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Commit 605bba8d authored by Cats's avatar Cats
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even more time_minutes

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CPAT.wdl
+ 3
− 0
View file @ 605bba8d
......@@ -31,6 +31,7 @@ task CPAT {
# CPAT should not index the reference genome.
Array[String]? startCodons
Array[String]? stopCodons
Int timeMinutes = 1 + ceil(size(gene, "G") * 30)
String dockerImage = "biocontainers/cpat:v1.2.4_cv1"
}
......@@ -55,6 +56,7 @@ task CPAT {
runtime {
docker: dockerImage
time_minutes: timeMinutes
}
parameter_meta {
......@@ -67,6 +69,7 @@ task CPAT {
category: "advanced"}
startCodons: {description: "Equivalent to CPAT's `--start` option.", category: "advanced"}
stopCodons: {description: "Equivalent to CPAT's `--stop` option.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
......
bcftools.wdl
+ 1
− 1
View file @ 605bba8d
......@@ -27,7 +27,7 @@ task Bcf2Vcf {
File bcf
String outputPath = "./bcftools/SV.vcf"
String memory = "2G"
Int timeMinutes = ceil(size(bcf, "G"))
Int timeMinutes = 1 + ceil(size(bcf, "G"))
String dockerImage = "quay.io/biocontainers/bcftools:1.9--ha228f0b_3"
}
......
bedtools.wdl
+ 33
− 29
View file @ 605bba8d
......@@ -24,8 +24,10 @@ task Complement {
input {
File faidx
File inputBed
String dockerImage = "quay.io/biocontainers/bedtools:2.23.0--hdbcaa40_3"
String outputBed = basename(inputBed, "\.bed") + ".complement.bed"
String memory = "2G"
Int timeMinutes = 1 + ceil(size([inputBed, faidx], "G"))
String dockerImage = "quay.io/biocontainers/bedtools:2.23.0--hdbcaa40_3"
}
# Use a fasta index file to get the genome sizes. And convert that to the
......@@ -44,20 +46,19 @@ task Complement {
}
runtime {
memory: memory
time_minutes: timeMinutes
docker: dockerImage
}
parameter_meta {
faidx: {description: "The fasta index (.fai) file from which to extract the genome sizes",
category: "required"}
inputBed: {description: "The inputBed to complement",
category: "required"}
outputBed: {description: "The path to write the output to",
category: "advanced"}
dockerImage: {
description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"
}
faidx: {description: "The fasta index (.fai) file from which to extract the genome sizes.", category: "required"}
inputBed: {description: "The inputBed to complement.", category: "required"}
outputBed: {description: "The path to write the output to.", category: "advanced"}
memory: {description: "The amount of memory needed for the job.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
}
......@@ -97,6 +98,8 @@ task MergeBedFiles {
input {
Array[File]+ bedFiles
String outputBed = "merged.bed"
String memory = "2G"
Int timeMinutes = 1 + ceil(size(bedFiles, "G"))
String dockerImage = "quay.io/biocontainers/bedtools:2.23.0--hdbcaa40_3"
}
......@@ -111,17 +114,17 @@ task MergeBedFiles {
}
runtime {
memory: memory
time_minutes: timeMinutes
docker: dockerImage
}
parameter_meta {
bedFiles: {description: "The bed files to merge",
category: "required"}
outputBed: {description: "The path to write the output to",
category: "advanced"}
dockerImage: {
description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"
}
bedFiles: {description: "The bed files to merge.", category: "required"}
outputBed: {description: "The path to write the output to.", category: "advanced"}
memory: {description: "The amount of memory needed for the job.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
}
......@@ -172,6 +175,8 @@ task Intersect {
# Giving a faidx file will set the sorted option.
File? faidx
String outputBed = "intersect.bed"
String memory = "2G"
Int timeMinutes = 1 + ceil([regionsA, regionsB], "G"))
String dockerImage = "quay.io/biocontainers/bedtools:2.23.0--hdbcaa40_3"
}
Boolean sorted = defined(faidx)
......@@ -192,21 +197,20 @@ task Intersect {
}
runtime {
memory: memory
time_minutes: timeMinutes
docker: dockerImage
}
parameter_meta {
faidx: {description: "The fasta index (.fai) file that is used to create the genome file required for sorted output. Implies sorted option.",
category: "common"}
regionsA: {description: "Region file a to intersect",
category: "required"}
regionsB: {description: "Region file b to intersect",
category: "required"}
outputBed: {description: "The path to write the output to",
category: "advanced"}
dockerImage: {
description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"
}
regionsA: {description: "Region file a to intersect", category: "required"}
regionsB: {description: "Region file b to intersect", category: "required"}
outputBed: {description: "The path to write the output to", category: "advanced"}
memory: {description: "The amount of memory needed for the job.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
}
bowtie.wdl
+ 1
− 1
View file @ 605bba8d
......@@ -37,7 +37,7 @@ task Bowtie {
String? samRG
Int threads = 1
Int timeMinutes = ceil(size(flatten([readsUpstream, readsDownstream]), "G") * 300 / threads)
Int timeMinutes = 1 + ceil(size(flatten([readsUpstream, readsDownstream]), "G") * 300 / threads)
String memory = "10G"
String picardXmx = "4G"
# Image contains bowtie=1.2.2 and picard=2.9.2
......
bwa.wdl
+ 2
− 2
View file @ 605bba8d
......@@ -31,7 +31,7 @@ task Mem {
Int threads = 4
String memory = "20G"
String picardXmx = "4G"
Int timeMinutes = ceil(size([read1, read2], "G") * 200 / threads)
Int timeMinutes = 1 + ceil(size([read1, read2], "G") * 200 / threads)
# A mulled container is needed to have both picard and bwa in one container.
# This container contains: picard (2.18.7), bwa (0.7.17-r1188)
String dockerImage = "quay.io/biocontainers/mulled-v2-002f51ea92721407ef440b921fb5940f424be842:43ec6124f9f4f875515f9548733b8b4e5fed9aa6-0"
......@@ -100,7 +100,7 @@ task Kit {
String sortMemoryPerThread = "4G"
Int compressionLevel = 1
String memory = "20G"
Int timeMinutes = ceil(size([read1, read2], "G") * 220 / threads)
Int timeMinutes = 1 + ceil(size([read1, read2], "G") * 220 / threads)
String dockerImage = "biocontainers/bwakit:v0.7.15_cv1"
}
......
clever.wdl
+ 1
− 0
View file @ 605bba8d
......@@ -78,6 +78,7 @@ task Mateclever {
outputPath: {description: "The location the output VCF file should be written.", category: "common"}
threads: {description: "The the number of threads required to run a program", category: "advanced"}
memory: {description: "The memory required to run the programs", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
}
}
......
cutadapt.wdl
+ 65
− 222
View file @ 605bba8d
......@@ -173,227 +173,70 @@ task Cutadapt {
}
parameter_meta {
read1: {
description: "The first or single end fastq file to be run through cutadapt.",
category: "required"
}
read2: {
description: "An optional second end fastq file to be run through cutadapt.",
category: "common"
}
read1output: {
description: "The name of the resulting first or single end fastq file.",
category: "common"
}
read2output: {
description: "The name of the resulting second end fastq file.",
category: "common"
}
adapter: {
description: "A list of 3' ligated adapter sequences to be cut from the given first or single end fastq file.",
category: "common"
}
front: {
description: "A list of 5' ligated adapter sequences to be cut from the given first or single end fastq file.",
category: "advanced"
}
anywhere: {
description: "A list of 3' or 5' ligated adapter sequences to be cut from the given first or single end fastq file.",
category: "advanced"
}
adapterRead2: {
description: "A list of 3' ligated adapter sequences to be cut from the given second end fastq file.",
category: "common"
}
frontRead2: {
description: "A list of 5' ligated adapter sequences to be cut from the given second end fastq file.",
category: "advanced"
}
anywhereRead2: {
description: "A list of 3' or 5' ligated adapter sequences to be cut from the given second end fastq file.",
category: "advanced"
}
interleaved: {
description: "Equivalent to cutadapt's --interleaved flag.",
category: "advanced"
}
pairFilter: {
description: "Equivalent to cutadapt's --pair-filter option.",
category: "advanced"
}
errorRate: {
description: "Equivalent to cutadapt's --error-rate option.",
category: "advanced"
}
noIndels: {
description: "Equivalent to cutadapt's --no-indels flag.",
category: "advanced"
}
times: {
description: "Equivalent to cutadapt's --times option.",
category: "advanced"
}
overlap: {
description: "Equivalent to cutadapt's --overlap option.",
category: "advanced"
}
matchReadWildcards: {
description: "Equivalent to cutadapt's --match-read-wildcards flag.",
category: "advanced"
}
noMatchAdapterWildcards: {
description: "Equivalent to cutadapt's --no-match-adapter-wildcards flag.",
category: "advanced"
}
noTrim: {
description: "Equivalent to cutadapt's --no-trim flag.",
category: "advanced"
}
maskAdapter: {
description: "Equivalent to cutadapt's --mask-adapter flag.",
category: "advanced"
}
cut: {
description: "Equivalent to cutadapt's --cut option.",
category: "advanced"
}
nextseqTrim: {
description: "Equivalent to cutadapt's --nextseq-trim option.",
category: "advanced"
}
qualityCutoff: {
description: "Equivalent to cutadapt's --quality-cutoff option.",
category: "advanced"
}
qualityBase: {
description: "Equivalent to cutadapt's --quality-base option.",
category: "advanced"
}
length: {
description: "Equivalent to cutadapt's --length option.",
category: "advanced"
}
trimN: {
description: "Equivalent to cutadapt's --trim-n flag.",
category: "advanced"
}
lengthTag: {
description: "Equivalent to cutadapt's --length-tag option.",
category: "advanced"
}
stripSuffix: {
description: "Equivalent to cutadapt's --strip-suffix option.",
category: "advanced"
}
prefix: {
description: "Equivalent to cutadapt's --prefix option.",
category: "advanced"
}
suffix: {
description: "Equivalent to cutadapt's --suffix option.",
category: "advanced"
}
minimumLength: {
description: "Equivalent to cutadapt's --minimum-length option.",
category: "advanced"
}
maximumLength: {
description: "Equivalent to cutadapt's --maximum-length option.",
category: "advanced"
}
maxN: {
description: "Equivalent to cutadapt's --max-n option.",
category: "advanced"
}
discardTrimmed: {
description: "Equivalent to cutadapt's --quality-cutoff option.",
category: "advanced"
}
discardUntrimmed: {
description: "Equivalent to cutadapt's --discard-untrimmed option.",
category: "advanced"
}
infoFilePath: {
description: "Equivalent to cutadapt's --info-file option.",
category: "advanced"
}
restFilePath: {
description: "Equivalent to cutadapt's --rest-file option.",
category: "advanced"
}
wildcardFilePath: {
description: "Equivalent to cutadapt's --wildcard-file option.",
category: "advanced"
}
tooShortOutputPath: {
description: "Equivalent to cutadapt's --too-short-output option.",
category: "advanced"
}
tooLongOutputPath: {
description: "Equivalent to cutadapt's --too-long-output option.",
category: "advanced"
}
untrimmedOutputPath: {
description: "Equivalent to cutadapt's --untrimmed-output option.",
category: "advanced"
}
tooShortPairedOutputPath: {
description: "Equivalent to cutadapt's --too-short-paired-output option.",
category: "advanced"
}
tooLongPairedOutputPath: {
description: "Equivalent to cutadapt's --too-long-paired-output option.",
category: "advanced"
}
untrimmedPairedOutputPath: {
description: "Equivalent to cutadapt's --untrimmed-paired-output option.",
category: "advanced"
}
colorspace: {
description: "Equivalent to cutadapt's --colorspace flag.",
category: "advanced"
}
doubleEncode: {
description: "Equivalent to cutadapt's --double-encode flag.",
category: "advanced"
}
stripF3: {
description: "Equivalent to cutadapt's --strip-f3 flag.",
category: "advanced"
}
maq: {
description: "Equivalent to cutadapt's --maq flag.",
category: "advanced"
}
bwa: {
description: "Equivalent to cutadapt's --bwa flag.",
category: "advanced"
}
zeroCap: {
description: "Equivalent to cutadapt's --zero-cap flag.",
category: "advanced"
}
noZeroCap: {
description: "Equivalent to cutadapt's --no-zero-cap flag.",
category: "advanced"
}
reportPath: {
description: "The name of the file to write cutadapts's stdout to, this contains some metrics.",
category: "common"
}
compressionLevel: {description: "The compression level if gzipped output is used.",
category: "advanced"}
cores: {
description: "The number of cores to use.",
category: "advanced"
}
memory: {
description: "The amount of memory this job will use.",
category: "advanced"
}
dockerImage: {
description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"
}
read1: {description: "The first or single end fastq file to be run through cutadapt.", category: "required"}
read2: {description: "An optional second end fastq file to be run through cutadapt.", category: "common"}
read1output: {description: "The name of the resulting first or single end fastq file.", category: "common"}
read2output: {description: "The name of the resulting second end fastq file.", category: "common"}
adapter: {description: "A list of 3' ligated adapter sequences to be cut from the given first or single end fastq file.",
category: "common"}
front: {description: "A list of 5' ligated adapter sequences to be cut from the given first or single end fastq file.",
category: "advanced"}
anywhere: {description: "A list of 3' or 5' ligated adapter sequences to be cut from the given first or single end fastq file.",
category: "advanced"}
adapterRead2: {description: "A list of 3' ligated adapter sequences to be cut from the given second end fastq file.",
category: "common"}
frontRead2: {description: "A list of 5' ligated adapter sequences to be cut from the given second end fastq file.",
category: "advanced"}
anywhereRead2: {description: "A list of 3' or 5' ligated adapter sequences to be cut from the given second end fastq file.",
category: "advanced"}
interleaved: {description: "Equivalent to cutadapt's --interleaved flag.", category: "advanced"}
pairFilter: {description: "Equivalent to cutadapt's --pair-filter option.", category: "advanced"}
errorRate: {description: "Equivalent to cutadapt's --error-rate option.", category: "advanced"}
noIndels: {description: "Equivalent to cutadapt's --no-indels flag.", category: "advanced"}
times: {description: "Equivalent to cutadapt's --times option.", category: "advanced"}
overlap: {description: "Equivalent to cutadapt's --overlap option.", category: "advanced"}
matchReadWildcards: {description: "Equivalent to cutadapt's --match-read-wildcards flag.", category: "advanced"}
noMatchAdapterWildcards: {description: "Equivalent to cutadapt's --no-match-adapter-wildcards flag.", category: "advanced"}
noTrim: {description: "Equivalent to cutadapt's --no-trim flag.", category: "advanced"}
maskAdapter: {description: "Equivalent to cutadapt's --mask-adapter flag.", category: "advanced"}
cut: {description: "Equivalent to cutadapt's --cut option.", category: "advanced"}
nextseqTrim: {description: "Equivalent to cutadapt's --nextseq-trim option.", category: "advanced"}
qualityCutoff: {description: "Equivalent to cutadapt's --quality-cutoff option.", category: "advanced"}
qualityBase: {description: "Equivalent to cutadapt's --quality-base option.", category: "advanced"}
length: {description: "Equivalent to cutadapt's --length option.", category: "advanced"}
trimN: {description: "Equivalent to cutadapt's --trim-n flag.", category: "advanced"}
lengthTag: {description: "Equivalent to cutadapt's --length-tag option.", category: "advanced"}
stripSuffix: {description: "Equivalent to cutadapt's --strip-suffix option.", category: "advanced"}
prefix: {description: "Equivalent to cutadapt's --prefix option.", category: "advanced"}
suffix: {description: "Equivalent to cutadapt's --suffix option.", category: "advanced"}
minimumLength: {description: "Equivalent to cutadapt's --minimum-length option.", category: "advanced"}
maximumLength: {description: "Equivalent to cutadapt's --maximum-length option.", category: "advanced"}
maxN: {description: "Equivalent to cutadapt's --max-n option.", category: "advanced"}
discardTrimmed: {description: "Equivalent to cutadapt's --quality-cutoff option.", category: "advanced"}
discardUntrimmed: {description: "Equivalent to cutadapt's --discard-untrimmed option.", category: "advanced"}
infoFilePath: {description: "Equivalent to cutadapt's --info-file option.", category: "advanced"}
restFilePath: {description: "Equivalent to cutadapt's --rest-file option.", category: "advanced"}
wildcardFilePath: {description: "Equivalent to cutadapt's --wildcard-file option.", category: "advanced"}
tooShortOutputPath: {description: "Equivalent to cutadapt's --too-short-output option.", category: "advanced"}
tooLongOutputPath: {description: "Equivalent to cutadapt's --too-long-output option.", category: "advanced"}
untrimmedOutputPath: {description: "Equivalent to cutadapt's --untrimmed-output option.", category: "advanced"}
tooShortPairedOutputPath: {description: "Equivalent to cutadapt's --too-short-paired-output option.", category: "advanced"}
tooLongPairedOutputPath: {description: "Equivalent to cutadapt's --too-long-paired-output option.", category: "advanced"}
untrimmedPairedOutputPath: {description: "Equivalent to cutadapt's --untrimmed-paired-output option.", category: "advanced"}
colorspace: {description: "Equivalent to cutadapt's --colorspace flag.", category: "advanced"}
doubleEncode: {description: "Equivalent to cutadapt's --double-encode flag.", category: "advanced"}
stripF3: {description: "Equivalent to cutadapt's --strip-f3 flag.", category: "advanced"}
maq: {description: "Equivalent to cutadapt's --maq flag.", category: "advanced"}
bwa: {description: "Equivalent to cutadapt's --bwa flag.", category: "advanced"}
zeroCap: {description: "Equivalent to cutadapt's --zero-cap flag.", category: "advanced"}
noZeroCap: {description: "Equivalent to cutadapt's --no-zero-cap flag.", category: "advanced"}
reportPath: {description: "The name of the file to write cutadapts's stdout to, this contains some metrics.",
category: "common"}
compressionLevel: {description: "The compression level if gzipped output is used.", category: "advanced"}
cores: {description: "The number of cores to use.", category: "advanced"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
}
fastqc.wdl
+ 2
− 1
View file @ 605bba8d
......@@ -40,7 +40,7 @@ task Fastqc {
Int threads = 1
# Fastqc uses 250MB per thread in its wrapper.
String memory = "~{250 + 250 * threads}M"
Int? timeMinutes = 1 + ceil(size(seqFile, "G")) * 4
Int timeMinutes = 1 + ceil(size(seqFile, "G")) * 4
String dockerImage = "quay.io/biocontainers/fastqc:0.11.9--0"
Array[File]? NoneArray
File? NoneFile
......@@ -106,6 +106,7 @@ task Fastqc {
dir: {description: "Equivalent to fastqc's --dir option.", category: "advanced"}
threads: {description: "The number of cores to use.", category: "advanced"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
......
gatk.wdl
+ 1
− 1
View file @ 605bba8d
......@@ -416,7 +416,7 @@ task CombineGVCFs {
String memory = "5G"
String javaXmx = "4G"
Int timeMinutes = ceil(size(gvcfFiles, "G") * 8)
Int timeMinutes = 1 + ceil(size(gvcfFiles, "G") * 8)
String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
}
......
gffcompare.wdl
+ 3
− 0
View file @ 605bba8d
......@@ -44,6 +44,7 @@ task GffCompare {
Boolean verbose = false
Boolean debugMode = false
Int timeMinutes = 1 + ceil(size(inputGtfFiles, "G") * 30)
String dockerImage = "quay.io/biocontainers/gffcompare:0.10.6--h2d50403_0"
# This workaround only works in the input section.
......@@ -110,6 +111,7 @@ task GffCompare {
}
runtime {
time_minutes: timeMinutes
docker: dockerImage
}
......@@ -134,6 +136,7 @@ task GffCompare {
noTmap: {description: "Equivalent to gffcompare's `-T` flag.", category: "advanced"}
verbose: {description: "Equivalent to gffcompare's `-V` flag.", category: "advanced"}
debugMode: {description: "Equivalent to gffcompare's `-D` flag.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
......
gffread.wdl
+ 3
− 0
View file @ 605bba8d
......@@ -30,6 +30,7 @@ task GffRead {
String? proteinFastaPath
String? filteredGffPath
Boolean outputGtfFormat = false
Int timeMinutes = 1 + ceil(size(inputGff) * 10)
String dockerImage = "quay.io/biocontainers/gffread:0.9.12--0"
}
......@@ -62,6 +63,7 @@ task GffRead {
runtime {
docker: dockerImage
time_minutes: timeMinutes
}
parameter_meta {
......@@ -73,6 +75,7 @@ task GffRead {
proteinFastaPath: {description: "The location the protein fasta should be written to.", category: "advanced"}
filteredGffPath: {description: "The location the filtered GFF should be written to.", category: "advanced"}
outputGtfFormat: {description: "Equivalent to gffread's `-T` flag.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
......
hisat2.wdl
+ 4
− 1
View file @ 605bba8d
......@@ -32,8 +32,9 @@ task Hisat2 {
String platform = "illumina"
Boolean downstreamTranscriptomeAssembly = true
Int threads = 1
Int threads = 4
String memory = "48G"
Int timeMinutes = 1 + ceil(size([inputR1, inputR2], "G") * 180 / threads)
# quay.io/biocontainers/mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1
# is a combination of hisat2 and samtools
# hisat2=2.1.0, samtools=1.8
......@@ -67,6 +68,7 @@ task Hisat2 {
runtime {
memory: memory
cpu: threads + 1
time_minutes: timeMinutes
docker: dockerImage
}
......@@ -82,6 +84,7 @@ task Hisat2 {
downstreamTranscriptomeAssembly: {description: "Equivalent to hisat2's `--dta` flag.", category: "advanced"}
threads: {description: "The number of threads to use.", category: "advanced"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
......
htseq.wdl
+ 15
− 44
View file @ 605bba8d
......@@ -33,6 +33,7 @@ task HTSeqCount {
Array[String] additionalAttributes = []
String memory = "40G"
Int timeMinutes = 1 + ceil(size(inputBams, "G") * 60)
String dockerImage = "quay.io/biocontainers/htseq:0.11.2--py37h637b7d7_1"
}
......@@ -56,54 +57,24 @@ task HTSeqCount {
}
runtime {
time_minutes: timeMinutes
memory: memory
docker: dockerImage
}
parameter_meta {
inputBams: {
description: "The input BAM files.",
category: "required"
}
gtfFile: {
description: "A GTF/GFF file containing the features of interest.",
category: "required"
}
outputTable: {
description: "The path to which the output table should be written.",
category: "common"
}
format: {
description: "Equivalent to the -f option of htseq-count.",
category: "advanced"
}
order: {
description: "Equivalent to the -r option of htseq-count.",
category: "advanced"
}
stranded: {
description: "Equivalent to the -s option of htseq-count.",
category: "common"
}
featureType: {
description: "Equivalent to the --type option of htseq-count.",
category: "advanced"
}
idattr: {
description: "Equivalent to the --idattr option of htseq-count.",
category: "advanced"
}
additionalAttributes: {
description: "Equivalent to the --additional-attr option of htseq-count.",
category: "advanced"
}
memory: {
description: "The amount of memory the job requires in GB.",
category: "advanced"
}
dockerImage: {
description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"
}
inputBams: {description: "The input BAM files.", category: "required"}
gtfFile: {description: "A GTF/GFF file containing the features of interest.", category: "required"}
outputTable: {description: "The path to which the output table should be written.", category: "common"}
format: {description: "Equivalent to the -f option of htseq-count.", category: "advanced"}
order: {description: "Equivalent to the -r option of htseq-count.", category: "advanced"}
stranded: {description: "Equivalent to the -s option of htseq-count.", category: "common"}
featureType: {description: "Equivalent to the --type option of htseq-count.", category: "advanced"}
idattr: {description: "Equivalent to the --idattr option of htseq-count.", category: "advanced"}
additionalAttributes: {description: "Equivalent to the --additional-attr option of htseq-count.", category: "advanced"}
memory: {description: "The amount of memory the job requires in GB.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
}
picard.wdl
+ 6
− 6
View file @ 605bba8d
......@@ -87,7 +87,7 @@ task CollectMultipleMetrics {
String memory = "10G"
String javaXmx = "8G"
Int timeMinutes = ceil(size(inputBam, "G") * 6)
Int timeMinutes = 1 + ceil(size(inputBam, "G") * 6)
String dockerImage = "quay.io/biocontainers/picard:2.20.5--0"
}
......@@ -208,7 +208,7 @@ task CollectRnaSeqMetrics {
String memory = "10G"
String javaXmx = "8G"
Int timeMinutes = ceil(size(inputBam, "G") * 6)
Int timeMinutes = 1 + ceil(size(inputBam, "G") * 6)
String dockerImage = "quay.io/biocontainers/picard:2.20.5--0"
}
......@@ -268,7 +268,7 @@ task CollectTargetedPcrMetrics {
String memory = "5G"
String javaXmx = "4G"
Int timeMinutes = ceil(size(inputBam, "G") * 6)
Int timeMinutes = 1 + ceil(size(inputBam, "G") * 6)
String dockerImage = "quay.io/biocontainers/picard:2.20.5--0"
}
......@@ -333,7 +333,7 @@ task GatherBamFiles {
String memory = "5G"
String javaXmx = "4G"
Int timeMinutes = ceil(size(inputBams, "G") * 0.5)
Int timeMinutes = 1 + ceil(size(inputBams, "G") * 0.5)
String dockerImage = "quay.io/biocontainers/picard:2.20.5--0"
}
......@@ -428,7 +428,7 @@ task MarkDuplicates {
String memory = "10G"
String javaXmx = "8G"
Int timeMinutes = ceil(size(inputBams, "G")* 8)
Int timeMinutes = 1 + ceil(size(inputBams, "G")* 8)
String dockerImage = "quay.io/biocontainers/picard:2.20.5--0"
# The program default for READ_NAME_REGEX is appropriate in nearly every case.
......@@ -499,7 +499,7 @@ task MergeVCFs {
String memory = "5G"
String javaXmx = "4G"
Int timeMinutes = ceil(size(inputVCFs, "G"))
Int timeMinutes = 1 + ceil(size(inputVCFs, "G"))
String dockerImage = "quay.io/biocontainers/picard:2.20.5--0"
}
......
samtools.wdl
+ 9
− 2
View file @ 605bba8d
......@@ -61,6 +61,8 @@ task Index {
input {
File bamFile
String? outputBamPath
String memory = "2G"
Int timeMinutes = 1 + ceil(size(bamFile, "G") * 4)
String dockerImage = "quay.io/biocontainers/samtools:1.8--h46bd0b3_5"
}
......@@ -87,6 +89,8 @@ task Index {
}
runtime {
memory: memory
time_minutes: timeMinutes
docker: dockerImage
}
......@@ -95,6 +99,8 @@ task Index {
bamFile: {description: "The BAM file for which an index should be made.", category: "required"}
outputBamPath: {description: "The location where the BAM file should be written to. The index will appear alongside this link to the BAM file.",
category: "common"}
memory: {description: "The amount of memory needed for the job.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
......@@ -203,7 +209,7 @@ task FilterShortReadsBam {
File bamFile
String outputPathBam
String memory = "1G"
Int timeMinutes = ceil(size(bamFile, "G") * 8)
Int timeMinutes = 1 + ceil(size(bamFile, "G") * 8)
String dockerImage = "quay.io/biocontainers/samtools:1.8--h46bd0b3_5"
}
......@@ -244,7 +250,7 @@ task Flagstat {
String outputPath
String memory = "1G"
Int timeMinutes = ceil(size(inputBam, "G"))
Int timeMinutes = 1 + ceil(size(inputBam, "G"))
String dockerImage = "quay.io/biocontainers/samtools:1.8--h46bd0b3_5"
}
......@@ -268,6 +274,7 @@ task Flagstat {
# inputs
inputBam: {description: "The BAM file for which statistics should be retrieved.", category: "required"}
outputPath: {description: "The location the ouput should be written to.", category: "required"}
memory: {description: "The amount of memory needed for the job.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
......
star.wdl
+ 3
− 0
View file @ 605bba8d
......@@ -36,6 +36,7 @@ task Star {
Int runThreadN = 4
String memory = "48G"
Int timeMinutes = 1 + ceil(size([inputR1, inputR2], "G") * 180 / runThreadN)
String dockerImage = "quay.io/biocontainers/star:2.7.3a--0"
}
......@@ -66,6 +67,7 @@ task Star {
runtime {
cpu: runThreadN
memory: memory
time_minutes: timeMinutes
docker: dockerImage
}
......@@ -83,6 +85,7 @@ task Star {
limitBAMsortRAM: {description: "Equivalent to star's `--limitBAMsortRAM` option.", category: "advanced"}
runThreadN: {description: "The number of threads to use.", category: "advanced"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
......
stringtie.wdl
+ 31
− 92
View file @ 605bba8d
......@@ -33,6 +33,7 @@ task Stringtie {
Int threads = 1
String memory = "10G"
Int timeMinutes = 1 + ceil(size(bam, "G") * 60 / threads)
String dockerImage = "quay.io/biocontainers/stringtie:1.3.4--py35_0"
}
......@@ -58,54 +59,24 @@ task Stringtie {
runtime {
cpu: threads
memory: memory
time_minutes: timeMinutes
docker: dockerImage
}
parameter_meta {
bam: {
description: "The input BAM file.",
category: "required"
}
bamIndex: {
description: "The input BAM file's index.",
category: "required"
}
referenceGtf: {
description: "A reference GTF file to be used as guide.",
category: "common"
}
skipNovelTranscripts: {
description: "Whether new transcripts should be assembled or not.",
category: "common"
}
assembledTranscriptsFile: {
description: "Where the output of the assembly should be written.",
category: "required"
}
firstStranded: {
description: "Equivalent to the --rf flag of stringtie.",
category: "required"
}
secondStranded: {
description: "Equivalent to the --fr flag of stringtie.",
category: "required"
}
geneAbundanceFile: {
description: "Where the abundance file should be written.",
category: "common"
}
threads: {
description: "The number of threads to use.",
category: "advanced"
}
memory: {
description: "The amount of memory needed for this task in GB.",
category: "advanced"
}
dockerImage: {
description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"
}
bam: {description: "The input BAM file.", category: "required"}
bamIndex: {description: "The input BAM file's index.", category: "required"}
referenceGtf: {description: "A reference GTF file to be used as guide.", category: "common"}
skipNovelTranscripts: {description: "Whether new transcripts should be assembled or not.", category: "common"}
assembledTranscriptsFile: {description: "Where the output of the assembly should be written.", category: "required"}
firstStranded: {description: "Equivalent to the --rf flag of stringtie.", category: "required"}
secondStranded: {description: "Equivalent to the --fr flag of stringtie.", category: "required"}
geneAbundanceFile: {description: "Where the abundance file should be written.", category: "common"}
threads: {description: "The number of threads to use.", category: "advanced"}
memory: {description: "The amount of memory needed for this task in GB.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
}
......@@ -123,6 +94,7 @@ task Merge {
String? label
String memory = "10G"
Int timeMinutes = 1 + ceil(size(gtfFiles, "G") * 20)
String dockerImage = "quay.io/biocontainers/stringtie:1.3.4--py35_0"
}
......@@ -148,57 +120,24 @@ task Merge {
runtime {
memory: memory
time_minutes: timeMinutes
docker: dockerImage
}
parameter_meta {
gtfFiles: {
description: "The GTF files produced by stringtie.",
category: "required"
}
outputGtfPath: {
description: "Where the output should be written.",
category: "required"
}
guideGtf: {
description: "Equivalent to the -G option of 'stringtie --merge'.",
category: "advanced"
}
minimumLength: {
description: "Equivalent to the -m option of 'stringtie --merge'.",
category: "advanced"
}
minimumCoverage: {
description: "Equivalent to the -c option of 'stringtie --merge'.",
category: "advanced"
}
minimumFPKM: {
description: "Equivalent to the -F option of 'stringtie --merge'.",
category: "advanced"
}
minimumTPM: {
description: "Equivalent to the -T option of 'stringtie --merge'.",
category: "advanced"
}
minimumIsoformFraction: {
description: "Equivalent to the -f option of 'stringtie --merge'.",
category: "advanced"
}
keepMergedTranscriptsWithRetainedIntrons: {
description: "Equivalent to the -i flag of 'stringtie --merge'.",
category: "advanced"
}
label: {
description: "Equivalent to the -l option of 'stringtie --merge'.",
category: "advanced"
}
memory: {
description: "The amount of memory needed for this task in GB.",
category: "advanced"
}
dockerImage: {
description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"
}
gtfFiles: {description: "The GTF files produced by stringtie.", category: "required"}
outputGtfPath: {description: "Where the output should be written.", category: "required"}
guideGtf: {description: "Equivalent to the -G option of 'stringtie --merge'.", category: "advanced"}
minimumLength: {description: "Equivalent to the -m option of 'stringtie --merge'.", category: "advanced"}
minimumCoverage: {description: "Equivalent to the -c option of 'stringtie --merge'.", category: "advanced"}
minimumFPKM: {description: "Equivalent to the -F option of 'stringtie --merge'.", category: "advanced"}
minimumTPM: {description: "Equivalent to the -T option of 'stringtie --merge'.", category: "advanced"}
minimumIsoformFraction: {description: "Equivalent to the -f option of 'stringtie --merge'.", category: "advanced"}
keepMergedTranscriptsWithRetainedIntrons: {description: "Equivalent to the -i flag of 'stringtie --merge'.", category: "advanced"}
label: {description: "Equivalent to the -l option of 'stringtie --merge'.", category: "advanced"}
memory: {description: "The amount of memory needed for this task in GB.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
}
umi-tools.wdl
+ 1
− 1
View file @ 605bba8d
......@@ -76,7 +76,7 @@ task Dedup {
Boolean paired = true
String memory = "5G"
Int timeMinutes = ceil(size(inputBam, "G") * 18)
Int timeMinutes = 1 + ceil(size(inputBam, "G") * 18)
# Use a multi-package-container which includes umi_tools (0.5.5) and samtools (1.9)
String dockerImage = "quay.io/biocontainers/mulled-v2-509311a44630c01d9cb7d2ac5727725f51ea43af:6089936aca6219b5bb5f54210ac5eb456c7503f2-0"
......
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