- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
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 | ||
sequencing_run_id | String | ||
assembly_mem_limit | Integer |
in Gb |
|
fraggenescan_model | https://w3id.org/cwl/view/git/1b0851e6456ccb1fca237a805ff85c53bc9d58c9/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 |
---|---|---|---|
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 |
fraggenescan |
../tools/FragGeneScan1_20.cwl
(CommandLineTool)
|
FragGeneScan: find (fragmented) genes in short reads |
FragGeneScan is an application for finding (fragmented) genes in short
reads. It can also be applied to predict prokaryotic genes in incomplete
assemblies or complete genomes. |
interproscan |
../tools/InterProScan5.21-60.cwl
(CommandLineTool)
|
InterProScan: protein sequence classifier |
Version 5.21-60 can be downloaded here:
https://github.com/ebi-pf-team/interproscan/wiki/HowToDownload |
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_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)
|
||
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)
|
||
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 |
---|---|---|---|
SSUs | File | ||
pCDS | File | ||
scaffolds | File | ||
annotations | File | ||
other_ncRNAs | File | ||
classifications | File | ||
otu_counts_hdf5 | File | ||
otu_counts_json | File | ||
otu_visualization | File |
https://w3id.org/cwl/view/git/1b0851e6456ccb1fca237a805ff85c53bc9d58c9/workflows/emg-assembly.cwl