Workflow Type: Galaxy

This workflow performs the scaffolding of a genome assembly using HiC data with YAHS. Can be used on any assembly with Hi-C data, and the assembly in the gfa format. You can generate a gfa from a fasta using the gfastat tool. Part of the VGP set of workflows, it is meant to be run after the contigging (workflows 3,4, or 5), optional purging step (Workflow 6 or 6b), and an optionnal scaffolding with Bionano data (Workflow 7). This workflow includes QC with Assembly statistics, Busco, and Hi-C maps.

Steps

ID Name Description
10 Species Name: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1
11 Assembly Name: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1
12 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0
13 Map parameter value toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0
14 Haplotype: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1
15 Lineage used for Busco toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1
16 Parse parameter value param_value_from_file
17 Trim and Align Hi-C paired collection n/a
18 Compose text parameter value toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1
19 Samtools merge toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.20+galaxy2
20 YAHS toolshed.g2.bx.psu.edu/repos/iuc/yahs/yahs/1.2a.2+galaxy2
21 Hi-C Alignment Stats pre-scaffolding toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5
22 PretextMap toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy1
23 Replace toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy0
24 Pretext Snapshot toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.4+galaxy0
25 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0
26 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0
27 Extract dataset __EXTRACT_DATASET__
28 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0
29 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0
30 gfastats toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0
31 BWA-MEM2 toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy4
32 Busco toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy1
33 compleasm toolshed.g2.bx.psu.edu/repos/iuc/compleasm/compleasm/0.2.6+galaxy2
34 gfastats_data_prep n/a
35 Replace toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy0
36 Samtools merge toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.20+galaxy2
37 Cut Cut1
38 Cut Cut1
39 PretextMap toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy1
40 Hi-C Alignment Stats scaffolds toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5
41 Size Plot toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.5.1+galaxy2
42 Nx Plot toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.5.1+galaxy2
43 Pretext Snapshot toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.4+galaxy0
44 MultiQC toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy3
45 Extract dataset __EXTRACT_DATASET__

Version History

v1.8 (latest) Created 29th May 2025 at 03:02 by WorkflowHub Bot

Updated to v1.8


Frozen v1.8 640117b

v1.7 Created 15th May 2025 at 03:02 by WorkflowHub Bot

Updated to v1.7


Frozen v1.7 4830c82

v1.6 Created 15th May 2025 at 03:02 by WorkflowHub Bot

Updated to v1.6


Frozen v1.6 f877e86

v1.5 Created 2nd May 2025 at 03:02 by WorkflowHub Bot

Updated to v1.5


Frozen v1.5 494f08c

v1.4 Created 8th Apr 2025 at 03:01 by WorkflowHub Bot

Updated to v1.4


Frozen v1.4 174afcf

v1.3 Created 29th Mar 2025 at 03:02 by WorkflowHub Bot

Updated to v1.3


Frozen v1.3 6ac1ca9

v1.2 Created 26th Mar 2025 at 12:00 by WorkflowHub Bot

Updated to v1.2


Frozen v1.2 13406fa

v1.1 Created 26th Mar 2025 at 12:00 by WorkflowHub Bot

Updated to v1.1


Frozen v1.1 42b038b

v1.0 Created 26th Mar 2025 at 12:00 by WorkflowHub Bot

Updated to v1.0


Frozen v1.0 ff48f3e

v0.3 Created 5th Feb 2025 at 03:02 by WorkflowHub Bot

Updated to v0.3


Frozen v0.3 60a248b

v0.2.8 Created 7th Oct 2024 at 16:33 by WorkflowHub Bot

Updated to v0.2.8


Frozen v0.2.8 53e128f

v0.2.7 Created 7th Oct 2024 at 16:33 by WorkflowHub Bot

Updated to v0.2.7


Frozen v0.2.7 5accfa6

v0.2.6 Created 7th Oct 2024 at 16:33 by WorkflowHub Bot

Updated to v0.2.6


Frozen v0.2.6 8b4b766

v0.2.5 Created 1st Aug 2024 at 03:01 by WorkflowHub Bot

Updated to v0.2.5


Frozen v0.2.5 f76e5c5

v0.2.4 Created 30th May 2024 at 11:35 by WorkflowHub Bot

Updated to v0.2.4


Frozen v0.2.4 03dd848

v0.2.3 Created 24th Apr 2024 at 03:01 by WorkflowHub Bot

Updated to v0.2.3


Frozen v0.2.3 7479a72

v0.2.2 Created 27th Mar 2024 at 03:02 by WorkflowHub Bot

Updated to v0.2.2


Frozen v0.2.2 8b8fe66

v0.2.1 Created 24th Nov 2023 at 03:02 by WorkflowHub Bot

Updated to v0.2.1


Frozen v0.2.1 faa9803

v0.2 Created 17th Nov 2023 at 03:02 by WorkflowHub Bot

Updated to v0.2


Frozen v0.2 b9afa62

v0.1.2 Created 16th Nov 2023 at 03:02 by WorkflowHub Bot

Updated to v0.1.2


Frozen v0.1.2 81d58fc

v0.1.1 Created 31st Oct 2023 at 03:02 by WorkflowHub Bot

Updated to v0.1.1


Frozen v0.1.1 bde67a2

v0.1 (earliest) Created 27th Oct 2023 at 03:01 by WorkflowHub Bot

Updated to v0.1


Frozen v0.1 95a269d
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VGP, Galaxy

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Views: 11150   Downloads: 3254   Runs: 5

Created: 27th Oct 2023 at 03:01

Last updated: 29th May 2025 at 03:02

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