Runs CrossMap.py script to project input BAM, BED, BIGWIG file based on input chain file. Not supported input file types: SAM, GFF, VCF, WIG

If `output_basename` is not set, call get_output_filename() and get_log_filename() functions to get default output and log filenames. Input `output_basename` should not include extension.

Runs CrossMap.py script to project input BAM, BED, BIGWIG file based on input chain file. Not supported input file types: SAM, GFF, VCF, WIG

If `output_basename` is not set, call get_output_filename() and get_log_filename() functions to get default output and log filenames. Input `output_basename` should not include extension.

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

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

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

Workflow converts input BAM file into bigWig and bedGraph files

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 sort BAM/SAM file (set as input `sort_input`). If input `trigger` is set to `true` or isn't set at all (`true` is used by default), run `samtools sort`, return newly generated sorted BAM/SAM/CRAM file (the actual format of the output file depends on `out_format` value and extension of a filename set in `sort_output_filename`). If input `trigger` is set to `false`, return unchanged BAM/SAM file, previously staged into output directory.

Before `baseCommand` is executed, input BAM/SAM file is staged into output directory (docker parameter `--workdir`), using `InitialWorkDirRequirement`. Setting `writable: true` makes cwl-runner to copy input BAM/SAM 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). Because `samtools sort` can overwrite input BAM/SAM file and save output with the same name, we don't need to rename it (as we did for samtools rmdup).

Trigger logic is implemented in bash script set by default in input `bash_script`. If first argment $0 (which is `trigger` input) is true, run `samtools sort` with the rest of the arguments. If $0 is not true, skip `samtools sort` and return input BAM/SAM file, previously 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 logic in bash script saved in `bash_script` input.

`default_output_name` function is used for generating output filename if input `sort_output_filename` is not set or in case when `trigger` is false and we need to return original BAM/SAM file staged into output directory.

`ext` function returns output filename extension on the base of `out_format` value. If input `out_format` is not set, use `.bam` by default. If input `trigger` is false, `out_format` is ignored.

If `trigger` is set to true (or true is used by default), but both `sort_output_filename` and `out_format` are not set, the output file format will be BAM by default.

If `trigger` is set to true (or true is used by default) and `sort_output_filename` is set to some value, but `out_format` is not set, the actual format of output file will be defined on the filename extension set in `sort_output_filename` (if filename doesn't have any extension, BAM is used by default). When `out_format` is also set, it overwrites extension generated on the base of `sort_output_filename` value.

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