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 processes and combines log files generated by Trimgalore, Bowtie, Samtools and MACS2.

`get_output_prefix` function returns output file prefix equal to `output_prefix`+`_collected_statistics_report` (if this input is provided) or generated on the base of bowtie log basename with `_collected_statistics_report` extension.

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.

If input trigger was set to false, skip running trimaglore and return unchanged input files

If the number of reads in the trimmed_fastq_file is less then min_reads_count, tool will return original_fastq_file and null as selected_report_file. Otherwise, the trimmed_fastq_file and trimming_report_file will be returned. Might be usefull in case of trimgalore removed all reads from the original_fastq_file

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`.

Tool to decompress input FASTQ file(s). If several FASTQ files are provided, they will be concatenated in the order that corresponds to files in input. 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 \"\", otherwise use '.fastq' - 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

Runs R script to produce gene body average tag density plot and RPKM distribution histogram Doesn't fail even when we couldn't produce any plots

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 get_gene_n_tss.R script to group isoforms by gene and common TSS

Tool calculates RPKM values grouped by isoforms or genes.

`default_output_prefix` function returns default prefix based on `bam_file` basename, if `output_prefix` is not provided.

genePredToGtf - Convert genePred table or file to gtf

Generates statistics for the input BAM file.

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 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.

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).

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. 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

Workflow converts input BAM file into bigWig and bedGraph files.

Input BAM file should be sorted by coordinates (required by `bam_to_bedgraph` step).

If `split` input is not provided use true by default. Default logic is implemented in `valueFrom` field of `split` input inside `bam_to_bedgraph` step to avoid possible bug in cwltool with setting default values for workflow inputs.

`scale` has higher priority over the `mapped_reads_number`. The last one is used to calculate `-scale` parameter for `bedtools genomecov` (step `bam_to_bedgraph`) only in a case when input `scale` is not provided. All logic is implemented inside `bedtools-genomecov.cwl`.

`bigwig_filename` defines the output name only for generated bigWig file. `bedgraph_filename` defines the output name for generated bedGraph file and can influence on generated bigWig filename in case when `bigwig_filename` is not provided.

All workflow inputs and outputs don't have `format` field to avoid format incompatibility errors when workflow is used as subworkflow.

Workflow converts input BAM file into bigWig and bedGraph files.

Input BAM file should be sorted by coordinates (required by `bam_to_bedgraph` step).

If `split` input is not provided use true by default. Default logic is implemented in `valueFrom` field of `split` input inside `bam_to_bedgraph` step to avoid possible bug in cwltool with setting default values for workflow inputs.

`scale` has higher priority over the `mapped_reads_number`. The last one is used to calculate `-scale` parameter for `bedtools genomecov` (step `bam_to_bedgraph`) only in a case when input `scale` is not provided. All logic is implemented inside `bedtools-genomecov.cwl`.

`bigwig_filename` defines the output name only for generated bigWig file. `bedgraph_filename` defines the output name for generated bedGraph file and can influence on generated bigWig filename in case when `bigwig_filename` is not provided.

All workflow inputs and outputs don't have `format` field to avoid format incompatibility errors when workflow is used as subworkflow.

For convenience to use in the workflow that sort and index BAM files by coordinate this tools expects coordinate sorted and indexed BAM file as input. For single-read dat it won't influence on anything, for paired-end the more memory will be used to keep reads while looking for their proper pairs (see --max-reads-in-buffer parameter).

Current limitations: - only one `--additional-attr` is supported - skip `--nprocesses` parameter as it's not helpful when we use only one input BAM file