Workflow Type: Galaxy
Frozen
This is part of a series of workflows to annotate a genome, tagged with TSI-annotation
.
These workflows are based on command-line code by Luke Silver, converted into Galaxy Australia workflows.
The workflows can be run in this order:
- Repeat masking
- RNAseq QC and read trimming
- Find transcripts
- Combine transcripts
- Extract transcripts
- Convert formats
- Fgenesh annotation
About this workflow:
- Inputs: transdecoder-peptides.fasta, transdecoder-nucleotides.fasta
- Runs many steps to convert outputs into the formats required for Fgenesh - .pro, .dat and .cdna
Inputs
ID | Name | Description | Type |
---|---|---|---|
transdecoder-nucleotides.fasta | transdecoder-nucleotides.fasta | n/a |
|
transdecoder-peptides.fasta | transdecoder-peptides.fasta | n/a |
|
Steps
ID | Name | Description |
---|---|---|
2 | STEP 1 Get IDs for complete, pos transcripts: Grep for lines starting with > | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy0 |
3 | grep for lines with complete | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy0 |
4 | Remove > from start of lines | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy0 |
5 | Keep lines that end in (+) | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy0 |
6 | STEP 2 | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy0 |
7 | Text reformatting | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy0 |
8 | Sort | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy0 |
9 | Text reformatting | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy0 |
10 | Cut | Cut1 |
11 | STEP 3. seqtk subseq | toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_subseq/1.4+galaxy0 |
12 | Text transformation | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy0 |
13 | FASTA-to-Tabular | toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1 |
14 | STEP 4. cut col 1, delimit by pipe | Cut1 |
15 | Sort | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy0 |
16 | seqtk_subseq | toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_subseq/1.4+galaxy0 |
17 | Tabular-to-FASTA | toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1 |
18 | FASTA-to-Tabular | toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1 |
19 | Text transformation | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy0 |
20 | Sort | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy0 |
21 | STEP 6 Grep headers | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy0 |
22 | STEP 9B. grep for > | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy0 |
23 | STEP 9A. grep for > | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy0 |
24 | Tabular-to-FASTA | toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1 |
25 | Sed to remove parentheses | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy0 |
26 | Cut | Cut1 |
27 | Text reformatting | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy0 |
28 | STEP 5 get seq lengths | toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.3 |
29 | STEP 10A. seqtk seq | toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_seq/1.4+galaxy0 |
30 | awk to extract last field in line | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy0 |
31 | Text transformation | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy0 |
32 | Text transformation | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy0 |
33 | Cut | Cut1 |
34 | FASTA-to-Tabular | toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1 |
35 | Cut | Cut1 |
36 | Cut | Cut1 |
37 | STEP 7. create chroms file with na lines | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy0 |
38 | STEP 8. create comments.txt | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy0 |
39 | paste starts and stops | Paste1 |
40 | STEP 9C. paste transcripts and chroms | Paste1 |
41 | paste comments and transcript-lengths | Paste1 |
42 | STEP 10B. paste starts stops and chroms | Paste1 |
43 | Paste | Paste1 |
44 | Paste | Paste1 |
45 | Paste | Paste1 |
46 | Paste | Paste1 |
47 | Cut | Cut1 |
48 | Tabular-to-FASTA | toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1 |
Outputs
ID | Name | Description | Type |
---|---|---|---|
output | output | n/a |
|
Version History
Version 1 (earliest) Created 8th May 2024 at 08:23 by Anna Syme
Initial commit
Frozen
Version-1
caf683f
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Citation
Silver, L., & Syme, A. (2024). Convert formats - TSI. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.880.1
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Views: 1834 Downloads: 203 Runs: 0
Created: 8th May 2024 at 08:23
Last updated: 9th May 2024 at 05:09
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