SSQuAWK4.0.2 Version 1
Visit source
Download RO-CrateSARS-CoV-2 Sequence Quality Assurance Workflow Kontraption, version 4.0.2
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Input dataset collection | Input dataset collection | n/a |
|
| Primer.bed | Primer.bed | n/a |
|
| 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 |
|
| _anonymous_output_2 | _anonymous_output_2 | n/a |
|
| _anonymous_output_3 | _anonymous_output_3 | n/a |
|
| _anonymous_output_4 | _anonymous_output_4 | n/a |
|
| _anonymous_output_5 | _anonymous_output_5 | n/a |
|
| _anonymous_output_6 | _anonymous_output_6 | n/a |
|
| _anonymous_output_7 | _anonymous_output_7 | n/a |
|
| _anonymous_output_8 | _anonymous_output_8 | n/a |
|
| _anonymous_output_9 | _anonymous_output_9 | n/a |
|
| _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
Open
masterdb9183b
Creators and Submitter
Views: 846 Downloads: 210
Created: 14th Mar 2023 at 11:09
TagsThis item has not yet been tagged.
AttributionsNone
Related items
https://orcid.org/0000-0001-9842-9718
Teams: Testing, Finn's test team, PNDB, LifeMonitorDev, iPC: individualizedPaediatricCure, test, Test Team, Australian BioCommons Dev, opscientia, V-pipe, UX study leave, DALiuGE workflows, Team1, UX study, My Fancy Team, Team UX Study11, My team, ux study team, UX study koehorst, Team Koehorst, UX Study (satra), Steve's UX Study Test Team, TestSaandra, KJ-workflow-test, NewTeam, team, UXStudy, A Team, UX study K, UXStudy99, Study team, Another new team, UX study2, Team 20220225, my new team, UX Study AU, Testing_proteomics, A test space (KKH), Pleiade, QSM4SENIOR, IGG-Bioinfo, Defragmentation training school, FWCC-D@HZDR, Submission Tutorial, Testing team, Galaxy Training Network, Exploring SEEK SOP functionality, MyTest, Tsinghua University BCI group, Test Team Number Nine, Eli's test team, EMBL Bioimage analysis service, Hu's Test
Web page: Not specified
