- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
BSD 3-clause "New" or "Revised" License
Note that the tools invoked by the workflow may have separate licenses.
Inputs
ID | Type | Title | Doc |
---|---|---|---|
read1s | 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 | ||
hard_trim_length | Integer | ||
speciesGenomeDir | Directory | ||
repeatElementGenomeDir | Directory | ||
trimagain_overlap_length | String | ||
trimfirst_overlap_length | String |
Steps
ID | Runs | Label | Doc |
---|---|---|---|
step_wf_trim_partial_and_map |
wf_trim_partial_and_map_se.cwl
(Workflow)
|
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 |
Outputs
ID | Type | Label | Doc |
---|---|---|---|
A_output_sorted_bam | File[] | ||
X_output_sorted_bam | File[] | ||
X_output_trim_first | 600a5aacbf54752c9b940076fa7d0210[] | ||
A_output_mapgenome_stats | File[] | ||
A_output_maprepeats_stats | File[] | ||
X_output_trim_first_metrics | File[] | ||
X_output_barcodecollapsese_bam | File[] | ||
A_output_sort_repunmapped_fastq | File[] | ||
A_output_mapgenome_star_settings | File[] | ||
A_output_maprepeats_star_settings | File[] | ||
A_output_mapgenome_mapped_to_genome | File[] | ||
A_output_maprepeats_mapped_to_genome | File[] |
Permalink:
https://w3id.org/cwl/view/git/49a9bcda10de8f55fab2481f424eb9cdf2e5b256/cwl/wf_trim_partial_and_map_se_scatter.cwl