Workflow: trim-rnaseq-pe-dutp.cwl

Fetched 2024-11-09 20:34:34 GMT

Runs RNA-Seq BioWardrobe basic analysis with strand specific pair-end data file.

children parents
Workflow as SVG
  • Selected
  • Default Values
  • Nested Workflows
  • Tools
  • Inputs/Outputs

Inputs

ID Type Title Doc
threads Integer (Optional) Number of threads

Number of threads for those steps that support multithreading

clip_3p_end Integer (Optional) Clip from 3p end

Number of bases to clip from the 3p end

clip_5p_end Integer (Optional) Clip from 5p end

Number of bases to clip from the 5p end

exclude_chr String (Optional) Chromosome to be excluded in rpkm calculation

Chromosome to be excluded in rpkm calculation

annotation_file File [GTF] Annotation file

GTF or TAB-separated annotation file

chrom_length_file File [Textual format] Chromosome length file

Chromosome length file

fastq_file_upstream File [FASTQ] FASTQ upstream input file

Upstream reads data in a FASTQ format, received after paired end sequencing

star_indices_folder Directory STAR indices folder

Path to STAR generated indices

bowtie_indices_folder Directory BowTie Ribosomal Indices

Path to Bowtie generated indices

fastq_file_downstream File [FASTQ] FASTQ downstream input file

Downstream reads data in a FASTQ format, received after paired end sequencing

Steps

ID Runs Label Doc
get_stat
../tools/python-get-stat-rnaseq.cwl (CommandLineTool)

Tool processes and combines log files generated by STAR/Bowtie aligners and GEEP rpkm results file.

`get_output_filename` function returns output filename equal to `output_filename` (if input is provided) or generated on the base of STAR log basename with `.stat` extension.

`get_formatted_output_filename` function returns output filename equal to `formatted_output_filename` (if input is provided) or generated on the base of STAR log basename with `_stats.tsv` extension.

trim_fastq
../tools/trimgalore.cwl (CommandLineTool)

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

star_aligner
../tools/star-alignreads.cwl (CommandLineTool)

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`.

bowtie_aligner
../tools/bowtie-alignreads.cwl (CommandLineTool)

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.

group_isoforms
../tools/group-isoforms.cwl (CommandLineTool)

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

rename_upstream
../tools/rename.cwl (CommandLineTool)

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

rpkm_calculation
../tools/geep.cwl (CommandLineTool)
geep

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.

rename_downstream
../tools/rename.cwl (CommandLineTool)

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

samtools_sort_index
../tools/samtools-sort-index.cwl (CommandLineTool)

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

bam_to_bigwig_upstream

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.

extract_fastq_upstream
../tools/extract-fastq.cwl (CommandLineTool)

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

bam_to_bigwig_downstream

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.

extract_fastq_downstream
../tools/extract-fastq.cwl (CommandLineTool)

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

fastx_quality_stats_upstream
../tools/fastx-quality-stats.cwl (CommandLineTool)

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.

fastx_quality_stats_downstream
../tools/fastx-quality-stats.cwl (CommandLineTool)

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.

Outputs

ID Type Label Doc
bowtie_log File [Textual format] Bowtie alignment log

Bowtie alignment log file

rpkm_genes File [TSV] RPKM, grouped by gene name

Calculated rpkm values, grouped by gene name

bambai_pair File [BAM] Coordinate sorted BAM alignment file (+index BAI)

Coordinate sorted BAM file and BAI index file

star_sj_log File (Optional) [Textual format] STAR sj log

STAR SJ.out.tab

get_stat_log File (Optional) [Textual format] Bowtie, STAR and GEEP combined log

Processed and combined Bowtie & STAR aligner and GEEP logs

star_out_log File (Optional) [Textual format] STAR log out

STAR Log.out

rpkm_isoforms File [CSV] RPKM, grouped by isoforms

Calculated rpkm values, grouped by isoforms

star_final_log File [Textual format] STAR final log

STAR Log.final.out

bigwig_upstream File [bigWig] BigWig file

Generated upstream BigWig file

rpkm_common_tss File [TSV] RPKM, grouped by common TSS

Calculated rpkm values, grouped by common TSS

star_stdout_log File (Optional) [Textual format] STAR stdout log

STAR Log.std.out

bigwig_downstream File [bigWig] BigWig file

Generated downstream BigWig file

star_progress_log File (Optional) [Textual format] STAR progress log

STAR Log.progress.out

trim_report_upstream File TrimGalore report Upstream

TrimGalore generated log for upstream FASTQ

get_stat_formatted_log File (Optional) [TSV] Bowtie, STAR and GEEP combined formatted log

Processed and combined Bowtie & STAR aligner and GEEP formatted logs

trim_report_downstream File TrimGalore report Downstream

TrimGalore generated log for downstream FASTQ

fastx_statistics_upstream File [Textual format] FASTQ upstream statistics

fastx_quality_stats generated upstream FASTQ quality statistics file

fastx_statistics_downstream File [Textual format] FASTQ downstream statistics

fastx_quality_stats generated downstream FASTQ quality statistics file

Permalink: https://w3id.org/cwl/view/git/94c6ea7bf4b64599746d778568efbd8e10f0d5ba/workflows/trim-rnaseq-pe-dutp.cwl