Workflow: allele-alignreads-se-pe.cwl

Fetched 2023-01-08 22:10:45 GMT

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.

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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
hal_file File HAL file

HAL file that includes strain information
ref_strain String Reference strain name

Reference strain name to be projected to
fastq_files File[] Input FASTQ file(s)

Input FASTQ file or array of files
chrom_length_file File Chromosome length file for reference genome

Chromosome length file for reference genome
insilico_star_indices_folder Directory STAR indices folder for insilico genome

Path to STAR generated indices folder for insilico genome
reference_star_indices_folder Directory STAR indices folder for reference genome

Path to STAR generated indices folder for reference genome

Steps

ID Runs Label Doc
strain1_process
strain2_process
reference_process
insilico_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`.

reference_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`.

Outputs

ID Type Label Doc
strain1_bigwig File I strain bigWig file

Generated bigWig file for the first strain, projected to reference genome
strain2_bigwig File II strain bigWig file

Generated bigWig file for the second strain, projected to reference genome
reference_bigwig File Reference bigWig file

Generated BigWig file for the reference genome
strain1_bambai_pair File I strain output BAM

Coordinate sorted BAM file mapped to the first strain genome, not projected to reference genome
strain2_bambai_pair File II strain output BAM

Coordinate sorted BAM file mapped to the second strain genome, not projected to reference genome
insilico_star_out_log File (Optional) STAR log out for insilico genome

STAR Log.out for insilico genome
reference_bambai_pair File Reference output BAM

Coordinate sorted BAM file mapped to reference genome
reference_star_out_log File (Optional) STAR log out for reference genome

STAR Log.out for reference genome
insilico_star_final_log File STAR final log for insilico genome

STAR Log.final.out for insilico genome
insilico_star_stdout_log File (Optional) STAR stdout log for insilico genome

STAR Log.std.out for insilico genome
reference_star_final_log File STAR final log for reference genome

STAR Log.final.out for reference genome
reference_star_stdout_log File (Optional) STAR stdout log for reference genome

STAR Log.std.out for reference genome
insilico_star_progress_log File (Optional) STAR progress log for insilico genome

STAR Log.progress.out for insilico genome
reference_star_progress_log File (Optional) STAR progress log for reference genome

STAR Log.progress.out for reference genome
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Permalink: https://w3id.org/cwl/view/git/00ced0fc44ceeb3495e891232e1000235e56ee6b/subworkflows/allele-alignreads-se-pe.cwl