Workflow: EMG assembly for paired end Illumina

Fetched 2019-05-20 20:57:12 GMT
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Inputs

ID Type Title Doc
ncRNA_ribosomal_models File[]
go_summary_config File
forward_reads File (Optional) [FASTQ]
ncRNA_other_models File[]
unpaired_reads File (Optional) [FASTQ]
mapseq_taxonomy_otu_table File
mapseq_ref File [FASTA]
sequencing_run_id String
ncRNA_ribosomal_model_clans File
mapseq_taxonomy File
ncRNA_other_model_clans File
reverse_reads File (Optional) [FASTQ]
fraggenescan_model https://w3id.org/cwl/view/git/4d2e0a49a7581fb2a73c60a6833e8cb97a282e55/tools/FragGeneScan-model.yaml#model

Steps

ID Runs Label Doc
unified_processing EMG core analysis
discard_short_scaffolds
../tools/discard_short_seqs.cwl (CommandLineTool)
drop short seqs
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

Outputs

ID Type Label Doc
go_summary File
match_count Integer
numberOrfs Integer
stats_reads File
qc_stats_gc_pcbin File
qc_stats_seq_len_bin File
LSU_sequences File
interproscan File
qc_stats_nuc_dist File
other_ncRNAs File
no_functions_seqs File
numberReadsWithOrf Integer
scaffolds File
predicted_CDS File
CDS_with_match_count Integer
5S_sequences File
qc_stats_seq_len_pbcbin File
qc_stats_gc File
reads_with_match_count Integer
qc_stats_seq_len File
pCDS_seqs File
readsWithOrf File
SSU_sequences File
qc_stats_gc_bin File
ssu_classifications File
qc_stats_summary File
go_summary_slim File
functional_annotations File
Permalink: https://w3id.org/cwl/view/git/4d2e0a49a7581fb2a73c60a6833e8cb97a282e55/workflows/emg-pipeline-v4-assembly-metaSPAdes.cwl