Workflow: trim-rnaseq-pe-dutp.cwl
Runs RNA-Seq BioWardrobe basic analysis with strand specific pair-end data file.
- Selected
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- 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. |
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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. |
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star_aligner |
../tools/star-alignreads.cwl
(CommandLineTool)
|
Tool runs STAR alignReads. |
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bowtie_aligner |
../tools/bowtie-alignreads.cwl
(CommandLineTool)
|
Tool maps input raw reads files to reference genome using Bowtie. |
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group_isoforms |
../tools/group-isoforms.cwl
(CommandLineTool)
|
Tool runs get_gene_n_tss.R script to group isoforms by gene and common TSS |
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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 |
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rpkm_calculation |
../tools/geep.cwl
(CommandLineTool)
|
geep |
Tool calculates RPKM values grouped by isoforms or genes. |
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. |
|
bam_to_bigwig_upstream |
../tools/bam-bedgraph-bigwig.cwl
(Workflow)
|
Workflow converts input BAM file into bigWig and bedGraph files. |
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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 |
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bam_to_bigwig_downstream |
../tools/bam-bedgraph-bigwig.cwl
(Workflow)
|
Workflow converts input BAM file into bigWig and bedGraph files. |
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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. |
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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 |
https://w3id.org/cwl/view/git/94c6ea7bf4b64599746d778568efbd8e10f0d5ba/workflows/trim-rnaseq-pe-dutp.cwl