Workflow: EMG assembly for paired end Illumina

Fetched 2024-11-09 10:35:04 GMT
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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/7bb76f33bf40b5cd2604001cac46f967a209c47f/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

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

Outputs

ID Type Label Doc
pCDS_seqs File
scaffolds 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
Permalink: https://w3id.org/cwl/view/git/7bb76f33bf40b5cd2604001cac46f967a209c47f/workflows/emg-pipeline-v4-assembly-metaSPAdes.cwl