Workflow: QuantSeq 3' FWD, FWD-UMI or REV for single-read mRNA-Seq data
### Devel version of QuantSeq 3' FWD, FWD-UMI or REV for single-read mRNA-Seq data
- 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 multi-threading |
use_umi | Boolean (Optional) | Use UMIs |
Use UMIs (for FWD-UMI libraries) |
fastq_file | File [FASTQ] | FASTQ input file |
Reads data in a FASTQ format |
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 |
minimum_rpkm | Float (Optional) | Minimum RPKM for Gene Body Average Tag Density Plot |
Minimum RPKM for Gene Body Average Tag Density Plot |
annotation_file | File [GTF] | Annotation file |
GTF or TAB-separated annotation file |
chrom_length_file | File [Textual format] | Chromosome length file |
Chromosome length file |
strand_specificity | Strand specificity. 'Yes' for FWD or FWD-UMI analyses, 'Reverse' for REV, 'No' to disable |
Whether the data is from a strand-specific assay. For stranded=no, a read is considered overlapping with a feature regardless of whether it is mapped to the same or the opposite strand as the feature. For stranded=yes and single-end reads, the read has to be mapped to the same strand as the feature. For paired-end reads, the first read has to be on the same strand and the second read on the opposite strand. For stranded=reverse, these rules are reversed. |
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annotation_gtf_file | File [GTF] | GTF annotation file |
GTF annotation file |
star_indices_folder | Directory | STAR indices folder |
Path to STAR generated indices |
bowtie_indices_folder | Directory | BowTie Ribosomal Indices |
Path to Bowtie generated indices |
Steps
ID | Runs | Label | Doc |
---|---|---|---|
get_stat |
../tools/collect-statistics-rna-quantseq.cwl
(CommandLineTool)
|
Tool processes and combines log files generated by Trimgalore, Bowtie, Samtools and MACS2. |
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star_aligner |
../tools/star-alignreads.cwl
(CommandLineTool)
|
Tool runs STAR alignReads. |
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extract_fastq |
../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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get_gene_body |
../tools/plugin-plot-rna.cwl
(CommandLineTool)
|
Gene body average tag density plot and RPKM distribution histogram |
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 |
trim_adapters |
trim-quantseq-mrnaseq-se-strand-specific.cwl#trim_adapters/a431e959-2427-41a1-81f8-39387f0b51a2
(CommandLineTool)
|
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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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umi_tools_dedup |
../tools/umi-tools-dedup.cwl
(CommandLineTool)
|
Deduplicate BAM files based on the first mapping co-ordinate and the UMI attached to the read Only -I, --paired and -S parameters are implemented. |
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get_bam_statistics |
../tools/samtools-stats.cwl
(CommandLineTool)
|
Generates statistics for the input BAM file. |
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fastx_quality_stats |
../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. |
|
move_umi_to_read_name |
../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 |
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bam_to_bigwig_upstream |
../tools/bam-bedgraph-bigwig.cwl
(Workflow)
|
Workflow converts input BAM file into bigWig and bedGraph files. |
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bam_to_bigwig_downstream |
../tools/bam-bedgraph-bigwig.cwl
(Workflow)
|
Workflow converts input BAM file into bigWig and bedGraph files. |
|
feature_expression_merge |
../tools/feature-merge.cwl
(CommandLineTool)
|
Feature merge - merges feature files based on the specified columns |
Tool merges input feature files based on the columns provided in --mergeby
input. All input feature CSV/TSV files should have the header (case-sensitive)
Format of the input files is identified based on file's extension
*.csv - CSV
*.tsv - TSV
Otherwise used CSV by default |
group_transcript_expression |
trim-quantseq-mrnaseq-se-strand-specific.cwl#group_transcript_expression/b625ab9a-4bc5-4aa1-96d9-d8830551dffa
(CommandLineTool)
|
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samtools_sort_index_after_dedup |
../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. |
|
geep_count_transcript_expression |
../tools/geep.cwl
(CommandLineTool)
|
geep |
Tool calculates RPKM values grouped by isoforms or genes. |
group_geep_transcript_expression |
trim-quantseq-mrnaseq-se-strand-specific.cwl#group_geep_transcript_expression/0bcba6ff-25bd-4e95-9948-4f1c129dd853
(CommandLineTool)
|
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samtools_sort_index_before_dedup |
../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. |
|
htseq_count_transcript_expression |
../tools/htseq-count.cwl
(CommandLineTool)
|
HTSeq: Analysing high-throughput sequencing data |
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). |
Outputs
ID | Type | Label | Doc |
---|---|---|---|
bowtie_log | File [Textual format] | Bowtie alignment log |
Bowtie alignment log file |
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) [YAML] | YAML formatted combined log |
YAML formatted combined log |
star_out_log | File (Optional) [Textual format] | STAR log out |
STAR Log.out |
star_final_log | File [Textual format] | STAR final log |
STAR Log.final.out |
bigwig_upstream | File [bigWig] | Upstream bigWig file |
bigWig file from the 5' - 3' strand |
star_stdout_log | File (Optional) [Textual format] | STAR stdout log |
STAR Log.std.out |
fastx_statistics | File [Textual format] | FASTQ statistics |
fastx_quality_stats generated FASTQ file quality statistics file |
gene_body_report | File (Optional) [TSV] | Gene body average tag density plot for all isoforms longer than 1000 bp |
Gene body average tag density plot for all isoforms longer than 1000 bp in TSV format |
bigwig_downstream | File [bigWig] | Downstream bigWig file |
bigWig file from the 3' - 5' strand |
get_stat_markdown | File (Optional) [TIDE TXT] | Markdown formatted combined log |
Markdown formatted combined log |
star_progress_log | File (Optional) [Textual format] | STAR progress log |
STAR Log.progress.out |
gene_body_plot_pdf | File (Optional) [PDF] | Gene body average tag density plot for all isoforms longer than 1000 bp |
Gene body average tag density plot for all isoforms longer than 1000 bp in PDF format |
get_formatted_stats | File (Optional) [Textual format] | Bowtie, STAR and GEEP mapping stats |
Processed and combined Bowtie & STAR aligner and GEEP logs |
gene_expression_file | File [TSV] | Gene expression |
Gene expression |
bam_statistics_report | File [Textual format] | BAM statistics report |
BAM statistics report (after deduplication step) |
umi_tools_dedup_stats | File[] (Optional) | umi_tools dedup statistics |
umi_tools dedup statistics |
htseq_count_stderr_log | File [Textual format] | HTSeq: stderr log |
HTSeq: stderr log |
htseq_count_stdout_log | File [Textual format] | HTSeq: stdout log |
HTSeq: stdout log |
trim_adapters_stderr_log | File | cutadapt: stderr log |
cutadapt: stderr log |
trim_adapters_stdout_log | File | cutadapt: stdout log |
cutadapt: stdout log |
geep_gene_expression_file | File [TSV] | GEEP: expression grouped by gene name |
GEEP: expression grouped by gene name |
rpkm_distribution_plot_pdf | File (Optional) [PDF] | RPKM distribution plot for isoforms |
RPKM distribution plot for isoforms in PDF format |
umi_tools_dedup_stderr_log | File | umi_tools dedup: stderr log |
umi_tools dedup: stderr log |
umi_tools_dedup_stdout_log | File | umi_tools dedup: stdout log |
umi_tools dedup: stdout log |
combined_gene_expression_file | File [TSV] | HTSeq vs GEEP gene expression comparison |
Merged by GeneId, Chrom, TxStart, TxEnd and Strand gene expression files with reported and renamed TotalReads columns. |
feature_expression_merge_stderr_log | File [Textual format] | HTSeq vs GEEP gene expression comparison stderr log |
HTSeq vs GEEP gene expression comparison stderr log |
feature_expression_merge_stdout_log | File [Textual format] | HTSeq vs GEEP gene expression comparison stdout log |
HTSeq vs GEEP gene expression comparison stdout log |
https://w3id.org/cwl/view/git/581156366f91861bd4dbb5bcb59f67d468b32af3/workflows/trim-quantseq-mrnaseq-se-strand-specific.cwl