star_workflow

Inputs

Required

• fastq1 (File, required)

• prefix (String, required)

• star_index (File, required)

Optional

• fastq2 (File?)

• star.sjdbFileChrStartEnd (File?)

• star.varVCFfile (File?)

• star.waspOutputMode (String?)

Defaults

• star.alignIntronMax (Int, default=1000000)

• star.alignIntronMin (Int, default=20)

• star.alignMatesGapMax (Int, default=1000000)

• star.alignSJDBoverhangMin (Int, default=1)

• star.alignSJoverhangMin (Int, default=8)

• star.alignSoftClipAtReferenceEnds (String, default=”Yes”)

• star.chimJunctionOverhangMin (Int, default=15)

• star.chimMainSegmentMultNmax (Int, default=1)

• star.chimOutJunctionFormat (Int, default=1)

• star.chimOutType (String, default=”Junctions WithinBAM SoftClip”)

• star.chimSegmentMin (Int, default=15)

• star.disk_space (Int, default=500)

• star.limitSjdbInsertNsj (Int, default=1200000)

• star.memory (Int, default=64)

• star.num_preempt (Int, default=1)

• star.num_threads (Int, default=16)

• star.outFilterIntronMotifs (String, default=”None”)

• star.outFilterMatchNminOverLread (Float, default=0.33)

• star.outFilterMismatchNmax (Int, default=999)

• star.outFilterMismatchNoverLmax (Float, default=0.1)

• star.outFilterMultimapNmax (Int, default=20)

• star.outFilterScoreMinOverLread (Float, default=0.33)

• star.outFilterType (String, default=”BySJout”)

• star.outSAMattrRGline (String, default=”ID:rg1 SM:sm1”)

• star.outSAMattributes (String, default=”NH HI AS nM NM ch”)

• star.outSAMstrandField (String, default=”intronMotif”)

• star.quantMode (String, default=”TranscriptomeSAM GeneCounts”)

Outputs

• bam_file (File)

• bam_index (File)

• transcriptome_bam (File)

• chimeric_junctions (File)

• chimeric_bam_file (File)

• chimeric_bam_index (File)

• read_counts (File)

• junctions (File)

• junctions_pass1 (File)

• logs (Array[File])

star

author : Francois Aguet

Inputs

Required

• fastq1 (File, required)

• prefix (String, required)

• star_index (File, required)

Optional

• fastq2 (File?)

• sjdbFileChrStartEnd (File?)

• varVCFfile (File?)

• waspOutputMode (String?)

Defaults

• alignIntronMax (Int, default=1000000)

• alignIntronMin (Int, default=20)

• alignMatesGapMax (Int, default=1000000)

• alignSJDBoverhangMin (Int, default=1)

• alignSJoverhangMin (Int, default=8)

• alignSoftClipAtReferenceEnds (String, default=”Yes”)

• chimJunctionOverhangMin (Int, default=15)

• chimMainSegmentMultNmax (Int, default=1)

• chimOutJunctionFormat (Int, default=1)

• chimOutType (String, default=”Junctions WithinBAM SoftClip”)

• chimSegmentMin (Int, default=15)

• disk_space (Int, default=500)

• limitSjdbInsertNsj (Int, default=1200000)

• memory (Int, default=64)

• num_preempt (Int, default=1)

• num_threads (Int, default=16)

• outFilterIntronMotifs (String, default=”None”)

• outFilterMatchNminOverLread (Float, default=0.33)

• outFilterMismatchNmax (Int, default=999)

• outFilterMismatchNoverLmax (Float, default=0.1)

• outFilterMultimapNmax (Int, default=20)

• outFilterScoreMinOverLread (Float, default=0.33)

• outFilterType (String, default=”BySJout”)

• outSAMattrRGline (String, default=”ID:rg1 SM:sm1”)

• outSAMattributes (String, default=”NH HI AS nM NM ch”)

• outSAMstrandField (String, default=”intronMotif”)

• quantMode (String, default=”TranscriptomeSAM GeneCounts”)

Outputs

• bam_file (File)

• bam_index (File)

• transcriptome_bam (File)

• chimeric_junctions (File)

• chimeric_bam_file (File)

• chimeric_bam_index (File)

• read_counts (File)

• junctions (File)

• junctions_pass1 (File)

• logs (Array[File])