1 #!/usr/bin/env cwl-runner
7 dockerPull: "quay.io/biocontainers/star:2.7.5c--0"
14 prefix: "--runThreadN"
26 prefix: "--readFilesIn"
29 # If paired-end reads (like Illumina), both 1 and 2 must be provided.
45 prefix: "--sjdbGTFfile"
50 prefix: "--sjdbOverhang"
60 prefix: "--outFilterType"
62 OutFilterIntronMotifs:
69 - RemoveNoncanonicalUnannotated
71 prefix: "--outFilterIntronMotifs"
81 prefix: "--outSAMtype"
93 prefix: "SortedByCoordinate"
99 prefix: "--readFilesCommand"
104 prefix: "--alignIntronMin"
109 prefix: "--alignIntronMax"
114 prefix: "--alignMatesGapMax"
119 prefix: "--alignSJoverhangMin"
121 AlignSJDBoverhangMin:
124 prefix: "--alignSJDBoverhangMin"
129 prefix: "--seedSearchStartLmax"
139 - "WithinBAM HardClip"
140 - "WithinBAM SoftClip"
145 prefix: "--chimSegmentMin"
147 ChimJunctionOverhangMin:
150 prefix: "--chimJunctionOverhangMin"
152 OutFilterMultimapNmax:
155 prefix: "--outFilterMultimapNmax"
157 OutFilterMismatchNmax:
160 prefix: "--outFilterMismatchNmax"
162 OutFilterMismatchNoverLmax:
165 prefix: "--outFilterMismatchNoverLmax"
175 prefix: "--outReadsUnmapped"
185 prefix: "--outSAMstrandField"
196 prefix: "--outSAMunmapped"
201 prefix: "--outSAMmapqUnique"
212 prefix: "--outSAMmode"
214 LimitOutSAMoneReadBytes:
217 prefix: "--limitOutSAMoneReadBytes"
222 prefix: "--outFileNamePrefix"
235 prefix: "--genomeLoad"
237 baseCommand: [STAR, --runMode, alignReads]
248 glob: "Unmapped.out*"