SSQuAWK4.0.2 Version 1
Visit source
Download RO-Crate
Run on GalaxySARS-CoV-2 Sequence Quality Assurance Workflow Kontraption, version 4.0.2
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Input dataset collection | Input dataset collection | n/a |
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| Primer.bed | Primer.bed | n/a |
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| Reference Genome FASTA | Reference Genome FASTA | n/a |
|
Steps
| ID | Name | Description |
|---|---|---|
| 3 | Kraken2 | toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1 |
| 4 | Bowtie2 | toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.2+galaxy0 |
| 5 | Text reformatting | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2 |
| 6 | Filter human, synthetic, and sarscov2 seqs | Filter1 |
| 7 | Text reformatting | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2 |
| 8 | Samtools stats | testtoolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2 |
| 9 | ivar trim | toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.3.1+galaxy2 |
| 10 | Collapse Collection | toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0 |
| 11 | Collapse Collection | toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0 |
| 12 | Collapse Collection | toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0 |
| 13 | Samtools sort | toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.3 |
| 14 | Replace Text | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3 |
| 15 | Filter | Filter1 |
| 16 | resortedStats | testtoolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2 |
| 17 | QualiMap BamQC | toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2d+galaxy3 |
| 18 | Text reformatting | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2 |
| 19 | Replace Text | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3 |
| 20 | Collapse Collection | toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0 |
| 21 | Text reformatting | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2 |
| 22 | Filter | Filter1 |
| 23 | Collapse Collection | toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0 |
| 24 | Replace Text | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3 |
| 25 | Concatenate datasets | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1 |
| 26 | Text reformatting | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2 |
| 27 | Join | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2 |
| 28 | SNRQK | toolrepo.galaxytrakr.org/repos/jasmine_amir/snrqk/snrqk/1 |
| 29 | Cut | toolshed.g2.bx.psu.edu/repos/devteam/cut_columns/Cut1/1.0.2 |
| 30 | Transpose | testtoolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.1.0 |
| 31 | Sort | sort1 |
| 32 | Transpose | testtoolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.1.0 |
| 33 | Text reformatting | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2 |
| 34 | Join | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2 |
| 35 | Join | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| _anonymous_output_1 | _anonymous_output_1 | n/a |
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| _anonymous_output_2 | _anonymous_output_2 | n/a |
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| _anonymous_output_3 | _anonymous_output_3 | n/a |
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| _anonymous_output_4 | _anonymous_output_4 | n/a |
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| _anonymous_output_5 | _anonymous_output_5 | n/a |
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| _anonymous_output_6 | _anonymous_output_6 | n/a |
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| _anonymous_output_7 | _anonymous_output_7 | n/a |
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| _anonymous_output_8 | _anonymous_output_8 | n/a |
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| _anonymous_output_9 | _anonymous_output_9 | n/a |
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| _anonymous_output_10 | _anonymous_output_10 | n/a |
|
Version History
Version 1 (earliest) Created 14th Mar 2023 at 11:09 by Stian Soiland-Reyes
Initial commit
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Views: 1480 Downloads: 426 Runs: 0
Created: 14th Mar 2023 at 11:09
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