Workflow: wf_trim_partial_and_map_se_scatter.cwl
Fetched 2024-04-24 08:17:49 GMT
Verified with cwltool version 3.1.20221201130942
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This workflow is Open Source and may be reused according to the terms of:
https://raw.githubusercontent.com/yeolab/eclip/master/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 | 1bb8fb7aa84f91e019d3b412947c0a54[] | ||
| 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/c0fffc4979a92371dc0667a03e3d957bf7f77600/cwl/wf_trim_partial_and_map_se_scatter.cwl
