Workflow: EMG assembly for paired end Illumina
Fetched 2026-04-15 04:52:09 GMT
Verified with cwltool version 3.1.20221201130942
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- Default Values
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- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
Apache License 2.0
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| mapseq_ref | File [FASTA] | ||
| forward_reads | File (Optional) [FASTQ] | ||
| reverse_reads | File (Optional) [FASTQ] | ||
| unpaired_reads | File (Optional) [FASTQ] | ||
| mapseq_taxonomy | File | ||
| go_summary_config | File | ||
| sequencing_run_id | String | ||
| fraggenescan_model | https://w3id.org/cwl/view/git/6430df56f7345f837d3f9c3f7fb5af5aa9dadc90/tools/FragGeneScan-model.yaml#model | ||
| ncRNA_other_models | File[] | ||
| ncRNA_ribosomal_models | File[] | ||
| ncRNA_other_model_clans | File | ||
| mapseq_taxonomy_otu_table | File | ||
| ncRNA_ribosomal_model_clans | File |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| assembly |
../tools/metaspades.cwl
(CommandLineTool)
|
metaSPAdes: de novo metagenomics assembler |
https://arxiv.org/abs/1604.03071 http://cab.spbu.ru/files/release3.10.1/manual.html#meta |
| extract_SSUs |
../tools/esl-sfetch-manyseqs.cwl
(CommandLineTool)
|
extract by names from an indexed sequence file |
https://github.com/EddyRivasLab/easel |
| classify_SSUs |
../tools/mapseq.cwl
(CommandLineTool)
|
MAPseq |
sequence read classification tools designed to assign taxonomy and OTU classifications to ribosomal RNA sequences. http://meringlab.org/software/mapseq/ |
| ORF_prediction |
orf_prediction.cwl
(Workflow)
|
Find reads with predicted coding sequences above 60 AA in length | |
| get_SSU_coords |
../tools/SSU-from-tablehits.cwl
(Workflow)
|
||
| index_scaffolds |
../tools/esl-sfetch-index.cwl
(CommandLineTool)
|
index a sequence file for use by esl-sfetch |
https://github.com/EddyRivasLab/easel |
| find_other_ncRNAs |
cmsearch-multimodel.cwl
(Workflow)
|
||
| functional_analysis |
functional_analysis.cwl
(Workflow)
|
functional analysis prediction with InterProScan | |
| visualize_otu_counts |
../tools/krona.cwl
(CommandLineTool)
|
visualize using krona | |
| find_ribosomal_ncRNAs |
cmsearch-multimodel.cwl
(Workflow)
|
||
| discard_short_scaffolds |
../tools/discard_short_seqs.cwl
(CommandLineTool)
|
drop short seqs | |
| convert_otu_counts_to_hdf5 |
../tools/biom-convert.cwl
(CommandLineTool)
|
||
| convert_otu_counts_to_json |
../tools/biom-convert.cwl
(CommandLineTool)
|
||
| convert_classifications_to_otu_counts |
../tools/mapseq2biom.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| SSUs | File | ||
| pCDS | File | ||
| scaffolds | File | ||
| annotations | File | ||
| other_ncRNAs | File | ||
| classifications | File | ||
| otu_counts_hdf5 | File | ||
| otu_counts_json | File | ||
| otu_visualization | File |
Permalink:
https://w3id.org/cwl/view/git/6430df56f7345f837d3f9c3f7fb5af5aa9dadc90/workflows/emg-assembly.cwl
