Workflow: Subworkflow for Annotation
Fetched 2025-11-06 11:31:53 GMT
Verified with cwltool version 3.1.20230201224320
\"Main workflow for Metagenome and Metatranscriptome Annotation related CWL file: ./Tools/00_fastp.cwl ./Tools/05_bwa_mem_index.cwl ./Tools/13_subread.cwl ./Workflow/annotation_sw.cwl ./Workflow/megahit_prodigal_sw.cwl ./Workflow/metagenomic_contig_mapping_sw.cwl\"
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| EVALUE | Float | evalue |
E-value threshold of BLASTP (diamond) and BLASTN alignment |
| THREADS | Integer | threads |
number of threads to use in main workflow |
| TRIM_TAIL | Integer | Number of bases trimmed from fastq1 tail |
Number of bases trimmed from fastq1 tail |
| MAP_FASTQ_1 | File | mapping reads fastq1 |
metagenomic or metatranscriptomic fastq1 file which you want to map metagenomic contigs |
| MAP_FASTQ_2 | File | mapping reads fastq2 |
metagenomic or metatranscriptomic fastq2 file which you want to map metagenomic contigs |
| TRIM_QUALITY | Integer | qualified quality phred |
Qualifying threshold value of quality phred |
| GTF_FILE_NAME | String | Output GTF file name |
Output GTF file name |
| CONTIG_FASTQ_1 | File | metagenomic fastq1 |
metagenomic fastq1 file which you want to construct metagenomic contigs for |
| CONTIG_FASTQ_2 | File | metagenomic fastq2 |
metagenomic fastq2 file which you want to construct metagenomic contigs for |
| DIAMOND_FASTA_FILE | File | Protein fasta file for diamond index |
Protein fasta file for diamond index |
| 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. |
| BLASTN_rRNA_FASTA_FILE1 | File | SILVA_138.1_LSUParc_tax_silva |
SILVA_138.1_LSUParc_tax_silva |
| BLASTN_rRNA_FASTA_FILE2 | File | SILVA_138.1_SSUParc_tax_silva |
SILVA_138.1_SSUParc_tax_silva |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| MAPPING |
metagenomic_contig_mapping_sw.cwl
(Workflow)
|
contig construction and protein prediction |
\"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/06_bwa_mem.cwl ./Tools/07_samtools_sort.cwl ./Tools/08_samtools_flagstat.cwl\" |
| ANNOTATION |
annotation_sw.cwl
(Workflow)
|
Subworkflow for Annotation |
\"Subworkflow for Metagenome Annotation This subworkflow is for annotation of predicted protein coding sequences. \" |
| CONTIG_INDEX |
../Tools/05_bwa_mem_index.cwl
(CommandLineTool)
|
bwa index process |
\"bwa index create process from predicted protein conding sequences for executing BWA-MEM process modified from https://github.com/common-workflow-library/bio-cwl-tools/blob/release/bwa/BWA-Index.cwl original script: https://github.com/RyoMameda/workflow/blob/main/05_mapping.sh original command: bwa index -p index_${f}_bwa ${f}.fna\" |
| TRIMMING_MAP |
../Tools/00_fastp.cwl
(CommandLineTool)
|
trimming by fastp (paired-end fastq data) |
\"quality-trimming pair-end fastq data using fastp version 0.23.4. Modified from https://github.com/nigyta/bact_genome/blob/master/cwl/tool/fastp/fastp.cwl Original script: https://github.com/RyoMameda/workflow/blob/main/02_readsQC.sh original command: fastp -i ${f}_1.fastq.gz -I ${f}_2.fastq.gz -o ${f}_1_trim.fastq.gz -O ${f}_2_trim.fastq.gz -q 20 -h ${f}_fastp.html -w ${threads} -t 1 -T 1\" |
| READS_COUNTIG |
../Tools/13_subread.cwl
(CommandLineTool)
|
counting mapped reads using featureCounts |
\"counting mapped reads using featureCounts command in Subread Original script: https://github.com/RyoMameda/workflow/blob/main/08_quantification.sh\" |
| TRIMMING_CONTIG |
../Tools/00_fastp.cwl
(CommandLineTool)
|
trimming by fastp (paired-end fastq data) |
\"quality-trimming pair-end fastq data using fastp version 0.23.4. Modified from https://github.com/nigyta/bact_genome/blob/master/cwl/tool/fastp/fastp.cwl Original script: https://github.com/RyoMameda/workflow/blob/main/02_readsQC.sh original command: fastp -i ${f}_1.fastq.gz -I ${f}_2.fastq.gz -o ${f}_1_trim.fastq.gz -O ${f}_2_trim.fastq.gz -q 20 -h ${f}_fastp.html -w ${threads} -t 1 -T 1\" |
| CONTIG_CONST_PROT_PREDICT |
megahit_prodigal_sw.cwl
(Workflow)
|
contig construction and protein prediction |
\"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\" |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| BAM | File | bam file |
sorted bam formated file |
| CDS | File | predicted coding sequences |
Predicted conding sequences of metagenomic contigs |
| GTF | File | Output GTF file |
GTF file contains gene annotation of metagenomic contigs |
| INDEX | Directory | index bwa dir |
index files will be contained in this directry |
| PROTEINS | File | predicted proteins |
Predicted proteins of metagenomic contigs |
| READ_COUNT | File | read counts txt file |
txt file containing mapped read counts to metagenomic predicted protein coding sequences |
| BAM_STATS_FILE | File | flagstat file |
flagstat file containing mapping efficiency information |
| CONTIG_FASTA_FILE | File | metagenomic contig |
Constructed metagenomic contigs fasta file |
| CONTIG_STATS_FILE | File | stats of metagenomic contig |
Statical analysis file of metagenomic contigs |
| TRIMMING_MAP_HTML | File | Output HTML file of reads for mapping |
Trimming output HTML file of metagenomic reads for mapping to contigs |
| TRIMMING_CONTIG_HTML | File | Output HTML file of reads for contig construction |
Trimming output HTML file of metagenomic reads for contig construction |
https://w3id.org/cwl/view/git/1838569c1d6d3c15f58c254667d4c6258e67e5a6/Workflow/main_w.cwl
