Workflow Type: Galaxy
Frozen
Frozen
Scaffolding using HiC data with YAHS.
Inputs
ID | Name | Description | Type |
---|---|---|---|
Estimated genome size - Parameter File | Estimated genome size - Parameter File | Estimated genome size from contiging workflow |
|
HiC Forward reads | HiC Forward reads | Forward reads as a single dataset in fastq format |
|
HiC reverse reads | HiC reverse reads | Reverse reads as a single dataset in fastq format |
|
Input GFA | Input GFA | The input GFA must conform to gfa1.2 standards, i.e. should have 'P' lines defined. Output GFAs from assemblers can be run through a GFA->GFA conversion using gfastats to ensure this. |
|
Lineage | Lineage | Taxonomic lineage for the organism being assembled for Busco analysis |
|
Restriction enzymes | Restriction enzymes | Restriction enzymes used in preparation of Hi-C libraries. |
|
SAK input file | SAK input file | n/a |
|
Sequence graph | Sequence graph | n/a |
|
Steps
ID | Name | Description |
---|---|---|
8 | Parse parameter value | param_value_from_file |
9 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0 |
10 | BWA-MEM2 | toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1 |
11 | BWA-MEM2 | toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1 |
12 | Filter and merge | toolshed.g2.bx.psu.edu/repos/iuc/bellerophon/bellerophon/1.0+galaxy1 |
13 | PretextMap | toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy1 |
14 | YAHS | toolshed.g2.bx.psu.edu/repos/iuc/yahs/yahs/1.2a.2+galaxy2 |
15 | Pretext Snapshot | toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.3+galaxy2 |
16 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0 |
17 | Extract dataset | __EXTRACT_DATASET__ |
18 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0 |
19 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0 |
20 | gfastats | toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0 |
21 | BWA-MEM2 | toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1 |
22 | BWA-MEM2 | toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1 |
23 | Busco | toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0 |
24 | Replace | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1 |
25 | gfastats_data_prep | n/a |
26 | Filter and merge | toolshed.g2.bx.psu.edu/repos/iuc/bellerophon/bellerophon/1.0+galaxy1 |
27 | Cut | Cut1 |
28 | Cut | Cut1 |
29 | PretextMap | toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy1 |
30 | bedtools BAM to BED | toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.31.1+galaxy0 |
31 | Nx Plot | toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.4.0+galaxy1 |
32 | Size Plot | toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.4.0+galaxy1 |
33 | Pretext Snapshot | toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.3+galaxy2 |
34 | Sort | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy1 |
35 | Extract dataset | __EXTRACT_DATASET__ |
Outputs
ID | Name | Description | Type |
---|---|---|---|
YAHS on input dataset(s): Final scaffolds agp output | YAHS on input dataset(s): Final scaffolds agp output | n/a |
|
Reconciliated Scaffolds: gfa | Reconciliated Scaffolds: gfa | n/a |
|
Pretext Map Before HiC scaffolding | Pretext Map Before HiC scaffolding | n/a |
|
Reconciliated Scaffolds: fasta | Reconciliated Scaffolds: fasta | n/a |
|
Assembly Statistics for s2 | Assembly Statistics for s2 | n/a |
|
Scaffold sizes for s2 | Scaffold sizes for s2 | n/a |
|
Busco Summary image | Busco Summary image | n/a |
|
Busco Summary | Busco Summary | n/a |
|
clean_stats | clean_stats | n/a |
|
Nx Plot | Nx Plot | n/a |
|
Size Plot | Size Plot | n/a |
|
Pretext Map After HiC scaffolding | Pretext Map After HiC scaffolding | n/a |
|
Version History
v0.2.8 (latest) Created 7th Oct 2024 at 16:33 by WorkflowHub Bot
Updated to v0.2.8
Frozen
v0.2.8
53e128f
v0.1 (earliest) Created 27th Oct 2023 at 03:01 by WorkflowHub Bot
Updated to v0.1
Frozen
v0.1
95a269d
Creators and Submitter
Creators
Not specifiedAdditional credit
VGP, Galaxy
Submitter
Activity
Views: 5556 Downloads: 1386 Runs: 0
Created: 27th Oct 2023 at 03:01
Last updated: 7th Oct 2024 at 16:33
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