Problem 6

process '2_rnaseq_mapping_star' {

  input:
      file genome from genome_file (1)
      file genomeDir from genome_dir_ch (2)
      set replicateId, file(reads) from reads_ch (3)

  output:
      set replicateId, file('Aligned.sortedByCoord.out.bam'), file('Aligned.sortedByCoord.out.bam.bai') into aligned_bam_ch (4)

  script:
  """
  # ngs-nf-dev Align reads to genome
  STAR --genomeDir $genomeDir \
       --readFilesIn $reads \
       --runThreadN ${task.cpus} \
       --readFilesCommand zcat \
       --outFilterType BySJout \
       --alignSJoverhangMin 8 \
       --alignSJDBoverhangMin 1 \
       --outFilterMismatchNmax 999

  # 2nd pass (improve alignmets using table of splice junctions and create a new index)
  mkdir genomeDir
  STAR --runMode genomeGenerate \
       --genomeDir genomeDir \
       --genomeFastaFiles $genome \
       --sjdbFileChrStartEnd SJ.out.tab \
       --sjdbOverhang 75 \
       --runThreadN ${task.cpus}

  # Final read alignments
  STAR --genomeDir genomeDir \
       --readFilesIn $reads \
       --runThreadN ${task.cpus} \
       --readFilesCommand zcat \
       --outFilterType BySJout \
       --alignSJoverhangMin 8 \
       --alignSJDBoverhangMin 1 \
       --outFilterMismatchNmax 999 \
       --outSAMtype BAM SortedByCoordinate \
       --outSAMattrRGline ID:$replicateId LB:library PL:illumina PU:machine SM:GM12878

  # Index the BAM file
  samtools index Aligned.sortedByCoord.out.bam (5)
  """
}