Generates FAI index file for input FASTA file Output file has the same basename, as input file, but with updated `.fai` extension. `samtools faidx` exports output file alognside the input file. To prevent tool from failing, `input_file` should be staged into output directory using `\"writable\": true`. Setting `writable: true` makes cwl-runner to make a copy of input file and mount it to docker container with `rw` mode as part of `--workdir` (if set to false, the file staged into output directory will be mounted to docker container separately with `ro` mode)

twoBitToFa - Convert all or part of .2bit file to fasta. Outputs only those chromosomes that are set in chr_list intput. Tool will fail if you include in chr_list those chromosomes that are absent in 2bit file. If gz is provided - use gunzip instead of twoBitToFa If FASTA file is provided, do nothing

Tool sorts data from `unsorted_file` by key

`default_output_filename` function returns file name identical to `unsorted_file`, if `output_filename` is not provided.

Tool returns directory with indices generated by STAR. If genome_dir input is not provided, use default output directory name star_indices. Output chr_name_length should not be moved outside the indices folder.

Tool runs bowtie-build Not supported parameters: -c - reference sequences given on cmd line (as <seq_in>)

Tool converts bed file to bigBed

Before running `baseCommand` the following files are created in Docker working directory (using `InitialWorkDirRequirement`): `narrowpeak.as` - default BED file structure template for ENCODE narrowPeak format `broadpeak.as` - default BED file structure template for ENCODE broadPeak format

`default_output_filename` function returns default output file name based on `input_bed` basename with `*.bb` extension if `output_filename` is not provided.

`get_bed_type` function returns default BED file type if `bed_type` is not provided. Depending on `input_bed` file extension the following values are returned: `*.narrowpeak` --> bed6+4 `*.broadpeak` --> bed6+3 else --> null (`bedToBigBed` will use its own default value)

`get_bed_template` function returns default BED file template if `bed_template` is not provided. Depending on `input_bed` file extension the following values are returned: `*.narrowpeak` --> narrowpeak.as (previously staged into Docker working directory) `*.broadpeak` --> broadpeak.as (previously staged into Docker working directory) else --> null (`bedToBigBed` will use its own default value)

Tool runs bowtie-build Not supported parameters: -c - reference sequences given on cmd line (as <seq_in>)

twoBitToFa - Convert all or part of .2bit file to fasta. Outputs only those chromosomes that are set in chr_list intput. Tool will fail if you include in chr_list those chromosomes that are absent in 2bit file. If gz is provided - use gunzip instead of twoBitToFa If FASTA file is provided, do nothing

Tool returns directory with indices generated by STAR. If genome_dir input is not provided, use default output directory name star_indices. Output chr_name_length should not be moved outside the indices folder.