Tool to run custom script set as `script` input with arguments from `param`. Default script runs sed command over the input file and exports results to the file with the same name as input's basename

Workflow converts input BAM file into bigWig and bedGraph files

Tool runs trimmomatic with ILLUMINACLIP step by default.

`-basein` and `-baseout` inputs are skipped.

If set `lib_type` to `PE`, both of the inputs `fastq_file_upstream` and `fastq_file_downstream` shoul be provided.

If input `trigger` is set to `true` or isn't set at all (`true` is used by default), run `trimmomatic` and return FASTQ file[s] with trimmed adapters, alongside with the uppaired reads FASTQ files (if `lib_type` is set to `PE` and such files are present after running `trimmomatic`) If input `trigger` is set to `false`, return unchanged `fastq_file_upstream` and `fastq_file_downstream`, previously staged into output directory.

Before execution `baseCommand`, `fastq_file_upstream` and `fastq_file_downstream` (if provided) are staged into directory set as docker parameter `--workdir` (tool's output directory), using `InitialWorkDirRequirement`. They are mount to docker container with `ro` mode as part of `--workdir`, because all generated files will have `trimmed` suffix in their names, so the staged files will not be overwritten.

Trigger logic is implemented in a bash scripts set by default as `bash_script` input. If the first argument $0 (which is `trigger` input) is true, run `trimmomatic` with the rest of the arguments. If $0 is not true, skip `trimmomatic` and return `fastq_file_upstream` and `fastq_file_downstream` (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.

`default_output_name` function is used for generating output filename based on `input_file.basename` and provided extension.

Returns file the first file from input File[], that match input regex expression

Returns file the first file from input File[], that match input regex expression

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 runs FastQC from Babraham Bioinformatics

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 renames `source_file` to `target_filename`. Input `target_filename` should be set as string. If it's a full path, only basename will be used. If BAI file is present, it will be renamed too

Tool runs FastQC from Babraham Bioinformatics

Tool renames `source_file` to `target_filename`. Input `target_filename` should be set as string. If it's a full path, only basename will be used. If BAI file is present, it will be renamed too

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 to generate BioWardrobe compatible isoforms file from RSEM outputs. `rsem_annotation_file` and `rsem_isoforms_file` are supposed to have identical order and number of isoforms. FPKM value is used intead of RPKM.

Tool renames `source_file` to `target_filename`. Input `target_filename` should be set as string. If it's a full path, only basename will be used. If BAI file is present, it will be renamed too

Tool runs rsem-calculate-expression.

`reference_name` parameter for RSEM is resolved from `indices_folder` input. If `paired_end` input is not set, but both of the `upstream_read_file` and `downstream_read_file` are present, set `paired_end` automatically.

`default_output_filename` function return prefix fot output files generated by RSEM based on `upstream_read_file` or `downstream_read_file` basename, if `output_filename` input is not provided

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.