diff --git a/CPAT.wdl b/CPAT.wdl
index 098d9ca61cc84de480f0a407868541937def3650..8d212b074fe7896ea8eee03b389825a00a4904a1 100644
--- a/CPAT.wdl
+++ b/CPAT.wdl
@@ -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"}
}
diff --git a/bcftools.wdl b/bcftools.wdl
index d923885db5bf3cc1c07099fe29fba605d4690083..53165c6be2118579bc1705a11577b52e80c8591e 100644
--- a/bcftools.wdl
+++ b/bcftools.wdl
@@ -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"
}
diff --git a/bedtools.wdl b/bedtools.wdl
index 4f39e2a8907b3b8a713373a562e466905f727587..99bb351edce2583eb0835fac39a98ffcf654343f 100644
--- a/bedtools.wdl
+++ b/bedtools.wdl
@@ -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"}
}
}
diff --git a/bowtie.wdl b/bowtie.wdl
index 94a809fa6787d85eb355c38f969f02285b74a004..87427e7dc1261aff0473bd353958719710761ff0 100644
--- a/bowtie.wdl
+++ b/bowtie.wdl
@@ -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
diff --git a/bwa.wdl b/bwa.wdl
index 247386d87c8df17d2ec5d161d2323d7f280ece01..a39eb3e9ffc3b4ddb2180c2a4a2d712f00efe56d 100644
--- a/bwa.wdl
+++ b/bwa.wdl
@@ -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"
}
diff --git a/clever.wdl b/clever.wdl
index 2da9f4d2922435698f25f8580a1727b7a24fc141..7e1eac4686b72263de74c457831b03152742836d 100644
--- a/clever.wdl
+++ b/clever.wdl
@@ -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"}
}
}
diff --git a/cutadapt.wdl b/cutadapt.wdl
index 421259d9bf28b5a54e33d929c2f4e3b39977f5bd..ad32ff21aff4958f9955628753a7b68468a855cd 100644
--- a/cutadapt.wdl
+++ b/cutadapt.wdl
@@ -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"}
}
}
diff --git a/fastqc.wdl b/fastqc.wdl
index 6708a6bc5a26407cbf6718e6fb7ba45836c6fab2..606c1bd4207c42c38f745a4f437d4d85e2008857 100644
--- a/fastqc.wdl
+++ b/fastqc.wdl
@@ -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"}
}
diff --git a/gatk.wdl b/gatk.wdl
index cb26ca7511e1f1fb628208e84dea4185f52fa190..366b32ddb166a9f3de730804ae8d58cbad19cda4 100644
--- a/gatk.wdl
+++ b/gatk.wdl
@@ -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"
}
diff --git a/gffcompare.wdl b/gffcompare.wdl
index ca2b1669d64c2fe95c7068df00a8445fa9f6e21a..197dd9ade74cade9b67bb77bbd1eee2492a7924e 100644
--- a/gffcompare.wdl
+++ b/gffcompare.wdl
@@ -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"}
}
diff --git a/gffread.wdl b/gffread.wdl
index 6b23785c7ee37c0fb112ed59d45424d2bced07d0..d83e4d76564411d1edd8b3ef5a17ac208f8bad67 100644
--- a/gffread.wdl
+++ b/gffread.wdl
@@ -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"}
}
diff --git a/hisat2.wdl b/hisat2.wdl
index bc6be2e84315d05a05f9d14da75cbe4c0507bbd4..3ea18ee8a8d272e0af04ec59f3e79e6352538eba 100644
--- a/hisat2.wdl
+++ b/hisat2.wdl
@@ -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"}
}
diff --git a/htseq.wdl b/htseq.wdl
index 900a88a79b96fab968b1244d0b3d6e090db70df5..9fad1714a69edc988ed16aba5e4ff231185ff0ed 100644
--- a/htseq.wdl
+++ b/htseq.wdl
@@ -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"}
}
}
diff --git a/picard.wdl b/picard.wdl
index 2eb9d410e9be3248264c091bc8f5ce816a44a44b..d19e3ac41e17370eec001a8df0f1c2a44e8c7c7e 100644
--- a/picard.wdl
+++ b/picard.wdl
@@ -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"
}
diff --git a/samtools.wdl b/samtools.wdl
index dc462f824e5ea23878794c532c1aeb13b9ac8598..5ffebc9ced931a1edba9022e2bb9df2fafb8d1c2 100644
--- a/samtools.wdl
+++ b/samtools.wdl
@@ -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"}
diff --git a/star.wdl b/star.wdl
index e1e55a262388f7f22a9c800ce558a24dbb447c73..94cdfa80bf12b0ca1a9141c34d06e2935f721473 100644
--- a/star.wdl
+++ b/star.wdl
@@ -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"}
}
diff --git a/stringtie.wdl b/stringtie.wdl
index cfaccc92f80d1ab9d489e37e31ea2dd3e28c0584..f1d994b3d4600817af4b605a27a913a1e85944fc 100644
--- a/stringtie.wdl
+++ b/stringtie.wdl
@@ -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"}
}
}
diff --git a/umi-tools.wdl b/umi-tools.wdl
index c44635ce0ef7d3cab9d3c9023a64989bb0259d11..608924f3fdd8dc7f5592e54f9cddadc7044c9039 100644
--- a/umi-tools.wdl
+++ b/umi-tools.wdl
@@ -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"