: output/cellranger/homo_sapiens_chr22_reference/star/genomeParameters.txt
-      contains: ["genomeGenerate"]
-    - path: output/cellranger/homo_sapiens_chr22_reference/star/sjdbInfo.txt
-      md5sum: 5690ea9d9f09f7ff85b7fd47bd234903
-    - path: output/cellranger/homo_sapiens_chr22_reference/star/sjdbList.fromGTF.out.tab
-      md5sum: 9e4f991abbbfeb3935a2bb21b9e258f1
-    - path: output/cellranger/homo_sapiens_chr22_reference/star/sjdbList.out.tab
-      md5sum: 9e4f991abbbfeb3935a2bb21b9e258f1
-    - path: output/cellranger/homo_sapiens_chr22_reference/star/transcriptInfo.tab
-      md5sum: 6fa11b4d34f4680a1c23dbcea2e050d5
-    - path: output/cellranger/versions.yml
-    - path: output/universc/sample-123/outs/_err
-    - path: output/universc/sample-123/outs/_invocation
+    - path: output/universc/123/outs/_err
+    - path: output/universc/123/outs/_invocation
       md5sum: adbbbc1027756be9fdeebabf979863e5
-    - path: output/universc/sample-123/outs/_log
-    - path: output/universc/sample-123/outs/basic_stats.txt
+    - path: output/universc/123/outs/_log
+    - path: output/universc/123/outs/basic_stats.txt
       md5sum: 90004df04ec7b65a0dd8d26a08e55fd2
-    - path: output/universc/sample-123/outs/filtered_feature_bc_matrix.h5
-    - path: output/universc/sample-123/outs/filtered_feature_bc_matrix/barcodes.tsv.gz
-    - path: output/universc/sample-123/outs/filtered_feature_bc_matrix/features.tsv.gz
-    - path: output/universc/sample-123/outs/filtered_feature_bc_matrix/matrix.mtx.gz
-    - path: output/universc/sample-123/outs/metrics_summary.csv
+    - path: output/universc/123/outs/filtered_feature_bc_matrix.h5
+    - path: output/universc/123/outs/filtered_feature_bc_matrix/barcodes.tsv.gz
+    - path: output/universc/123/outs/filtered_feature_bc_matrix/features.tsv.gz
+    - path: output/universc/123/outs/filtered_feature_bc_matrix/matrix.mtx.gz
+    - path: output/universc/123/outs/metrics_summary.csv
       md5sum: bba1b122b15698d97a034af61e3fcd59
-    - path: output/universc/sample-123/outs/molecule_info.h5
-    - path: output/universc/sample-123/outs/possorted_genome_bam.bam
-    - path: output/universc/sample-123/outs/possorted_genome_bam.bam.bai
-    - path: output/universc/sample-123/outs/raw_feature_bc_matrix.h5
-    - path: output/universc/sample-123/outs/raw_feature_bc_matrix/barcodes.tsv.gz
-    - path: output/universc/sample-123/outs/raw_feature_bc_matrix/features.tsv.gz
-    - path: output/universc/sample-123/outs/raw_feature_bc_matrix/matrix.mtx.gz
-    - path: output/universc/sample-123/outs/web_summary.html
-      contains: ["sample-123"]
+    - path: output/universc/123/outs/molecule_info.h5
+    - path: output/universc/123/outs/possorted_genome_bam.bam
+    - path: output/universc/123/outs/possorted_genome_bam.bam.bai
+    - path: output/universc/123/outs/raw_feature_bc_matrix.h5
+    - path: output/universc/123/outs/raw_feature_bc_matrix/barcodes.tsv.gz
+    - path: output/universc/123/outs/raw_feature_bc_matrix/features.tsv.gz
+    - path: output/universc/123/outs/raw_feature_bc_matrix/matrix.mtx.gz
+    - path: output/universc/123/outs/web_summary.html
+      contains: ["123"]
     - path: output/universc/versions.yml