Workflow: contig construction and protein prediction
Fetched 2025-10-19 19:46:05 GMT
Verified with cwltool version 3.1.20230201224320
\"This workflow performs construction of metagenomic contigs and prediction protein sequences for metagenomic contigs. It executes 2 processes: contig construction and protein prediction. related CWL file: ./Tools/01_megahit.cwl ./Tools/02_rename.cwl ./Tools/03_seqkit_stats.cwl ./Tools/04_prodigal.cwl\"
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| FASTQ_1 | File | Forward reads file (_1_trim.fastq.gz) |
trimmed metagenomic forward reads file (_1_trim.fastq.gz) |
| FASTQ_2 | File | Reverse reads file (_2_trim.fastq.gz) |
trimmed metagenomic reverse reads file (_2_trim.fastq.gz) |
| THREADS | Integer | Threads |
Number of threads to use |
| MEGAHIT_OUTPUT_DIR | String | Output directory name (e.g., contig${sample_name}) |
Output directory name (e.g., contig${sample_name}), you should not make the directory before execution. |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| MEGAHIT |
../Tools/01_megahit.cwl
(CommandLineTool)
|
metagenome assembly process using MEGAHIT |
\"metagenome assembly process using MEGAHIT Input files are trimmed metagenomic fastq which obtained from 00_fastp.cwl, the metagenomic contigs are outputs. Original script: https://github.com/RyoMameda/workflow/blob/main/03_assembly.sh\" |
| SEQKIT_STATS |
../Tools/03_seqkit_stats.cwl
(CommandLineTool)
|
seqkit stats process |
\"statical analysis of metagenomic contigs using SeqKit Checking value (such as N50, length ...) to confirm the contigs quality Original script: https://github.com/RyoMameda/workflow/blob/main/03_assembly.sh\" |
| RENAME_CONTIG |
../Tools/02_rename.cwl
(CommandLineTool)
|
rename process |
\"assembled contig rename process\" |
| PROTEIN_PREDICTION |
../Tools/04_prodigal.cwl
(CommandLineTool)
|
prodigal process |
\"prediction of protein coding sequences from metagenomic contigs using Prodigal Original script: https://github.com/RyoMameda/workflow/blob/main/04_prodigal.sh prodigal -i ${contig} -o ${output}.gbk -p meta -q -a ${output}.faa -d ${output}.fna\" |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| CONTIG_STATS_FILE | File | stats file |
text file containing metagenoic contig stats |
| PREDICTED_PROTEINS | File | Output protein fasta file |
predicted protein sequences to the selected file. |
| PREDICTED_CODING_DNA | File | Output dna fasta file |
protein coding nucleotide sequences to the selected file |
| NAMED_CONTIG_FASTA_FILE | File | Output contigs fasta file |
Named metagenomic contigs fasta file |
| MEGAHIT_CONTIG_DIRECTORY | Directory | Output directory of megahit |
Output directory containing final metagenomic contigs fasta file (final.contigs.fa) |
https://w3id.org/cwl/view/git/1838569c1d6d3c15f58c254667d4c6258e67e5a6/Workflow/megahit_prodigal_sw.cwl
