Close merge request #28

src/nf_modules/star/main.nf

+// STAR is an ultrafast universal RNA-seq aligner
+// 
+// EXAMPLE:
+
+/*
+include {
+    index_with_gff as star_index_with_gff;
+    mapping_fastq as star_mapping_fastq
+ } from './nf_modules/star/main.nf'
+   addParams(
+    star_mapping_fastq_out: "star/"
+   )
+
+star_index_with_gff(
+  genome_file,
+  gff_file
+  )
+
+star_mapping_fastq(
+    star_index_with_gff.out.index,
+    reads
+)
+
+*/
+
+
+version = "2.7.3a"
+container_url = "lbmc/star:${version}"
+
+params.star_mapping_fastq_out = ""
+
+
+process gff3_2_gtf {
+  container = "dceoy/cufflinks"
+  label "small_mem_mono_cpus"
+
+    input:
+        tuple val(genome_id), path(gff3_file)
+    output:
+        path "${genome_id}.gtf", emit: gtf
+    script:
+"""
+gffread ${gff3_file} -T -o ${genome_id}.gtf
+"""
+}
+
+
+process index_with_gtf {
+  container = "${container_url}"
+  label "big_mem_multi_cpus"
+
+  input:
+    tuple val(genome_id), path(genome_fasta)
+    path gtf_file
+
+  output:
+    tuple val(genome_id), path ("*"), emit: index
+
+  script:
+"""
+STAR --runThreadN ${task.cpus} --runMode genomeGenerate \
+--genomeDir ./ \
+--genomeFastaFiles ${genome_fasta}  \
+--sjdbGTFfile ${gtf_file} \
+--genomeSAindexNbases 13 # min(14, log2(GenomeLength)/2 - 1)
+"""
+}
+
+workflow index_with_gff {
+  take:
+    genome_fasta
+    gff_file
+  main:
+    gff3_2_gtf(gff_file)
+    index_with_gtf(genome_fasta,gff3_2_gtf.out.gtf)
+  emit:
+    report = index_with_gtf.out.index
+}
+
+
+process index_without_gff {
+  container = "${container_url}"
+  label "big_mem_multi_cpus"
+
+  input:
+    tuple val(genome_id), path(genome_fasta)
+
+  output:
+    tuple val(genome_id), path ("*"), emit: index
+
+  script:
+"""
+STAR --runThreadN ${task.cpus} --runMode genomeGenerate \
+--genomeDir ./ \
+--genomeFastaFiles ${genome_fasta}  \
+--genomeSAindexNbases 13 # min(14, log2(GenomeLength)/2 - 1)
+"""
+}
+
+
+process mapping_fastq {
+  container = "${container_url}"
+  label "big_mem_multi_cpus"
+  if (params.star_mapping_fastq_out != "") {
+    publishDir "results/${params.star_mapping_fastq_out}", mode: 'copy'
+  }
+
+  input:
+    tuple val(index_id), path(index)
+    tuple val(reads_id), path(reads) 
+
+  output:
+    path "*.Log.final.out", emit: report
+    tuple val(reads_id), path("*.bam"), emit: bam
+
+  script:
+if (reads_id instanceof List){
+    file_prefix = reads_id[0]
+  } else {
+    file_prefix = reads_id
+  }
+
+if (reads.size() == 2)
+"""
+mkdir -p index
+mv ${index} index/
+STAR --runThreadN ${task.cpus} \
+--genomeDir index/ \
+--readFilesCommand zcat \
+--readFilesIn ${reads[0]} ${reads[1]} \
+--outFileNamePrefix ${reads_id}. \
+--alignIntronMax 10000 \
+--outSAMtype BAM SortedByCoordinate \
+--outSAMstrandField intronMotif
+
+mv ${reads_id}.Aligned.sortedByCoord.out.bam ${reads_id}.bam
+"""
+else
+"""
+mkdir -p index
+mv ${index} index/
+STAR --runThreadN ${task.cpus} \
+--genomeDir index/ \
+--readFilesCommand zcat \
+--readFilesIn ${reads} \
+--outFileNamePrefix ${reads_id}. \
+--alignIntronMax 10000 \
+--outSAMtype BAM SortedByCoordinate \
+--outSAMstrandField intronMotif
+
+mv ${reads_id}.Aligned.sortedByCoord.out.bam ${reads_id}.bam
+"""
+}
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