> toil-cwl-runner merge_fastq_0.1.7.cwl example_inputs.yaml
#Using CWLTOOL
> cwltool --singularity --non-strict /path/to/merge_fastq_0.1.7/merge_fastq_0.1.7.cwl /path/to/inputs.yaml
#Using toil-cwl-runner
> mkdir tool_toil_log
> toil-cwl-runner --singularity --logFile /path/to/tool_toil_log/cwltoil.log --jobStore /path/to/tool_jobStore --batchSystem lsf --workDir /path/to/tool_toil_log --outdir . --writeLogs /path/to/tool_toil_log --logLevel DEBUG --stats --retryCount 2 --disableCaching --maxLogFileSize 20000000000 /path/to/merge_fastq_0.1.7/merge_fastq_0.1.7.cwl /path/to/inputs.yaml > tool_toil.stdout 2> tool_toil.stderr &
> toil-cwl-runner merge_fastq_0.1.7.cwl --help
usage: merge_fastq_0.1.7.cwl [-h]
positional arguments:
job_order Job input json file
optional arguments:
-h, --help show this help message and exit
--memory_per_job MEMORY_PER_JOB
Memory per job in megabytes
--memory_overhead MEMORY_OVERHEAD
Memory overhead per job in megabytes
--number_of_threads NUMBER_OF_THREADS
--fastq1 FASTQ1 Full path to gziped READ1 fastq files, can be
specified multiple times for example: --fastq1
test_part1_R1.fastq.gz --fastq1 test_part2_R1.fastq.gz
[required]
--fastq2 FASTQ2 Full path to gziped READ2 fastq files, can be
specified multiple times for example: --fastq1
test_part1_R2.fastq.gz --fastq1 test_part2_R2.fastq.gz
[required]
--output_path OUTPUT_PATH
Full path to write the output files (default: Current
working directory)
--out_fastq1_name OUT_FASTQ1_NAME
Name of the merged output READ1 fastq file(default:
merged_fastq_R1.fastq.gz)
--out_fastq2_name OUT_FASTQ2_NAME
Name of the merged output READ2 fastq file(default:
merged_fastq_R2.fastq.gz)
