CLIPper is a tool to define peaks in your CLIP-seq dataset. CLIPper was developed in the Yeo Lab at the University of California, San Diego. Usage: clipper --bam CLIP-seq_reads.srt.bam --species hg19 --outfile CLIP-seq_reads.srt.peaks.bed

Tool: bedtools bamtobed (aka bamToBed) Version: v2.26.0 Summary: Converts BAM alignments to BED6 or BEDPE format.

Usage: bedtools bamtobed [OPTIONS] -i <bam>

Options: -bedpe Write BEDPE format. - Requires BAM to be grouped or sorted by query.

-mate1 When writing BEDPE (-bedpe) format, always report mate one as the first BEDPE \"block\".

-bed12 Write \"blocked\" BED format (aka \"BED12\"). Forces -split.

http://genome-test.cse.ucsc.edu/FAQ/FAQformat#format1

-split Report \"split\" BAM alignments as separate BED entries. Splits only on N CIGAR operations.

-splitD Split alignments based on N and D CIGAR operators. Forces -split.

-ed Use BAM edit distance (NM tag) for BED score. - Default for BED is to use mapping quality. - Default for BEDPE is to use the minimum of the two mapping qualities for the pair. - When -ed is used with -bedpe, the total edit distance from the two mates is reported.

-tag Use other NUMERIC BAM alignment tag for BED score. - Default for BED is to use mapping quality. Disallowed with BEDPE output.

-color An R,G,B string for the color used with BED12 format. Default is (255,0,0).

-cigar Add the CIGAR string to the BED entry as a 7th column.

dedup.py - Deduplicate reads that are coded with a UMI =========================================================

:Author: Ian Sudbery, Tom Smith :Release: $Id$ :Date: |today| :Tags: Python UMI

Purpose -------

The purpose of this command is to deduplicate BAM files based on the first mapping co-ordinate and the UMI attached to the read.

Selecting the representative read ---------------------------------

The following criteria are applied to select the read that will be retained from a group of duplicated reads:

1. The read with the lowest number of mapping coordinates (see --multimapping-detection-method option) 2. The read with the highest mapping quality

Otherwise a read is chosen at random.

detecting peaks from CLIP data Usage: tag2peak.pl [options] <tag.bed> <peak.bed> <tag.bed> : BED file of unique CLIP tags, input <peak.bed>: BED file of called peaks, output Options: -big : big input file -ss : separate the two strands --valley-seeking : find candidate peaks by valley seeking --valley-depth [float] : depth of valley if valley seeking (0.9) --out-boundary [string]: output cluster boundaries --out-half-PH [string]: output half peak height boundaries --dbkey [string]: species to retrieve the default gene bed file (mm10|hg19) --gene [string]: custom gene bed file for scan statistics (will override --dbkey) --use-expr : use expression levels given in the score column in the custom gene bed file for normalization -p [float] : threshold of p-value to call peak (0.01) --multi-test : do Bonferroni multiple test correction -minPH [int] : min peak height (2) -maxPH [int] : max peak height to calculate p-value(-1, no limit if < 0) --skip-out-of-range-peaks: skip peaks with PH > maxPH -gap [int] : merge cluster peaks closer than the gap (-1, no merge if < 0) --prefix [string]: prefix of peak id (Peak) -c [dir] : cache dir --keep-cache : keep cache when the job done -v : verbose

Tool runs Trimgalore - the wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files.

`default_log_name` function returns names for generated log files (for both paired-end and single-end cases). `trim_galore` itself doesn't support setting custom names for output files.

For paired-end data processing both `input_file_pair` and `paired` should be set. If either of them is not set, the other one becomes unset automatically.

extract.py - Extract UMI from fastq ====================================================

:Author: Ian Sudbery, Tom Smith :Release: $Id$ :Date: |today| :Tags: Python UMI

Purpose -------

Extract UMI barcode from a read and add it to the read name, leaving any sample barcode in place. Can deal with paired end reads and UMIs split across the paired ends. Can also optionally extract cell barcodes and append these to the read name also. See the section below for an explanation for how to encode the barcode pattern(s) to specficy the position of the UMI +/- cell barcode.

Filtering and correcting cell barcodes --------------------------------------

umi_tools extract can optionally filter cell barcodes (--filter-cell-barcode) against a user-supplied whitelist (--whitelist). If a whitelist is not available for your data, e.g if you have performed droplet-based scRNA-Seq, you can use the whitelist tool.

Cell barcodes which do not match the whitelist (user-generated or automatically generated) can also be optionally corrected using the --error-correct-cell option.

The whitelist should be in the following format (tab-separated):

AAAAAA AGAAAA AAAATC AAACAT AAACTA AAACTN,GAACTA AAATAC AAATCA GAATCA AAATGT AAAGGT,CAATGT

Where column 1 is the whitelisted cell barcodes and column 2 is the list (comma-separated) of other cell barcodes which should be corrected to the barcode in column 1. If the --error-correct-cell option is not used, this column will be ignored. Any additional columns in the whitelist input, such as the counts columns from the output of umi_tools whitelist, will be ignored.

Tool runs STAR alignReads.

`default_output_name_prefix` function returns output files prefix if `outFileNamePrefix` is not set. By default prefix is equal to basename of `readFilesIn`.

Workflow converts input BAM file into bigWig and bedGraph files

Tool to decompress input FASTQ file Bash script's logic: - disable case sensitive glob check - check if root name of input file already include '.fastq' or '.fq' extension. If yes, set DEFAULT_EXT to \"\" - check file type, decompress if needed - return 1, if file type is not recognized This script also works of input file doesn't have any extension at all

Tool assigns each peak obtained from MACS2 to a gene and region (upstream, promoter, exon, intron, intergenic)

`default_output_filename` function returns output filename with sufix set as `ext` argument. Function is called when either `output_filename` or `log_filename` inputs are not provided.

Tool to sort and index input BAM/SAM/CRAM. If input `trigger` is set to `true` or isn't set at all (`true` is used by default), run `samtools sort` and `samtools index`, return sorted BAM and BAI/CSI index file. If input `trigger` is set to `false`, return unchanged `sort_input` (BAM/SAM/CRAM) and index (BAI/CSI, if provided in `secondaryFiles`) files, previously staged into output directory.

Before execution `baseCommand`, `sort_input` and `secondaryFiles` (if provided) are staged into directory set as docker parameter `--workdir` (tool's output directory), using `InitialWorkDirRequirement`. Setting `writable: true` makes cwl-runner to make copies of the `sort_input` and `secondaryFiles` (if provided) and mount them to docker container with `rw` mode as part of `--workdir` (if set to false, the files staged into output directory will be mounted to docker container separately with `ro` mode). Because both `samtools sort` and `samtools index` can overwrite files with the same names (and in case of `samtools sort` even the input file can be overwritten), we don't need to rename any of the staged files.

Trigger logic is implemented in two bash scripts set by default as `bash_script_sort` and `bash_script_index` inputs. For both of then, if the first argument $0 (which is `trigger` input) is true, run `samtools sort/index` with the rest of the arguments. If $0 is not true, skip `samtools sort/index` and return `sort_input` and `secondaryFiles` (if provided) staged into output directory.

Input `trigger` is Boolean, but returns String, because of `valueFrom` field. The `valueFrom` is used, because if `trigger` is false, cwl-runner doesn't append this argument at all to the the `baseCommand` - new feature of CWL v1.0.2. Alternatively, `prefix` field could be used, but it causes changing in script logic.

If using `sort_output_filename`, the output file extension should be `*.bam`, because `samtools sort` defines the output file format on the base of the file extension. If `*.sam` is sed as output filename, it cannot be usefully indexed by `samtools index`.

`default_bam` function is used to generate output filename for `samtools sort` if input `sort_output_filename` is not set or when `trigger` is false and we need to return `sort_input` and `secondaryFiles` (if provided) files staged into output directory. Output filename is generated on the base of `sort_input` basename with `.bam` extension by default.

`ext` function is used to return the index file extension (BAI/CSI) based on `csi` and `bai` inputs according to the following logic `csi` && `bai` => BAI !`csi` && !`bai ` => BAI `csi` && !`bai ` => CSI

Tool to sort and index input BAM/SAM/CRAM. If input `trigger` is set to `true` or isn't set at all (`true` is used by default), run `samtools sort` and `samtools index`, return sorted BAM and BAI/CSI index file. If input `trigger` is set to `false`, return unchanged `sort_input` (BAM/SAM/CRAM) and index (BAI/CSI, if provided in `secondaryFiles`) files, previously staged into output directory.

Before execution `baseCommand`, `sort_input` and `secondaryFiles` (if provided) are staged into directory set as docker parameter `--workdir` (tool's output directory), using `InitialWorkDirRequirement`. Setting `writable: true` makes cwl-runner to make copies of the `sort_input` and `secondaryFiles` (if provided) and mount them to docker container with `rw` mode as part of `--workdir` (if set to false, the files staged into output directory will be mounted to docker container separately with `ro` mode). Because both `samtools sort` and `samtools index` can overwrite files with the same names (and in case of `samtools sort` even the input file can be overwritten), we don't need to rename any of the staged files.

Trigger logic is implemented in two bash scripts set by default as `bash_script_sort` and `bash_script_index` inputs. For both of then, if the first argument $0 (which is `trigger` input) is true, run `samtools sort/index` with the rest of the arguments. If $0 is not true, skip `samtools sort/index` and return `sort_input` and `secondaryFiles` (if provided) staged into output directory.

Input `trigger` is Boolean, but returns String, because of `valueFrom` field. The `valueFrom` is used, because if `trigger` is false, cwl-runner doesn't append this argument at all to the the `baseCommand` - new feature of CWL v1.0.2. Alternatively, `prefix` field could be used, but it causes changing in script logic.

If using `sort_output_filename`, the output file extension should be `*.bam`, because `samtools sort` defines the output file format on the base of the file extension. If `*.sam` is sed as output filename, it cannot be usefully indexed by `samtools index`.

`default_bam` function is used to generate output filename for `samtools sort` if input `sort_output_filename` is not set or when `trigger` is false and we need to return `sort_input` and `secondaryFiles` (if provided) files staged into output directory. Output filename is generated on the base of `sort_input` basename with `.bam` extension by default.

`ext` function is used to return the index file extension (BAI/CSI) based on `csi` and `bai` inputs according to the following logic `csi` && `bai` => BAI !`csi` && !`bai ` => BAI `csi` && !`bai ` => CSI

Tool maps input raw reads files to reference genome using Bowtie.

`default_output_filename` function returns default name for SAM output and log files. In case when `sam` and `output_filename` inputs are not set, default filename will have `.sam` extension but format may not correspond SAM specification. To set output filename manually use `output_filename` input. Default output filename is based on `output_filename` or basename of `upstream_filelist`, `downstream_filelist` or `crossbow_filelist` file (if array, the first file in array is taken). If function is called without argenments and `output_filename` input is set, it will be returned from the function.

For single-end input data any of the `upstream_filelist` or `downstream_filelist` inputs can be used.

Log filename (`log_file` output) is generated by `default_output_filename` function with ex='.bw'

`indices_folder` defines folder to contain Bowtie indices. Based on the first found file with `rev.1.ebwt` or `rev.1.ebwtl` extension, bowtie index prefix is returned from input's `valueFrom` field.

Tool calculates statistics on the base of FASTQ file quality scores. If `output_filename` is not provided call function `default_output_filename` to return default output file name generated as `input_file` basename + `.fastxstat` extension.

Tool calculates statistics on the base of FASTQ file quality scores. If `output_filename` is not provided call function `default_output_filename` to return default output file name generated as `input_file` basename + `.fastxstat` extension.