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Merge pull request #47 from chuan-wang/master
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 v1.3 config refactor and new options added
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@ewels
ewels authored Nov 6, 2017
2 parents ddf140a + 9dbaf21 commit 9d8b6b5
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Showing 6 changed files with 228 additions and 97 deletions.
2 changes: 1 addition & 1 deletion Dockerfile
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Expand Up @@ -109,7 +109,7 @@ RUN echo 'source("https://bioconductor.org/biocLite.R")' > /opt/packages.r && \
mkdir /usr/local/lib/R/site-library

# Install phantompeakqualtools
ENV SPP_VERSION="1.14"
ENV SPP_VERSION="1.15"
ENV PHANTOMPEAKQUALTOOLS_VERSION="v.1.1"
RUN curl -fsSL https://github.com/hms-dbmi/spp/archive/${SPP_VERSION}.tar.gz -o /opt/SPP_${SPP_VERSION}.tar.gz && \
Rscript -e "install.packages('/opt/SPP_${SPP_VERSION}.tar.gz',dependencies=TRUE)" && \
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41 changes: 28 additions & 13 deletions conf/base.config
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Expand Up @@ -11,8 +11,6 @@ vim: syntax=groovy
* run on the logged in environment.
*/



process {
cpus = { check_max( 1 * task.attempt, 'cpus' ) }
memory = { check_max( 8.GB * task.attempt, 'memory' ) }
Expand All @@ -22,46 +20,63 @@ process {
maxRetries = 1
maxErrors = '-1'

// Process specific configuration
// Environment modules and resource requirements
$fastqc {
errorStrategy = { task.exitStatus == 143 ? 'retry' : 'ignore' }
}
$trim_galore {
cpus = { check_max( 2 * task.attempt, 'cpus' ) }
memory = { check_max( 16.GB * task.attempt, 'memory' ) }
time = { check_max( 8.h * task.attempt, 'time' ) }
errorStrategy = { task.exitStatus == 143 ? 'retry' : 'terminate' }
}
$bwa{
cpus = { check_max( 8 * task.attempt, 'cpus' ) }
memory = { check_max( 64.GB * task.attempt, 'memory' ) }
time = { check_max( 48.h * task.attempt, 'time' ) }
time = { check_max( 24.h * task.attempt, 'time' ) }
}
$samtools {
time = { check_max( 120.h * task.attempt, 'time' ) }
cpus = { check_max( 4 * task.attempt, 'cpus' ) }
memory = { check_max( 32.GB * task.attempt, 'memory' ) }
time = { check_max( 8.h * task.attempt, 'time' ) }
}
$bwa_unmapped{
cpus = { check_max( 4 * task.attempt, 'cpus' ) }
memory = { check_max( 32.GB * task.attempt, 'memory' ) }
time = { check_max( 8.h * task.attempt, 'time' ) }
errorStrategy = { task.exitStatus == 143 ? 'retry' : 'ignore' }
}
$picard {
time = { check_max( 24.h * task.attempt, 'time' ) }
cpus = { check_max( 4 * task.attempt, 'cpus' ) }
memory = { check_max( 32.GB * task.attempt, 'memory' ) }
time = { check_max( 8.h * task.attempt, 'time' ) }
}
$countstat {
memory = { check_max( 4.GB * task.attempt, 'memory' ) }
time = { check_max( 8.h * task.attempt, 'time' ) }
errorStrategy = { task.exitStatus == 143 ? 'retry' : 'ignore' }
}
$phantompeakqualtools {
time = { check_max( 24.h * task.attempt, 'time' ) }
time = { check_max( 8.h * task.attempt, 'time' ) }
errorStrategy = { task.exitStatus == 143 ? 'retry' : 'ignore' }
}
$calculateNSCRSC {
memory = { check_max( 2.GB * task.attempt, 'memory' ) }
errorStrategy = { task.exitStatus == 143 ? 'retry' : 'ignore' }
}
$deepTools {
cpus = { check_max( 4 * task.attempt, 'cpus' ) }
memory = { check_max( 32.GB * task.attempt, 'memory' ) }
time = { check_max( 120.h * task.attempt, 'time' ) }
time = { check_max( 8.h * task.attempt, 'time' ) }
errorStrategy = { task.exitStatus == 143 ? 'retry' : 'ignore' }
}
$ngsplot {
time = { check_max( 120.h * task.attempt, 'time' ) }
cpus = { check_max( 4 * task.attempt, 'cpus' ) }
memory = { check_max( 32.GB * task.attempt, 'memory' ) }
time = { check_max( 8.h * task.attempt, 'time' ) }
errorStrategy = { task.exitStatus == 143 ? 'retry' : 'ignore' }
}
$macs {
cpus = { check_max( 4 * task.attempt, 'cpus' ) }
memory = { check_max( 32.GB * task.attempt, 'memory' ) }
time = { check_max( 24.h * task.attempt, 'time' ) }
time = { check_max( 8.h * task.attempt, 'time' ) }
}
$multiqc {
executor = 'local'
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2 changes: 1 addition & 1 deletion conf/docker.config
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Expand Up @@ -14,7 +14,7 @@ docker {
}
process {
container = 'scilifelab/ngi-chipseq'
// Not sure that this always works. May be better to config this manually.
executor = 'local'
cpus = $executor.cpus
memory = $executor.memory
time = 48.h
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34 changes: 19 additions & 15 deletions conf/uppmax.config
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Expand Up @@ -4,56 +4,60 @@ vim: syntax=groovy
* -------------------------------------------------
* Nextflow config file for UPPMAX (milou / irma)
* -------------------------------------------------
* Defines reference genomes, using iGenome paths
* Imported under the default 'standard' Nextflow
* profile in nextflow.config
*/


process {
executor = 'slurm'
clusterOptions = { "-A $params.project " + (params.clusterOptions ?: '') }
clusterOptions = { "-A $params.project ${params.clusterOptions ?: ''}" }

// Process specific configuration
// Environment modules and resource requirements
$fastqc {
module = ['bioinfo-tools', 'FastQC']
module = ['bioinfo-tools', 'FastQC/0.7.2']
}
$trim_galore {
module = ['bioinfo-tools', 'FastQC', 'TrimGalore']
module = ['bioinfo-tools', 'TrimGalore/0.4.1', 'FastQC/0.7.2']
}
$bwa{
module = ['bioinfo-tools', 'bwa', 'samtools/1.3']
module = ['bioinfo-tools', 'bwa/0.7.8', 'samtools/1.5']
}
$samtools {
module = ['bioinfo-tools', 'samtools/1.3', 'BEDTools']
module = ['bioinfo-tools', 'samtools/1.5', 'BEDTools/2.26.0']
}
$bwa_unmapped {
module = ['bioinfo-tools', 'samtools/1.5']
}
$picard {
module = ['bioinfo-tools', 'picard/2.0.1', 'samtools/1.3', 'BEDTools']
module = ['bioinfo-tools', 'picard/2.10.3', 'samtools/1.5', 'BEDTools/2.26.0']
}
$countstat {
}
$phantompeakqualtools {
module = ['bioinfo-tools', 'R/3.2.3', 'phantompeakqualtools']
module = ['bioinfo-tools', 'R/3.2.3', 'phantompeakqualtools/1.1']
}
$calculateNSCRSC {
}
$deepTools {
module = ['bioinfo-tools', 'deepTools']
module = ['bioinfo-tools', 'deepTools/2.5.1']
}
$ngsplot {
module = ['bioinfo-tools', 'samtools/1.3', 'R/3.2.3', 'ngsplot']
module = ['bioinfo-tools', 'samtools/1.5', 'R/3.2.3', 'ngsplot/2.61']
}
$macs {
module = ['bioinfo-tools', 'MACS', 'samtools/1.3']
module = ['bioinfo-tools', 'MACS/2.1.0', 'samtools/1.5']
}
// NB: Overwrite this in a config file in the working directory (nextflow.config) or with -c
// if you have your own installation of MultiQC outside of the environment module system.
// eg: Add the line: process.$multiqc.module = []
$multiqc {
module = ['bioinfo-tools', 'MultiQC']
module = ['bioinfo-tools', 'MultiQC/1.2']
}
}

params {
clusterOptions = false
rlocation = "$HOME/R/nxtflow_libs/"
saveReference = true
// Max resources requested by a normal node on milou. If you need more memory, run on a fat node using:
// --clusterOptions "-C mem512GB" --max_memory "512GB"
max_memory = 128.GB
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