Refactor workflows into subworkflows

lib/WorkflowScrnaseq.groovy

@@ -8,10 +8,10 @@ class WorkflowScrnaseq {
     // Check and validate parameters
     //
     public static void initialise(params, log) {
-        genomeExistsError(params, log)
+        genomeExists(params, log)
 
-        if (!params.genome_fasta) {
-            log.error "Genome fasta file not specified with e.g. '--genome_fasta genome.fa' or via a detectable config file."
+        if (!params.input) {
+            log.error "Please provide an input samplesheet with --input"
             System.exit(1)
         }
     }
@@ -43,18 +43,111 @@ class WorkflowScrnaseq {
         return yaml_file_text
     }
 
-    //
+
+    // Citation string
+    private static String citation(workflow) {
+        return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" +
+                '* The pipeline\n' +
+                '  https://doi.org/10.5281/zenodo.3901628\n\n' +
+                '* The nf-core framework\n' +
+                '  https://doi.org/10.1038/s41587-020-0439-x\n\n' +
+                '* Software dependencies\n' +
+                "  https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md"
+    }
+
     // Exit pipeline if incorrect --genome key provided
-    //
-    private static void genomeExistsError(params, log) {
+    static void genomeExists(params, log) {
         if (params.genomes && params.genome && !params.genomes.containsKey(params.genome)) {
             log.error '=============================================================================\n' +
-                "  Genome '${params.genome}' not found in any config files provided to the pipeline.\n" +
-                '  Currently, the available genome keys are:\n' +
-                "  ${params.genomes.keySet().join(', ')}\n" +
-                '==================================================================================='
+                    "  Genome '${params.genome}' not found in any config files provided to the pipeline.\n" +
+                    '  Currently, the available genome keys are:\n' +
+                    "  ${params.genomes.keySet().join(', ')}\n" +
+                    '==================================================================================='
             System.exit(1)
         }
     }
 
+
+    /*
+    * Format the protocol
+    * Given the protocol paramter (params.protocol) and the aligner (params.aligner),
+    * this function formats the protocol such that it is fit for the respective
+    * subworkflow
+    */
+    static formatProtocol(protocol, aligner) {
+        String new_protocol = protocol
+        String chemistry = ''
+
+        // alevin
+        if (aligner == 'alevin') {
+            switch (protocol) {
+                case '10XV1':
+                    new_protocol = 'chromium'
+                    chemistry = 'V1'
+                    break
+                case '10XV2':
+                    new_protocol = 'chromium'
+                    chemistry = 'V2'
+                    break
+                case '10XV3':
+                    new_protocol = 'chromiumV3'
+                    chemistry = 'V3'
+                    break
+                case 'dropseq':
+                    new_protocol = 'dropseq'
+            }
+        }
+
+        // star
+        else if (aligner == 'star') {
+            switch (protocol) {
+                case '10XV1':
+                    new_protocol = 'CB_UMI_Simple'
+                    chemistry = 'V1'
+                    break
+                case '10XV2':
+                    new_protocol = 'CB_UMI_Simple'
+                    chemistry = 'V2'
+                    break
+                case '10XV3':
+                    new_protocol = 'CB_UMI_Simple'
+                    chemistry = 'V3'
+                    break
+                case 'dropseq':
+                    new_protocol = 'CB_UMI_Simple'
+                    break
+                case 'smartseq':
+                    new_protocol = 'SmartSeq'
+            }
+        }
+
+        // kallisto bustools
+        else if (aligner = 'kallisto' ) {
+            switch (protocol) {
+                case '10XV1':
+                    new_protocol = '10XV1'
+                    chemistry = 'V1'
+                    break
+                case '10XV2':
+                    new_protocol = '10XV2'
+                    chemistry = 'V2'
+                    break
+                case '10XV3':
+                    new_protocol = '10XV3'
+                    chemistry = 'V3'
+                    break
+                case 'dropseq':
+                    new_protocol = 'DROPSEQ'
+                    break
+                case 'smartseq':
+                    new_protocol = 'SMARTSEQ'
+            }
+        }
+        else {
+            exit 1, 'Aligner not recognized.'
+        }
+
+        return [new_protocol, chemistry]
+    }
+
 }

modules/local/multiqc_alevin.nf → modules/local/multiqc.nf

@@ -11,7 +11,8 @@ process MULTIQC {
     path multiqc_custom_config
     path software_versions
     path workflow_summary
-    path ('salmon_alevin/*')
+    path ("STAR/*")
+    path ("salmon_alevin/*")
 
     output:
     path "*multiqc_report.html"     , emit: report

modules/local/salmon_alevin.nf

@@ -34,7 +34,7 @@ process SALMON_ALEVIN {
         $args \\
         -o ${prefix}_alevin_results
 
-    mv ${whitelist} ${prefix}_alevin_results/alevin/whitelist.txt
+    gzip -cdf ${whitelist} > ${prefix}_alevin_results/alevin/whitelist.txt
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/local/star_align.nf

@@ -41,7 +41,7 @@ process STAR_ALIGN {
         --readFilesIn ${reads[1]} ${reads[0]}  \\
         --runThreadN $task.cpus \\
         --outFileNamePrefix $prefix. \\
-        --soloCBwhitelist $whitelist \\
+        --soloCBwhitelist <(gzip -cdf $whitelist) \\
         --soloType $protocol \\
         $out_sam_type \\
         $ignore_gtf \\

nextflow.config

@@ -32,6 +32,7 @@ params {
     kallisto_gene_map = null
     kallisto_index    = null
     skip_bustools     = false
+    kb_workflow       = "standard"
 
     // STARsolo parameters
     star_index          = null