Workflow: wf_trim_and_map_se.cwl
Fetched 2023-01-03 19:07:17 GMT
Verified with cwltool version 3.1.20221201130942
This workflow takes in appropriate trimming params and demultiplexed reads, and performs the following steps in order: trimx1, trimx2, fastq-sort, filter repeat elements, fastq-sort, genomic mapping, sort alignment, index alignment, namesort, PCR dedup, sort alignment, index alignment
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| read1 | File | ||
| read_name | String | ||
| a_adapters | File | ||
| bam_suffix | String | ||
| sort_names | Boolean | ||
| trim_times | String | ||
| dataset_name | String | ||
| fastq_suffix | String | ||
| trim_error_rate | String | ||
| speciesGenomeDir | Directory | ||
| repeatElementGenomeDir | Directory | ||
| trimagain_overlap_length | String | ||
| trimfirst_overlap_length | String |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| A_sort |
sort.cwl
(CommandLineTool)
|
This tool wraps samtools sort by coordinates (namesort flag is False by default). Usage: samtools sort [options...] [in.bam] |
|
| X_sort |
sort.cwl
(CommandLineTool)
|
This tool wraps samtools sort by coordinates (namesort flag is False by default). Usage: samtools sort [options...] [in.bam] |
|
| X_trim |
trim_se.cwl
(CommandLineTool)
|
This tool wraps cutadapt with default parameters set to single-end eCLIP processing defaults. Usage: cutadapt -a ADAPT1 -A ADAPT2 [options] -o out1.fastq -p out2.fastq in1.fastq in2.fastq |
|
| A_index |
samtools-index.cwl
(CommandLineTool)
|
samtools-index.cwl is developed for CWL consortium |
|
| A_map_genome |
star-genome.cwl
(CommandLineTool)
|
||
| X_sortlexico |
namesort.cwl
(CommandLineTool)
|
This tool wraps samtools sort, setting the by-name (-n) flag to be True by default. Usage: samtools sort -n <input.bam> <output.bam> |
|
| X_trim_again |
trim_se.cwl
(CommandLineTool)
|
This tool wraps cutadapt with default parameters set to single-end eCLIP processing defaults. Usage: cutadapt -a ADAPT1 -A ADAPT2 [options] -o out1.fastq -p out2.fastq in1.fastq in2.fastq |
|
| A_map_repeats |
star-repeatmapping.cwl
(CommandLineTool)
|
||
| get_a_adapters |
file2stringArray.cwl
(ExpressionTool)
|
Returns string array expression based on lines in a fasta file (SKIPS >). |
|
| index_rmdup_bam |
samtools-index.cwl
(CommandLineTool)
|
samtools-index.cwl is developed for CWL consortium |
|
| step_fastqc_trim |
wf_fastqc.cwl
(Workflow)
|
This workflow takes in single-end reads, and performs the following steps in order: demux_se.cwl (does not actually demux for single end, but mirrors the paired-end processing protocol) |
|
| X_barcodecollapsese |
barcodecollapse_se.cwl
(CommandLineTool)
|
The purpose of this command is to deduplicate BAM files based
on the first mapping co-ordinate and the UMI attached to the read.
It is assumed that the FASTQ files were processed with extract_umi.py
before mapping and thus the UMI is the last word of the read name. e.g: |
|
| A_sort_trimmed_fastq |
fastqsort.cwl
(CommandLineTool)
|
Sorts FASTQ files by their read name. Sorted fastq files are required to keep mapping steps
deterministic. |
|
| rename_mapped_genome |
rename.cwl
(CommandLineTool)
|
||
| rename_mapped_repeats |
rename.cwl
(CommandLineTool)
|
||
| step_gzip_sort_X_trim |
gzip.cwl
(CommandLineTool)
|
||
| step_fastqc_trim_again |
wf_fastqc.cwl
(Workflow)
|
This workflow takes in single-end reads, and performs the following steps in order: demux_se.cwl (does not actually demux for single end, but mirrors the paired-end processing protocol) |
|
| rename_unmapped_repeats |
rename.cwl
(CommandLineTool)
|
||
| A_sort_repunmapped_fastq |
fastqsort.cwl
(CommandLineTool)
|
Sorts FASTQ files by their read name. Sorted fastq files are required to keep mapping steps
deterministic. |
|
| step_gzip_sort_X_trim_again |
gzip.cwl
(CommandLineTool)
|
||
| step_gzip_sort_repunmapped_fastq |
gzip.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| A_output_sorted_bam | File | ||
| X_output_sorted_bam | File | ||
| X_output_trim_again | File[] | ||
| X_output_trim_first | File[] | ||
| A_output_mapgenome_stats | File | ||
| A_output_maprepeats_stats | File | ||
| X_output_trim_again_metrics | File | ||
| X_output_trim_first_metrics | File | ||
| X_output_barcodecollapsese_bam | File | ||
| A_output_sort_repunmapped_fastq | File | ||
| A_output_mapgenome_star_settings | File | ||
| X_output_trim_again_fastqc_stats | File | ||
| X_output_trim_first_fastqc_stats | File | ||
| A_output_maprepeats_star_settings | File | ||
| X_output_trim_again_fastqc_report | File | ||
| X_output_trim_first_fastqc_report | File | ||
| X_output_barcodecollapsese_metrics | File | ||
| A_output_mapgenome_mapped_to_genome | File | ||
| A_output_maprepeats_mapped_to_genome | File |
https://w3id.org/cwl/view/git/c0fffc4979a92371dc0667a03e3d957bf7f77600/cwl/wf_trim_and_map_se.cwl
