> For the complete documentation index, see [llms.txt](https://cmo-ci.gitbook.io/command-line-tools-cwl/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://cmo-ci.gitbook.io/command-line-tools-cwl/develop-1/trim-galore/trim_galore_0.6.2.md).
# v0.6.2
## Version of tools in docker image (/container/Dockerfile)
| Tool | Version | Location |
| ----------------- | ------- | ------------------------------------------------------------------------------ |
| Ubuntu base image | 18.04 | - |
| cutadapt | 2.3 | |
| FASTQC | 0.11.8 | |
| Trim Galore | 0.6.2 | |
## CWL
* CWL specification 1.0
* Use example\_inputs.yaml to see the inputs to the cwl
* Example Command using [toil](https://toil.readthedocs.io):
```bash
> toil-cwl-runner trim_galore_0.6.2.cwl example_inputs.yaml
```
**If at MSK, using the JUNO cluster you can use the following command**
```bash
#Using CWLTOOL
> cwltool --singularity --non-strict /path/to/trim_galore_0.6.2.cwl /path/to/inputs.yaml
#Using toil-cwl-runner
> mkdir trimgalore_toil_log
> toil-cwl-runner --singularity --logFile /path/to/trimgalore_toil_log/cwltoil.log --jobStore /path/to/trimgalore_jobStore --batchSystem lsf --workDir /path/to/trimgalore_toil_log --outdir . --writeLogs /path/to/trimgalore_toil_log --logLevel DEBUG --stats --retryCount 2 --disableCaching --maxLogFileSize 20000000000 /path/to/trim_galore_0.6.2.cwl /path/to/inputs.yaml > trimgalore_toil.stdout 2> trimgalore_toil.stderr &
```
### Usage
```
usage: trim_galore_0.6.2.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
--path_to_trim_galore PATH_TO_TRIM_GALORE
Path to trim_galore executable file
--adapter ADAPTER Adapter sequence to be trimmed. If not specified
explicitely, the first 13bp of the Illumina adapter
'AGATCGGAAGAGC' will be used by default.
--adapter2 ADAPTER2 Optional adapter sequence to be trimmed off read 2 of
paired-end files. This option requires '--paired' to
be specified as well
--fastq1 FASTQ1 READ1 of the paired-end run
--fastq2 FASTQ2 READ2 of the pair-end run
--length LENGTH Discard reads that became shorter than length INT
because of either quality or adapter trimming. A value
of '0' effectively disables this behaviour. Default:
20 bp.
--paired This option performs length trimming of
quality/adapter/RRBS trimmed reads for paired-end
files. To pass the validation test, both sequences of
a sequence pair are required to have a certain minimum
length which is governed by the option --length (see
above). If only one read passes this length threshold
the other read can be rescued (see option
--retain_unpaired). Using this option lets you discard
too short read pairs without disturbing the sequence-
by-sequence order of FastQ files which is required by
many aligners.
--gzip Compress the output file with gzip. If the input files
are gzip-compressed the output files will be
automatically gzip compressed as well.
--quality QUALITY Trim low-quality ends from reads in addition to
adapter removal. For RRBS samples, quality trimming
will be performed first, and adapter trimming is
carried in a second round. Other files are quality and
adapter trimmed in a single pass. The algorithm is the
same as the one used by BWA (Subtract INT from all
qualities; compute partial sums from all indices to
the end of the sequence; cut sequence at the index at
which the sum is minimal). Default Phred score: 20.
--stringency STRINGENCY
"Overlap with adapter sequence required to trim a
sequence. Defaults to a very stringent setting of '1',
i.e. even a single bp of overlapping sequence will be
trimmed of the 3' end of any read."
--suppress_warn If specified any output to STDOUT or STDERR will be
suppressed.
--error_rate ERROR_RATE
Maximum allowed error rate (no. of errors divided by
the length of the matching region) (default: 0.1)
```
---
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