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6ef74fe May 30, 2017
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/*
Clusterflow Config
-------------------
Default static variables for clusterflow.
Syntax - @key value
These will be overwritten by any with the same name in ~/.clusterflow/clusterflow.config
-------------------
*/
/****************/
/* Core Options */
/****************/
/* See the Cluster Flow documentation for descriptions */
@email 0
@colourful 0
/* @disable_update_check */
@notification suspend
@notification abort
@notification complete
@split_files 1
/* @priority -500 */
@total_cores 64
@total_mem 128G
@max_runs 12
@time_multiplier 1
@max_time 10-00
/***********************/
/* Cluster Environment */
/***********************/
/* Options: local, GRIDEngine, SLURM or LSF */
/* @cluster_environment GRIDEngine */
/* GRIDEngine parallel environment (default orte) */
/* @cluster_queue_environment mpislots */
/* GRIDEngine - specify memory per CPU (default false) */
/* @cluster_mem_per_cpu true */
/* Custom Job Submit Command - uncomment to customise parameters for job submission */
/* Accepted variable placeholders: {{command}} {{job_id}} {{outfn}} {{cores}} {{mem}} {{time}} {{priority}} {{email}} {{notifications}} {{project}} {{qname}} */
/* @custom_job_submit_command qsub -cwd -V -S /bin/bash -MY --CUSTOM --PARAMS -pe orte {{cores}} {{command}} */
/***********************/
/* Environment Modules */
/***********************/
/* To stop cluster flow trying to load environment modules, uncomment the following line: */
/* @ignore_modules true */
/* Sometimes, you always need to load certain modules. Add these here. */
/* @environment_module_always <mod name> */
/* If your modules have a different name to those being requested in a module, you can create aliases */
/* You can also use aliases to specify particular module versions */
/* @environment_module_alias <requested> <replacement> */
/****************/
/* File Merging */
/****************/
/* Many sequencing centres split samples across lanes, meaning starting FastQ files should */
/* be concatenated before processing. You can uncomment the following line and set a regex */
/* below to automatically do this at the start of every Cluster Flow run. */
/* If input files don't match the regex, the pipeline continues without any merging. Use */
/* one set of brackets to define the resulting merged file names. */
/* @merge_regex [1-8]_[0-9]{6}_[a-zA-Z0-9]+_(P\d+_\d+_[12]).fastq.gz */
/**********************/
/* Pipeline Reporting */
/**********************/
/* If specific flags are found in the pipeline output log, you can flag them as */
/* warnings or highlights in the report e-mail. Case insensitve. */
@log_highlight_string at least one reported alignment
@log_warning_string Error occured
@log_warning_string job failed