Workflow: EMG pipeline v3.0 (paired end version)

Fetched 2022-10-02 23:04:22 GMT
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Inputs

ID Type Title Doc
run_id String
5S_model File [HMMER format]
16S_model File [HMMER format]
23S_model File [HMMER format]
tRNA_model File [HMMER format]
forward_reads File [FASTQ]
reverse_reads File [FASTQ]
go_summary_config File
fraggenescan_model https://w3id.org/cwl/view/git/7bb76f33bf40b5cd2604001cac46f967a209c47f/tools/FragGeneScan-model.yaml#model

Steps

ID Runs Label Doc
overlap_reads
../tools/seqprep.cwl (CommandLineTool)
unified_processing
emg-pipeline-v3.cwl (Workflow)
EMG pipeline v3.0 (single end version)
combine_overlaped_and_unmerged_reads
../tools/seqprep-merge.cwl (CommandLineTool)

Outputs

ID Type Label Doc
tree File
summary File
biom_tsv File
biom_hdf5 File
biom_json File
ipr_reads File
pCDS_seqs File
5S_matches File
go_summary File
16S_matches File
23S_matches File
ipr_summary File
krona_input File
qc_stats_gc File
tRNA_matches File
actual_run_id String
post_qc_reads File
kingdom_counts File
go_summary_slim File
ipr_match_count Integer
qc_stats_gc_bin File
annotated_CDS_aa File
predicted_CDS_aa File
qc_stats_seq_len File
qc_stats_summary File
annotated_CDS_nuc File
no_functions_seqs File
otu_table_summary File
otu_visualization File
qc_stats_gc_pcbin File
qc_stats_nuc_dist File
post_qc_read_count Integer
unannotated_CDS_aa File
processed_sequences File
unannotated_CDS_nuc File
interproscan_matches File
qc_stats_seq_len_bin File
functional_annotations File
qc_stats_seq_len_pbcbin File
qiime_assigned_taxonomy File
ipr_CDS_with_match_count Integer
ipr_reads_with_match_count Integer
qiime_sequences-filtered_otus File
qiime_sequences-filtered_clusters File
Permalink: https://w3id.org/cwl/view/git/7bb76f33bf40b5cd2604001cac46f967a209c47f/workflows/emg-pipeline-v3-paired.cwl