fastQC
Niassa-wrapped Cromwell (widdle) workflow for running FastQC tools on paired or unpaired reads.
Dependencies
Usage
Cromwell
java -jar cromwell.jar run fastqc.wdl --inputs inputs.json
Inputs
Required workflow parameters:
| Parameter | Value | Description |
|---|---|---|
fastqR1 |
File | Input file with the first mate reads. |
Optional workflow parameters:
| Parameter | Value | Default | Description |
|---|---|---|---|
fastqR2 |
File? | None | Input file with the second mate reads (if not set the experiments will be regarded as single-end). |
outputFileNamePrefix |
String | "" | Output prefix, customizable. Default is the first file's basename. |
r1Suffix |
String | "_R1" | Suffix for R1 file. |
r2Suffix |
String | "_R2" | Suffix for R2 file. |
Optional task parameters:
| Parameter | Value | Default | Description |
|---|---|---|---|
firstMateFastQC.jobMemory |
Int | 6 | Memory allocated to fastqc. |
firstMateFastQC.timeout |
Int | 20 | Timeout in hours, needed to override imposed limits. |
firstMateFastQC.javaHeap |
Int | 4 | Memory allocated to java heap, in G. |
firstMateFastQC.threads |
Int? | None | Threads param for fastqc |
firstMateFastQC.modules |
String | "perl/5.28 java/11 fastqc/0.11.9" | Names and versions of required modules. |
firstMateHtml.jobMemory |
Int | 2 | Memory allocated to this task. |
firstMateHtml.timeout |
Int | 1 | Timeout, in hours, needed to override imposed limits. |
firstMateZip.jobMemory |
Int | 2 | Memory allocated to this task. |
firstMateZip.timeout |
Int | 1 | Timeout, in hours, needed to override imposed limits. |
secondMateFastQC.jobMemory |
Int | 6 | Memory allocated to fastqc. |
secondMateFastQC.timeout |
Int | 20 | Timeout in hours, needed to override imposed limits. |
secondMateFastQC.javaHeap |
Int | 4 | Memory allocated to java heap, in G. |
secondMateFastQC.threads |
Int? | None | Threads param for fastqc |
secondMateFastQC.modules |
String | "perl/5.28 java/11 fastqc/0.11.9" | Names and versions of required modules. |
secondMateHtml.jobMemory |
Int | 2 | Memory allocated to this task. |
secondMateHtml.timeout |
Int | 1 | Timeout, in hours, needed to override imposed limits. |
secondMateZip.jobMemory |
Int | 2 | Memory allocated to this task. |
secondMateZip.timeout |
Int | 1 | Timeout, in hours, needed to override imposed limits. |
Outputs
| Output | Type | Description |
|---|---|---|
html_report_R1 |
File | HTML report for the first mate fastq file. |
zip_bundle_R1 |
File | zipped report from FastQC for the first mate reads. |
html_report_R2 |
File? | HTML report for read second mate fastq file. |
zip_bundle_R2 |
File? | zipped report from FastQC for the second mate reads. |
Commands
This section lists command(s) run by fastqc workflow
- Running fastqc
fastqc workflow runs the following command (excerpt from .wdl file). INPUT_FASTQ is a placeholder for an input file.
FASTQC=$(which fastqc)
JAVA=$(which java)
perl $FASTQC INPUT_FASTQ --java=$JAVA --noextract --outdir "."
Support
For support, please file an issue on the Github project or send an email to [email protected] .
Generated with generate-markdown-readme (https://github.com/oicr-gsi/gsi-wdl-tools/)
React
Typescript
Django
Laravel
Facebook
Microsoft
Google
Alibaba
D3
Tencent