Merge pull request #92 from drpatelh/salmon

Update Salmon modules

software/salmon/index/main.nf

@@ -5,7 +5,7 @@ params.options = [:]
 def options    = initOptions(params.options)
 
 process SALMON_INDEX {
-    tag "$fasta"
+    tag "$transcript_fasta"
     label "process_medium"
     publishDir "${params.outdir}",
         mode: params.publish_dir_mode,
@@ -15,21 +15,33 @@ process SALMON_INDEX {
     container "quay.io/biocontainers/salmon:1.3.0--hf69c8f4_0"
 
     input:
-    path fasta
+    path genome_fasta
+    path transcript_fasta
 
     output:
     path "salmon"       , emit: index
     path "*.version.txt", emit: version
 
     script:
-    def software = getSoftwareName(task.process) 
+    def software      = getSoftwareName(task.process)
+    def get_decoy_ids = "grep '^>' $genome_fasta | cut -d ' ' -f 1 > decoys.txt"
+    def gentrome      = "gentrome.fa"
+    if (genome_fasta.endsWith('.gz')) {
+        get_decoy_ids = "grep '^>' <(gunzip -c $genome_fasta) | cut -d ' ' -f 1 > decoys.txt"
+        gentrome      = "gentrome.fa.gz"
+    }
     """
+    $get_decoy_ids
+    sed -i.bak -e 's/>//g' decoys.txt
+    cat $transcript_fasta $genome_fasta > $gentrome
+
     salmon \\
         index \\
         --threads $task.cpus \\
-        -t $fasta \\
+        -t gentrome.fa \\
+        -d decoys.txt \\
         $options.args \\
         -i salmon
     salmon --version | sed -e "s/salmon //g" > ${software}.version.txt
     """
-}
+}

software/salmon/quant/main.nf

@@ -18,16 +18,24 @@ process SALMON_QUANT {
     tuple val(meta), path(reads)
     path  index
     path  gtf
+    path  transcript_fasta
+    val   alignment_mode
     
     output:
     tuple val(meta), path("${prefix}"), emit: results
     path  "*.version.txt"             , emit: version
 
     script:
-    def software  = getSoftwareName(task.process)
-    prefix        = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
-    def endedness = meta.single_end ? "-r $reads" : "-1 ${reads[0]} -2 ${reads[1]}"
+    def software    = getSoftwareName(task.process)
+    prefix          = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
 
+    def reference   = "--index $index"
+    def input_reads = meta.single_end ? "-r $reads" : "-1 ${reads[0]} -2 ${reads[1]}"
+    if (alignment_mode) {
+        reference   = "-t $transcript_fasta"
+        input_reads = "-a $reads"
+    }
+    
     def strandedness = meta.single_end ? 'U' : 'IU'
     if (meta.strandedness == 'forward') {
         strandedness = meta.single_end ? 'SF' : 'ISF'
@@ -39,8 +47,8 @@ process SALMON_QUANT {
         --geneMap $gtf \\
         --threads $task.cpus \\
         --libType=$strandedness \\
-        --index $index \\
-        $endedness \\
+        $reference \\
+        $input_reads \\
         $options.args \\
         -o $prefix
 

software/ucsc/bedgraphtobigwig/main.nf

@@ -6,7 +6,7 @@ def options    = initOptions(params.options)
 
 def VERSION = '377'
 
-process UCSC_BEDRAPHTOBIGWIG {
+process UCSC_BEDGRAPHTOBIGWIG {
     tag "$meta.id"
     label 'process_medium'
     publishDir "${params.outdir}",