Workflow: RNA-seq (VCF) alelle specific pipeline for paired-end data
Allele specific RNA-Seq (using vcf) paired-end workflow
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- Inputs/Outputs
Inputs
ID | Type | Title | Doc |
---|---|---|---|
strain1 | String | I strain name |
First strain name |
strain2 | String | II strain name |
Second strain name |
threads | Integer (Optional) | Number of threads |
Number of threads for those steps that support multithreading |
chrom_length_file | File [Textual format] | Chromosome length file for reference genome |
Chromosome length file for reference genome |
strain1_chain_file | File [Textual format] | I strain chain file |
Chain file to project strain I to reference genome |
strain2_chain_file | File [Textual format] | II strain chain file |
Chain file to project strain II to reference genome |
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 for reference genome |
Path to STAR generated indices for reference genome |
fastq_file_downstream | File [FASTQ] | FASTQ downstream input file |
Downstream reads data in a FASTQ format, received after paired end sequencing |
insilico_star_indices_folder | Directory | STAR indices folder for insilico genome |
Path to STAR generated indices for insilico genome |
Steps
ID | Runs | Label | Doc |
---|---|---|---|
extract_fastq_upstream |
../tools/extract-fastq.cwl
(CommandLineTool)
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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 |
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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 |
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allele_vcf_alignreads_se_pe |
Workflow maps FASTQ files from `fastq_files` input into reference genome `reference_star_indices_folder` and insilico generated `insilico_star_indices_folder` genome (concatenated genome for both `strain1` and `strain2` strains). For both genomes STAR is run with `outFilterMultimapNmax` parameter set to 1 to discard all of the multimapped reads. For insilico genome SAM file is generated. Then it's splitted into two SAM files based on strain names and then sorted by coordinates into the BAM format. For reference genome output BAM file from STAR slignment is also coordinate sorted. |
Outputs
ID | Type | Label | Doc |
---|---|---|---|
strain1_bigwig | File [bigWig] | I strain bigWig file |
Generated bigWig file for the first strain |
strain2_bigwig | File [bigWig] | II strain bigWig file |
Generated bigWig file for the second strain |
reference_bigwig | File [bigWig] | Reference bigWig file |
Generated BigWig file for the reference genome |
strain1_bambai_pair | File [BAM] | Strain I coordinate sorted BAM alignment file (+index BAI) |
Coordinate sorted BAM file and BAI index file for strain I |
strain2_bambai_pair | File [BAM] | Strain II coordinate sorted BAM alignment file (+index BAI) |
Coordinate sorted BAM file and BAI index file for strain II |
insilico_star_out_log | File (Optional) [Textual format] | STAR log out for insilico genome |
STAR Log.out for insilico genome |
reference_bambai_pair | File [BAM] | Reference coordinate sorted BAM alignment file (+index BAI) |
Coordinate sorted BAM file and BAI index file for reference genome |
reference_star_out_log | File (Optional) [Textual format] | STAR log out for reference genome |
STAR Log.out for reference genome |
insilico_star_final_log | File [Textual format] | STAR final log for insilico genome |
STAR Log.final.out for insilico genome |
insilico_star_stdout_log | File (Optional) [Textual format] | STAR stdout log for insilico genome |
STAR Log.std.out for insilico genome |
reference_star_final_log | File [Textual format] | STAR final log for reference genome |
STAR Log.final.out for reference genome |
reference_star_stdout_log | File (Optional) [Textual format] | STAR stdout log for reference genome |
STAR Log.std.out for reference genome |
insilico_star_progress_log | File (Optional) [Textual format] | STAR progress log for insilico genome |
STAR Log.progress.out for insilico genome |
reference_star_progress_log | File (Optional) [Textual format] | STAR progress log for reference genome |
STAR Log.progress.out for reference genome |
https://w3id.org/cwl/view/git/7518b100d8cbc80c8be32e9e939dfbb27d6b4361/workflows/allele-vcf-rnaseq-pe.cwl