Workflow: EMG core analysis
Fetched 2025-01-17 12:05:35 GMT
Verified with cwltool version 3.1.20221201130942
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- 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] | ||
| input_sequences | File [FASTA] | ||
| mapseq_taxonomy | File | ||
| go_summary_config | File | ||
| sequencing_run_id | String | ||
| fraggenescan_model | https://w3id.org/cwl/view/git/7bb76f33bf40b5cd2604001cac46f967a209c47f/tools/FragGeneScan-model.yaml#model | ||
| ncRNA_other_models | File[] | ||
| ncRNA_ribosomal_models | File[] | ||
| ncRNA_other_model_clans | File | ||
| ncRNA_ribosomal_model_clans | File |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| ipr_stats |
../tools/ipr_stats.cwl
(CommandLineTool)
|
gather stats from InterProScan | |
| orf_stats |
../tools/orf_stats.cwl
(CommandLineTool)
|
gather stats from ORF caller | |
| extract_5Ss |
../tools/esl-sfetch-manyseqs.cwl
(CommandLineTool)
|
extract by names from an indexed sequence file |
https://github.com/EddyRivasLab/easel |
| index_reads |
../tools/esl-sfetch-index.cwl
(CommandLineTool)
|
index a sequence file for use by esl-sfetch |
https://github.com/EddyRivasLab/easel |
| extract_LSUs |
../tools/esl-sfetch-manyseqs.cwl
(CommandLineTool)
|
extract by names from an indexed sequence file |
https://github.com/EddyRivasLab/easel |
| 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/ |
| get_5S_coords |
../tools/5S-from-tablehits.cwl
(Workflow)
|
||
| ORF_prediction |
orf_prediction.cwl
(Workflow)
|
Find reads with predicted coding sequences above 60 AA in length | |
| categorisation |
../tools/create_categorisations.cwl
(CommandLineTool)
|
categorise sequences | |
| get_LSU_coords |
../tools/LSU-from-tablehits.cwl
(Workflow)
|
||
| get_SSU_coords |
../tools/SSU-from-tablehits.cwl
(Workflow)
|
||
| sequence_stats |
../tools/qc-stats.cwl
(CommandLineTool)
|
Post QC-ed input analysis of sequence file | |
| 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)
|
||
| convert_otu_counts_to_hdf5 |
../tools/biom-convert.cwl
(CommandLineTool)
|
||
| convert_otu_counts_to_json |
../tools/biom-convert.cwl
(CommandLineTool)
|
||
| remove_asterisks_and_reformat |
../tools/esl-reformat.cwl
(CommandLineTool)
|
normalize to fasta |
normalizes input sequeces to FASTA with fixed number of sequence characters per line using esl-reformat from https://github.com/EddyRivasLab/easel |
| convert_classifications_to_otu_counts |
../tools/mapseq2biom.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| pCDS_seqs | File | ||
| go_summary | File | ||
| numberOrfs | Integer | ||
| match_count | Integer | ||
| qc_stats_gc | File | ||
| stats_reads | File | ||
| 5S_sequences | File | ||
| interproscan | File | ||
| other_ncRNAs | File | ||
| readsWithOrf | File | ||
| LSU_sequences | File | ||
| SSU_sequences | File | ||
| predicted_CDS | File | ||
| go_summary_slim | File | ||
| qc_stats_gc_bin | File | ||
| qc_stats_seq_len | File | ||
| qc_stats_summary | File | ||
| no_functions_seqs | File | ||
| qc_stats_gc_pcbin | File | ||
| qc_stats_nuc_dist | File | ||
| numberReadsWithOrf | Integer | ||
| ssu_classifications | File | ||
| ssu_otu_counts_hdf5 | File | ||
| ssu_otu_counts_json | File | ||
| CDS_with_match_count | Integer | ||
| qc_stats_seq_len_bin | File | ||
| ssu_otu_visualization | File | ||
| functional_annotations | File | ||
| qc_stats_seq_len_pcbin | File | ||
| reads_with_match_count | Integer |
Permalink:
https://w3id.org/cwl/view/git/7bb76f33bf40b5cd2604001cac46f967a209c47f/workflows/emg-core-analysis-v4.cwl
