Workflow: EMG pipeline v3.0 (single end version)
Fetched 2024-04-19 09:41:42 GMT
Verified with cwltool version 3.1.20221201130942
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- Default Values
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- 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 |
|---|---|---|---|
| reads | File [FASTQ] | ||
| run_id | String | ||
| 5S_model | File [HMMER format] | ||
| 16S_model | File [HMMER format] | ||
| 23S_model | File [HMMER format] | ||
| tRNA_model | File [HMMER format] | ||
| go_summary_config | File | ||
| fraggenescan_model | https://w3id.org/cwl/view/git/7bb76f33bf40b5cd2604001cac46f967a209c47f/tools/FragGeneScan-model.yaml#model |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| ipr_stats |
../tools/ipr_stats.cwl
(CommandLineTool)
|
gather stats from InterProScan | |
| orf_stats |
../tools/orf_stats.cwl
(CommandLineTool)
|
gather stats from ORF caller | |
| divide_faa |
../tools/faselector.cwl
(CommandLineTool)
|
||
| divide_ffn |
../tools/faselector.cwl
(CommandLineTool)
|
||
| count_reads |
../tools/count_fastq.cwl
(CommandLineTool)
|
||
| ORF_prediction |
orf_prediction.cwl
(Workflow)
|
Find reads with predicted coding sequences above 60 AA in length | |
| categorisation |
../tools/create_categorisations.cwl
(CommandLineTool)
|
categorise sequences | |
| sequence_stats |
../tools/qc-stats.cwl
(CommandLineTool)
|
Post QC-ed input analysis of sequence file | |
| generate_summary |
../tools/summary.cwl
(CommandLineTool)
|
gather stats from InterProScan | |
| count_masked_reads |
../tools/count_fasta.cwl
(CommandLineTool)
|
||
| find_SSUs_and_mask |
rna-selector.cwl
(Workflow)
|
RNASelector as a CWL workflow |
https://doi.org/10.1007/s12275-011-1213-z |
| clean_fasta_headers |
../tools/clean_fasta_headers.cwl
(CommandLineTool)
|
replace problem characters from FASTA headers with dashes | |
| functional_analysis |
functional_analysis.cwl
(Workflow)
|
functional analysis prediction with InterProScan | |
| generate_ipr_summary |
../tools/write_ipr_summary.cwl
(CommandLineTool)
|
gather stats from InterProScan | |
| trim_quality_control |
../tools/trimmomatic.cwl
(CommandLineTool)
|
Trimmomatic is a fast, multithreaded command line tool that can be used to trim and crop Illumina (FASTQ) data as well as to remove adapters. These adapters can pose a real problem depending on the library preparation and downstream application. There are two major modes of the program: Paired end mode and Single end mode. The paired end mode will maintain correspondence of read pairs and also use the additional information contained in paired reads to better find adapter or PCR primer fragments introduced by the library preparation process. Trimmomatic works with FASTQ files (using phred + 33 or phred + 64 quality scores, depending on the Illumina pipeline used). |
|
| count_processed_reads |
../tools/count_fasta.cwl
(CommandLineTool)
|
||
| 16S_taxonomic_analysis |
16S_taxonomic_analysis.cwl
(Workflow)
|
Functional analyis of sequences that match the 16S SSU | |
| extract_iprscan_coords |
../tools/extract_sig_coords.cwl
(CommandLineTool)
|
||
| relabel_annotated_cds_aa_seqs |
../tools/map_fa_headers.cwl
(CommandLineTool)
|
||
| convert_trimmed-reads_to_fasta |
../tools/fastq_to_fasta.cwl
(CommandLineTool)
|
||
| relabel_annotated_cds_nuc_seqs |
../tools/map_fa_headers.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 [FASTA] | ||
| go_summary | File | ||
| 16S_matches | File [FASTA] | ||
| 23S_matches | File [FASTA] | ||
| ipr_summary | File | ||
| krona_input | File | ||
| qc_stats_gc | File | ||
| tRNA_matches | File [FASTA] | ||
| actual_run_id | String | ||
| post_qc_reads | File | ||
| kingdom_counts | File | ||
| post_sequences | 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 [FASTA] | ||
| 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.cwl
