0.24.0
Version of tools in docker image
Tool
Version
Location
fastp
0.24.0
quay.io/biocontainers/fastp:0.24.0--heae3180_1
CWL
CWL specification 1.0
Use example_inputs.yaml to see the inputs to the cwl
Example Command using toil:
> toil-cwl-runner ./fastp_0.20.1.cwl example_inputs.yamlIf at MSK, using the JUNO cluster having installed toil version 3.19 and manually modifying lsf.py by removing type==X86_64 && you can use the following command
#Using CWLTOOL
> cwltool ./fastp_0.24.0.cwl example_inputs.yaml
#Using toil-cwl-runner
> mkdir toil_log
> toil-cwl-runner --singularity --logFile /path/to/toil_log/cwltoil.log --jobStore /path/to/jobStore --batchSystem lsf --workDir /path/to =toil_log --outdir . --writeLogs /path/to/toil_log --logLevel DEBUG --stats --retryCount 2 --disableCaching --maxLogFileSize 20000000000 /path/to/fastp-0_20_1/fastp-0_20_1.cwl /path/to/inputs.yaml > toil.stdout 2> toil.stderr &Usage
usage: fastp_0.24.0.cwl [-h] [--memory_per_job MEMORY_PER_JOB] [--memory_overhead MEMORY_OVERHEAD] [--number_of_threads NUMBER_OF_THREADS] --read1_input READ1_INPUT --read1_output_path READ1_OUTPUT_PATH
[--read2_input READ2_INPUT] [--read2_output_path READ2_OUTPUT_PATH] [--unpaired1_path UNPAIRED1_PATH] [--unpaired2_path UNPAIRED2_PATH] [--failed_reads_path FAILED_READS_PATH]
[--read1_adapter_sequence READ1_ADAPTER_SEQUENCE] [--read2_adapter_sequence READ2_ADAPTER_SEQUENCE] [--minimum_read_length MINIMUM_READ_LENGTH] [--maximum_read_length MAXIMUM_READ_LENGTH]
[--trim_tail1 TRIM_TAIL1] [----trim_tail2 TRIM_TAIL2] [--max_len_read1 MAX_LEN_READ1] [--max_len_read2 MAX_LEN_READ2] [--json_output_path JSON_OUTPUT_PATH] [--html_output_path HTML_OUTPUT_PATH]
[--disable_quality_filtering] [--disable_trim_poly_g] [--disable_adapter_trimming] [--dont_eval_duplication] [--disable_length_filtering] [--verbose VERBOSE]
[job_order]
Setup and execute Fastp
positional arguments:
job_order Job input json file
options:
-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
worker thread number, default is 2 (int [=2])
--read1_input READ1_INPUT
read1 input file name
--read1_output_path READ1_OUTPUT_PATH
read1 output file name
--read2_input READ2_INPUT
read2 input file name, for PE data
--read2_output_path READ2_OUTPUT_PATH
read2 output file name
--unpaired1_path UNPAIRED1_PATH
for PE input, if read1 passed QC but read2 not, it will be written to unpaired1.
--unpaired2_path UNPAIRED2_PATH
for PE input, if read2 passed QC but read1 not, it will be written to unpaired2.
--failed_reads_path FAILED_READS_PATH
specify the file to store reads that cannot pass the filters.
--read1_adapter_sequence READ1_ADAPTER_SEQUENCE
the adapter for read1. For SE data, if not specified, the adapter will be auto-detected. For PE data, this is used if R1/R2 are found not overlapped.
--read2_adapter_sequence READ2_ADAPTER_SEQUENCE
the adapter for read2. For PE data, this is used if R1/R2 are found not overlapped.
--minimum_read_length MINIMUM_READ_LENGTH
reads shorter than length_required will be discarded, default is 15.
--maximum_read_length MAXIMUM_READ_LENGTH
reads longer than length_limit will be discarded, default 0 means no limitation.
--trim_tail1 TRIM_TAIL1
trimming how many bases in tail for read1, default is 0 (int [=0])
----trim_tail2 TRIM_TAIL2
trimming how many bases in tail for read2. If it's not specified, it will follow read1's settings (int [=0])
--max_len_read1 MAX_LEN_READ1
if read1 is longer than max_len1, then trim read1 at its tail to make it as long as max_len1. Default 0 means no limitation
--max_len_read2 MAX_LEN_READ2
if read2 is longer than max_len2, then trim read2 at its tail to make it as long as max_len2. Default 0 means no limitation. If it's not specified, it will follow read1's settings
--json_output_path JSON_OUTPUT_PATH
the json format report file name
--html_output_path HTML_OUTPUT_PATH
the html format report file name
--disable_quality_filtering
quality filtering is enabled by default. If this option is specified, quality filtering is disabled
--disable_trim_poly_g
disable polyG tail trimming, by default trimming is automatically enabled for Illumina NextSeq/NovaSeq data
--disable_adapter_trimming
adapter trimming is enabled by default. If this option is specified, adapter trimming is disabled
--dont_eval_duplication
don't evaluate duplication rate to save time and use less memory.
--disable_length_filtering
length filtering is enabled by default. If this option is specified, length filtering is disabled
--verbose VERBOSE output verbose log information (i.e. when every 1M reads are processed)Last updated