included code to allow for the mapping to the transcriptome, as well as using cDNA rather than dRNA in minimap, but both are untested

Author: number-25

docs/usage.md

@@ -28,7 +28,7 @@ CONTROL1,2,data/long_reads_2.fastq.gz
 | ----------- | -------------------------- |
 | `sample`    | Sample name.               |
 | `replicate` | Technical replicate number |
-| `reads` | Full path to fastq reads.  |
+| `reads`     | Full path to fastq reads.  |
 
 An [example samplesheet](../assets/samplesheet.csv) has been provided with the pipeline.
 

modules/local/minimap2/align/main.nf

@@ -9,17 +9,10 @@ process MINIMAP2_ALIGN {
     input:
     tuple val(meta), path(fastq)
     path(genome_index)
-    // tuple val(meta2), path(reference)
-    // val bam_format
-    // val bam_index_extension
-    // val cigar_paf_format
-    // val cigar_bam
 
     output:
-    //tuple val(meta), path("*.paf")                       , optional: true, emit: paf
-    tuple val(meta), path("*.sam")                       , optional: true, emit: sam
-    //tuple val(meta), path("*.bam.${bam_index_extension}"), optional: true, emit: index
-    path "versions.yml"                                  , emit: versions
+    tuple val(meta), path("*.sam")  , optional: true, emit: sam
+    path "versions.yml"             , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -28,29 +21,13 @@ process MINIMAP2_ALIGN {
     // This can be expanded eventually to allow cDNA mapping, etc.
     def args        = task.ext.args ?: ''
     def prefix      = task.ext.prefix ?: "${meta.id}_${meta.replicate}_minimap2"
-    def dRNA_preset = task.ext.dRNA_preset ?: "-ax splice -uf"
-    def kmer        = task.ext.kmer ?: "-k 14"
-    //def mismatch_tag = (params.talon ) ? "--MD"
-    /*
-    def args2 = task.ext.args2 ?: ''
-    def args3 = task.ext.args3 ?: ''
-    def args4 = task.ext.args4 ?: ''
-    def bam_index = bam_index_extension ? "${prefix}.bam##idx##${prefix}.bam.${bam_index_extension} --write-index" : "${prefix}.bam"
-    def bam_output = bam_format ? "-a | samtools sort -@ ${task.cpus-1} -o ${bam_index} ${args2}" : "-o ${prefix}.paf"
-    def cigar_paf = cigar_paf_format && !bam_format ? "-c" : ''
-    def set_cigar_bam = cigar_bam && bam_format ? "-L" : ''
-    def bam_input = "${reads.extension}".matches('sam|bam|cram')
-    def samtools_reset_fastq = bam_input ? "samtools reset --threads ${task.cpus-1} $args3 $reads | samtools fastq --threads ${task.cpus-1} $args4 |" : ''
-    def query = bam_input ? "-" : reads
-    def target = reference ?: (bam_input ? error("BAM input requires reference") : reads)
-    */
+    //def dRNA_preset = task.ext.dRNA_preset ?: "-ax splice -uf"
+    def preset      = (params.sequencing_type == 'ont-drna') ?: "-ax splice -uf" : "-ax splice"
+    def kmer        = (params.sequencing_type == 'ont-drna') ?: "-k 14" : ""
 
-    //$samtools_reset_fastq \\
-    // $set_cigar_bam \\
-    // $bam_output
     """
     minimap2 \\
-        ${dRNA_preset} \\
+        ${preset} \\
         ${kmer} \\
         -t ${task.cpus} \\
         ${genome_index} \\
@@ -66,12 +43,8 @@ process MINIMAP2_ALIGN {
 
     stub:
     def prefix      = task.ext.prefix ?: "${meta.id}_${meta.replicate}_minimap2"
-    def dRNA_preset = task.ext.dRNA_preset ?: "-ax splice -uf"
-    def kmer        = task.ext.kmer ?: "-k 14"
-    //def output_file = bam_format ? "${prefix}.bam" : "${prefix}.paf"
-    //def bam_index = bam_index_extension ? "touch ${prefix}.bam.${bam_index_extension}" : ""
-    //def bam_input = "${reads.extension}".matches('sam|bam|cram')
-    //def target = reference ?: (bam_input ? error("BAM input requires reference") : reads)
+    def preset      = (params.sequencing_type == 'ont-drna') ?: "-ax splice -uf" : "-ax splice"
+    def kmer        = (params.sequencing_type == 'ont-drna') ?: "-k 14" : ""
 
     """
     touch ${prefix}.sam

nextflow.config

@@ -14,18 +14,18 @@ plugins {
 params {
     // Input options
     input                           = 'assets/samplesheet.csv'
-    sequencing_type                 = "ont-drna" // sequencing molecule [ont-drna OR ont-cdna]
-    bam_input                       = false
+    sequencing_type                 = "ont-drna" // sequencing library [ont-drna OR ont-cdna]
+    bam_input                       = false // input premapped bam files. default: [false]
     // References
     genome_fasta                    = null //'data/hg38.analysisSet.fa.gz'
     genome_fasta_index              = null //'data/hg38.analysisSet.fa.fai'
     genome_fasta_sizes              = null
     //custom_genome                 = false // only when providing novel genomes
     skip_prepare_reference          = false // even if paths are hardcoded, files need to be unzipped and so on
     genome_minimap2_index           = null
-    transcriptome_fasta             = null //'data/gencode.v46.transcripts.fa.gz'
+    transcriptome_fasta             = null // e.g. 'data/gencode.v46.transcripts.fa.gz'
     transcriptome_minimap2_index    = null
-    annotation_gtf                  = null // 'data/Homo_sapiens.GRCh38.112.gtf.gz'
+    annotation_gtf                  = null // e.g. 'data/Homo_sapiens.GRCh38.112.gtf.gz'
 
     //igenomes
     //igenomes_base                   = 's3://ngi-igenomes/igenomes/'
@@ -59,6 +59,7 @@ params {
     //extra_ngs_bits_options          = null
 
     // MAPPING
+    transcriptome_mapping           = false
     // minimap2 options
     skip_mapping                    = false
     //extra_minimap2_options          = null
@@ -141,14 +142,6 @@ params {
     //max_memory                      = '32.GB'
     //max_cpus                        = 10
     //max_time                        = '48.h'
-
-    // Schema validation default options
-    //validationFailUnrecognisedParams = false
-    //validationLenientMode            = false
-    //validationSchemaIgnoreParams     = 'genomes,igenomes_base'
-    //validationShowHiddenParams       = false
-    //validate_params                  = true
-
 }
 
 validation {

nextflow_schema.json

@@ -82,7 +82,7 @@
                     "type": "string",
                     "default": "ont-drna",
                     "description": "Type of Oxford Nanopore library.",
-                    "help_text": "Type of Oxford nanopore library. Either 'ont-drna' or 'ont-cdna'",
+                    "help_text": "Type of Oxford nanopore library. Either 'ont-drna' or 'ont-cdna'.",
                     "fa_icon": "fas fa-font"
                 }
             }