update UniverSC module

  add inputs, outputs and example calls for UniverSC and Cell Ranger v3.0.2
  calls versions for UniverSC and Cell Ranger

Author: TomKellyGenetics

modules/universc/main.nf

@@ -23,10 +23,10 @@ process UNIVERSC {
     //               Software MUST be pinned to channel (i.e. "bioconda"), version (i.e. "1.10").
     //               For Conda, the build (i.e. "h9402c20_2") must be EXCLUDED to support installation on different operating systems.
     // TODO nf-core: See section in main README for further information regarding finding and adding container addresses to the section below.
-    conda (params.enable_conda ? "YOUR-TOOL-HERE" : null)
+    conda (params.enable_conda ? "UniverSC" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE':
-        'quay.io/biocontainers/YOUR-TOOL-HERE' }"
+        'https://hub.docker.com/layers/tomkellygenetics/universc':
+        'docker.io/tomkellygenetics/universc:latest' }"
 
     input:
     // TODO nf-core: Where applicable all sample-specific information e.g. "id", "single_end", "read_group"
@@ -35,20 +35,25 @@ process UNIVERSC {
     //               https://github.com/nf-core/modules/blob/master/modules/bwa/index/main.nf
     // TODO nf-core: Where applicable please provide/convert compressed files as input/output
     //               e.g. "*.fastq.gz" and NOT "*.fastq", "*.bam" and NOT "*.sam" etc.
-    tuple val(meta), path(bam)
+    tuple val(meta), path(reads)
+    path  reference
 
     output:
     // TODO nf-core: Named file extensions MUST be emitted for ALL output channels
-    tuple val(meta), path("*.bam"), emit: bam
+    output:
+    path("sample-${meta.id}/outs/*"), emit: outs
     // TODO nf-core: List additional required output channels/values here
-    path "versions.yml"           , emit: versions
+    path "versions.yml"             , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    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]}"
     // TODO nf-core: Where possible, a command MUST be provided to obtain the version number of the software e.g. 1.10
     //               If the software is unable to output a version number on the command-line then it can be manually specified
     //               e.g. https://github.com/nf-core/modules/blob/master/modules/homer/annotatepeaks/main.nf
@@ -59,17 +64,87 @@ process UNIVERSC {
     // TODO nf-core: Please replace the example samtools command below with your module's command
     // TODO nf-core: Please indent the command appropriately (4 spaces!!) to help with readability ;)
     """
-    samtools \\
-        sort \\
-        $args \\
-        -@ $task.cpus \\
-        -o ${prefix}.bam \\
-        -T $prefix \\
-        $bam
+    bash /universc/launch_universc.sh \\
+        --technology '${meta.technology}' \\
+        --id 'sample-${meta.id}' \\
+        $input_reads \\
+        --reference ${reference_name} \\
+        --sample ${sample_arg} \\
+        --jobmode "local" \\
+        --localcores ${task.cpus} \\
+        --localmem ${task.memory.toGiga()} \\
+        --per-cell-data \\
+        $args
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        cellranger: cellranger count --version 2>&1 | head -n 2 | tail -n 1 | sed 's/^.* \(\(\d*\)\)/\1/'| sed 's/[)(]//g'
+        universc: bash /universc/launch_universc.sh --version | grep version | grep universc | sed 's/^.* \(\(\d*\)\)/\1/'
+    END_VERSIONS
+    """
+
+
+    stub:
+    """
+    mkdir -p "sample-${meta.id}/outs/"
+    touch sample-${meta.id}/outs/fake_file.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        cellranger: cellranger count --version 2>&1 | head -n 2 | tail -n 1 | sed 's/^.* \(\(\d*\)\)/\1/'| sed 's/[)(]//g'
+        universc: bash /universc/launch_universc.sh --version | grep version | grep universc | sed 's/^.* \(\(\d*\)\)/\1/'
+    END_VERSIONS
+}
+
+process CELLRANGER_COUNT_OS {
+    tag "$meta.id"
+    label 'process_medium'
+
+    if (params.enable_conda) {
+        exit 1, "Conda environments cannot be used when using the Cell Ranger tool. Please use docker or singularity containers."
+    }
+    container "tomkellygenetics/cellranger_clean:3.0.2.9001"
+
+    input:
+    tuple val(meta), path(reads)
+    path  reference
+
+    output:
+    path("sample-${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
+    """
+    cellranger \\
+        count \\
+        --id='sample-${meta.id}' \\
+        --fastqs=. \\
+        --transcriptome=$reference_name \\
+        --sample=$sample_arg \\
+        --localcores=$task.cpus \\
+        --localmem=${task.memory.toGiga()} \\
+        $args
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        cellranger: cellranger count --version 2>&1 | head -n 2 | tail -n 1 | sed 's/^.* \(\(\d*\)\)/\1/'| sed 's/[)(]//g'
+    END_VERSIONS
+    """
+
+    stub:
+    """
+    mkdir -p "sample-${meta.id}/outs/"
+    touch sample-${meta.id}/outs/fake_file.txt
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        universc: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' ))
+        cellranger: cellranger count --version 2>&1 | head -n 2 | tail -n 1 | sed 's/^.* \(\(\d*\)\)/\1/'| sed 's/[)(]//g'
     END_VERSIONS
     """
 }