- 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] | ||
forward_reads | File [FASTQ] | ||
reverse_reads | File [FASTQ] | ||
mapseq_taxonomy | File | ||
go_summary_config | File | ||
sequencing_run_id | String | ||
fraggenescan_model | https://w3id.org/cwl/view/git/ecf044f3a5a7589cb2238487a19f22863c2bcdb1/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 |
---|---|---|---|
overlap_reads |
../tools/seqprep.cwl
(CommandLineTool)
|
||
unified_processing |
emg-core-analysis-v4.cwl
(Workflow)
|
EMG core analysis | |
trim_and_reformat_reads |
trim_and_reformat_reads.cwl
(Workflow)
|
Trim and reformat reads (single and paired end version) | |
combine_overlaped_and_unmerged_reads |
../tools/seqprep-merge.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 | ||
CDS_with_match_count | Integer | ||
qc_stats_seq_len_bin | File | ||
functional_annotations | File | ||
reads_with_match_count | Integer | ||
qc_stats_seq_len_pbcbin | File | ||
processed_nucleotide_reads | File |
Permalink:
https://w3id.org/cwl/view/git/ecf044f3a5a7589cb2238487a19f22863c2bcdb1/workflows/emg-pipeline-v4-paired.cwl