post-curation-processing/main v0.1
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Tests Post-curation processing workflow for VGP assemblies. Takes a curated AGP file and combined haplotype FASTA, splits by haplotype, applies curation, assigns chromosome names, renames and reorients hap2 to match hap1, then generates QC outputs including Compleasm, Pretext maps, telomere analysis, and coverage tracks.
Steps
| ID | Name | Description |
|---|---|---|
| 21 | Assembly informations | toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1 |
| 22 | Curation Processing | n/a |
| 23 | True when no gene track generated | toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0 |
| 24 | Trim Hi-C reads 2 | toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/5.2+galaxy2 |
| 25 | Remove adapters from Hifi reads | toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/5.2+galaxy2 |
| 26 | Header Hap1 | toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1 |
| 27 | Compose text parameter value | toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1 |
| 28 | Header Hap2 | toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1 |
| 29 | Compose text parameter value | toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1 |
| 30 | Hap1 Stats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy2 |
| 31 | Hap2 Stats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy2 |
| 32 | Compressed Curated Hap1 | toolshed.g2.bx.psu.edu/repos/iuc/compress_file/compress_file/0.1.0 |
| 33 | Compressed Curated Hap2 | toolshed.g2.bx.psu.edu/repos/iuc/compress_file/compress_file/0.1.0 |
| 34 | mashmap | toolshed.g2.bx.psu.edu/repos/iuc/mashmap/mashmap/3.1.3+galaxy0 |
| 35 | Generate Chromosome File and Sequence assignment Hap1 | n/a |
| 36 | Generate Chromosome File and Sequence assignment Hap2 | n/a |
| 37 | Pick parameter value | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
| 38 | Pick parameter value | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
| 39 | Add Header to hap1 | toolshed.g2.bx.psu.edu/repos/bgruening/add_line_to_file/add_line_to_file/0.1.0 |
| 40 | Add Header to hap2 | toolshed.g2.bx.psu.edu/repos/bgruening/add_line_to_file/add_line_to_file/0.1.0 |
| 41 | Text transformation | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.5+galaxy3 |
| 42 | Compose text parameter value | toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1 |
| 43 | Compose text parameter value | toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1 |
| 44 | Text transformation | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.5+galaxy3 |
| 45 | Hic Map Hap1 | n/a |
| 46 | Hic Map Hap2 | n/a |
| 47 | Join two Datasets | join1 |
| 48 | Create text file | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.5+galaxy3 |
| 49 | Create text file | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.5+galaxy3 |
| 50 | Image Montage | toolshed.g2.bx.psu.edu/repos/bgruening/imagemagick_image_montage/imagemagick_image_montage/7.1.2-2+galaxy1 |
| 51 | Image Montage | toolshed.g2.bx.psu.edu/repos/bgruening/imagemagick_image_montage/imagemagick_image_montage/7.1.2-2+galaxy1 |
| 52 | JBrowse2 | toolshed.g2.bx.psu.edu/repos/fubar/jbrowse2/jbrowse2/3.7.0+galaxy0 |
| 53 | JBrowse2 | toolshed.g2.bx.psu.edu/repos/fubar/jbrowse2/jbrowse2/3.7.0+galaxy0 |
| 54 | Cut | Cut1 |
| 55 | Text reformatting | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy3 |
| 56 | Text reformatting | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy3 |
| 57 | Join | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.5+galaxy3 |
Version History
v0.1 (earliest) Created 30th May 2026 at 03:01 by WorkflowHub Bot
Updated to v0.1
Frozen
v0.1c8db20e
Creators and SubmitterViews: 44 Downloads: 164 Runs: 0
Created: 30th May 2026 at 03:01
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