AwkFastaConverter#
Add to module run order:
#BioModule biolockj.module.seq.AwkFastaConverter
Description#
Convert fastq files into fasta format.
Properties#
Properties are the name=value
pairs in the configuration file.
AwkFastaConverter properties:#
none
General properties applicable to this module:#
Property | Description |
---|---|
cluster.batchCommand | string Terminal command used to submit jobs on the cluster default: null |
cluster.jobHeader | string Header written at top of worker scripts default: null |
cluster.modules | list List of cluster modules to load at start of worker scripts default: null |
cluster.prologue | string To run at the start of every script after loading cluster modules (if any) default: null |
cluster.statusCommand | string Terminal command used to check the status of jobs on the cluster default: null |
docker.saveContainerOnExit | boolean If Y, docker run command will NOT include the --rm flag default: null |
docker.verifyImage | boolean In check dependencies, run a test to verify the docker image. default: null |
exe.awk | executable Path for the "awk" executable; if not supplied, any script that needs the awk command will assume it is on the PATH. default: null |
exe.gzip | executable Path for the "gzip" executable; if not supplied, any script that needs the gzip command will assume it is on the PATH. default: null |
script.defaultHeader | string Store default script header for MAIN script and locally run WORKER scripts. default: #!/bin/bash |
script.numThreads | integer Used to reserve cluster resources and passed to any external application call that accepts a numThreads parameter. default: 8 |
script.numWorkers | integer Set number of samples to process per script (if parallel processing) default: 1 |
script.permissions | string Used as chmod permission parameter (ex: 774) default: 770 |
script.timeout | integer Sets # of minutes before worker scripts times out. default: null |
Details#
version: 0.0.0 This module was first introduced because it was required for QIIME.
Adds modules#
pre-requisite modules
none found
post-requisite modules
none found
Docker#
If running in docker, this module will run in a docker container from this image:
biolockjdevteam/blj_basic:v1.3.18
This can be modified using the following properties:
AwkFastaConverter.imageOwner
AwkFastaConverter.imageName
AwkFastaConverter.imageTag
Citation#
BioLockJ v1.4.2
Module developed by Mike Sioda