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Commit 6c751607 authored by nservant's avatar nservant
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update help

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......@@ -34,7 +34,7 @@ def helpMessage() {
--save_reference [bool] Save reference genome to output folder. Default: False
Alignments
--split_fastq [bool] Size of read chuncks to use to speed up the workflow. Default: None
--split_fastq [int] Size of read chuncks to use to speed up the workflow. Default: None
--save_aligned_intermediates [bool] Save intermediates alignment files. Default: False
--bwt2_opts_end2end [str] Options for bowtie2 end-to-end mappinf (first mapping step). See hic.config for default.
--bwt2_opts_trimmed [str] Options for bowtie2 mapping after ligation site trimming. See hic.config for default.
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