Workflow: contig construction and protein prediction
Fetched 2025-11-10 22:46:41 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/06_bwa_mem.cwl ./Tools/07_samtools_sort.cwl ./Tools/08_samtools_flagstat.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 |
| INDEX_BWA_FILENAME | File | index bwa dir name |
directory containig index files for BWA-MEM |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| BAM_STATS |
../Tools/08_samtools_flagstat.cwl
(CommandLineTool)
|
samtools process |
\"checking mapping results (bam formated file) by SAMtools flagstat command original script: https://github.com/RyoMameda/workflow/blob/main/05_mapping.sh original command: samtools flagstat -@ ${threads} mg_${bam}.bam > flagstat_mg_${bam}\" |
| BWA_MEM_MAPPING |
../Tools/06_bwa_mem.cwl
(CommandLineTool)
|
bwa process |
\"Mapping trimmed metagenomic or metatranscriptomic reads to predicted protein coding sequences using BWA-MEM original script: https://github.com/RyoMameda/workflow/blob/main/05_mapping.sh original command: bwa mem -t ${threads} index_${f}_bwa ${fqdir}/${mgfq}_1_trim.fastq.gz ${fqdir}/${mgfq}_2_trim.fastq.gz\" |
| SORTING_SAM2BAM |
../Tools/07_samtools_sort.cwl
(CommandLineTool)
|
samtools process |
\"SAMtools sorting process from BWA-MEM output sam file to bam file original script: https://github.com/RyoMameda/workflow/blob/main/05_mapping.sh original command: samtools sort -@ ${threads} > mg_${bam}.bam\" |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| MAPPING_BAM | File | bam file |
sorted bam formated file |
| BAM_FLAGSTAT | File | flagstat file |
flagstat file containing mapping efficiency information |
https://w3id.org/cwl/view/git/1838569c1d6d3c15f58c254667d4c6258e67e5a6/Workflow/metagenomic_contig_mapping_sw.cwl
