Workflow: xenbase-rnaseq-pe.cwl
XenBase workflow for analysing RNA-Seq paired-end data
- 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 |
fasta_file_adapters | File [FASTA] | Adapters FASTA file |
Adapters FASTA file to be used by Trimmomatic |
fastq_file_upstream | File [FASTQ] | FASTQ upstream input file |
Upstream reads data in a FASTQ format, received after paired end sequencing |
rsem_indices_folder | Directory | RSEM indices folder |
Path to RSEM indices generated with BowTie2 |
bowtie_indices_folder | Directory | BowTie Ribosomal Indices |
Path to Bowtie generated indices for ribosomal FASTA |
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/custom-bash.cwl
(CommandLineTool)
|
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 |
|
bam_to_bigwig |
../subworkflows/bam-bedgraph-bigwig.cwl
(Workflow)
|
Workflow converts input BAM file into bigWig and bedGraph files |
|
trim_adapters |
../tools/trimmomatic.cwl
(CommandLineTool)
|
Tool runs trimmomatic with ILLUMINACLIP step by default. |
|
get_annotation_file |
../expressiontools/get-file-by-name.cwl
(ExpressionTool)
|
Returns file the first file from input File[], that match input regex expression |
|
get_chr_length_file |
../expressiontools/get-file-by-name.cwl
(ExpressionTool)
|
Returns file the first file from input File[], that match input regex expression |
|
ribo_bowtie_aligner |
../tools/bowtie-alignreads.cwl
(CommandLineTool)
|
Tool maps input raw reads files to reference genome using Bowtie. |
|
fastqc_stats_upstream |
../tools/fastqc.cwl
(CommandLineTool)
|
Tool runs FastQC from Babraham Bioinformatics |
|
extract_fastq_upstream |
../tools/extract-fastq.cwl
(CommandLineTool)
|
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 |
|
rename_rsem_genes_file |
../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 |
|
fastqc_stats_downstream |
../tools/fastqc.cwl
(CommandLineTool)
|
Tool runs FastQC from Babraham Bioinformatics |
|
rename_rsem_bambai_pair |
../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 |
|
extract_fastq_downstream |
../tools/extract-fastq.cwl
(CommandLineTool)
|
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 |
|
make_biowardrobe_isoforms |
../tools/python-make-biowardrobe-isoforms.cwl
(CommandLineTool)
|
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. |
|
rename_rsem_isoforms_file |
../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 |
|
rsem_calculate_expression |
../tools/rsem-calculate-expression.cwl
(CommandLineTool)
|
Tool runs rsem-calculate-expression. |
|
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] | Ribo Bowtie alignment log |
Ribo Bowtie alignment log file. Mostly for debug purposes |
bambai_pair | File [BAM] | Coordinate sorted BAM alignment file (+index BAI) |
Coordinate sorted BAM file and BAI index file |
bigwig_file | File [bigWig] | BigWig file |
Generated BigWig file |
get_stat_log | File [Textual format] | RSEM & Bowtie combined log |
Mapping statistics from RSEM & Bowtie logs |
rsem_genes_file | File [TSV] | RSEM genes expression file |
RSEM genes expression file |
rsem_stat_folder | Directory | RSEM alignment statistics |
RSEM generated statistics folder. Mostly for debug purposes |
rsem_isoforms_file | File [TSV] | RSEM isoforms expression file |
RSEM isoforms expression file |
biowardrobe_isoforms_file | File [CSV] | Biowardrobe compatible isoforms expression file |
Biowardrobe compatible isoforms expression file |
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/cf107bc24a37883ef01b959fd89c19456aaecc02/workflows/xenbase-rnaseq-pe.cwl