From 2105f0169134562581479451a65366d195991fb3 Mon Sep 17 00:00:00 2001
From: JasperBoom <jboom@infernum.nl>
Date: Wed, 29 Jan 2020 11:46:36 +0100
Subject: [PATCH] Update parameter_meta and fix centrifuge index locating.
---
centrifuge.wdl | 26 ++++++++++++++++++++++++--
minimap2.wdl | 6 ++----
talon.wdl | 32 ++++++++++++++++----------------
3 files changed, 42 insertions(+), 22 deletions(-)
diff --git a/centrifuge.wdl b/centrifuge.wdl
index 32ddff3..0d05fee 100644
--- a/centrifuge.wdl
+++ b/centrifuge.wdl
@@ -68,6 +68,7 @@ task Build {
}
parameter_meta {
+ # inputs
disableDifferenceCover: {description: "Disable use of the difference-cover sample.", category: "required"}
conversionTable: {description: "List of UIDs (unique ID) and corresponding taxonomic IDs.", category: "required"}
taxonomyTree: {description: "Taxonomic tree (e.g. nodes.dmp).", category: "required"}
@@ -79,6 +80,12 @@ task Build {
ftabChars: {description: "Calculate an initial BW range with respect to this character.", category: "common"}
kmerCount: {description: "Use <int> as kmer-size for counting the distinct number of k-mers in the input sequences.", category: "common"}
sizeTable: {description: "List of taxonomic IDs and lengths of the sequences belonging to the same taxonomic IDs.", category: "common"}
+ threads: {description: "The number of threads to be used.", category: "advanced"}
+ memory: {description: "The amount of memory available to the job.", 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"}
+
+ # outputs
+ outputIndex: {description: "Generated Centrifuge index."}
}
}
@@ -139,6 +146,7 @@ task Classify {
}
parameter_meta {
+ # inputs
inputFormat: {description: "The format of the read file(s).", category: "required"}
phred64: {description: "If set to true, Phred+64 encoding is used.", category: "required"}
minHitLength: {description: "Minimum length of partial hits.", category: "required"}
@@ -151,13 +159,21 @@ task Classify {
reportMaxDistinct: {description: "It searches for at most <int> distinct, primary assignments for each read or pair.", category: "common"}
hostTaxIDs: {description: "A comma-separated list of taxonomic IDs that will be preferred in classification procedure.", category: "common"}
excludeTaxIDs: {description: "A comma-separated list of taxonomic IDs that will be excluded in classification procedure.", category: "common"}
+ threads: {description: "The number of threads to be used.", category: "advanced"}
+ memory: {description: "The amount of memory available to the job.", 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"}
+
+ # outputs
+ outputMetrics: {description: "File with Centrifuge metrics."}
+ outputClassification: {description: "File with the classification results."}
+ outputReport: {description: "File with a classification summary."}
}
}
task Inspect {
input {
String printOption = "fasta"
- String indexBasename
+ Array[File]+ indexFiles
String outputPrefix
Int? across
@@ -174,7 +190,7 @@ task Inspect {
centrifuge-inspect \
~{outputOptions[printOption]} \
~{"--across " + across} \
- ~{indexBasename} \
+ ~{sub(indexFiles[0], "\.[0-9]\.cf", "")} \
> ~{outputPrefix + "/" + printOption}
}
@@ -188,10 +204,16 @@ task Inspect {
}
parameter_meta {
+ # inputs
printOption: {description: "The output option for inspect (fasta, summary, conversionTable, taxonomyTree, nameTable, sizeTable)", category: "required"}
indexBasename: {description: "The basename of the index to be inspected.", category: "required"}
outputPrefix: {description: "Output directory path + output file prefix.", category: "required"}
across: {description: "When printing FASTA output, output a newline character every <int> bases.", category: "common"}
+ memory: {description: "The amount of memory available to the job.", 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"}
+
+ # outputs
+ outputInspect: {description: "Output file according to output option."}
}
}
diff --git a/minimap2.wdl b/minimap2.wdl
index aff51dc..32c0666 100644
--- a/minimap2.wdl
+++ b/minimap2.wdl
@@ -68,8 +68,7 @@ task Indexing {
splitIndex: {description: "Split index for every ~NUM input bases.", category: "advanced"}
cores: {description: "The number of cores to be used.", category: "advanced"}
memory: {description: "The amount of memory available to the job.", 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"}
+ 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"}
# output
outputIndexFile: {description: "Indexed reference file."}
@@ -150,8 +149,7 @@ task Mapping {
queryFile: {description: "Input fasta file.", category: "required"}
cores: {description: "The number of cores to be used.", category: "advanced"}
memory: {description: "The amount of memory available to the job.", 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"}
+ 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"}
# output
outputAlignmentFile: {description: "Mapping and alignment between collections of DNA sequences file."}
diff --git a/talon.wdl b/talon.wdl
index c861e56..0501896 100644
--- a/talon.wdl
+++ b/talon.wdl
@@ -64,8 +64,7 @@ task CreateAbundanceFileFromDatabase {
whitelistFile: {description: "Whitelist file of transcripts to include in the output.", category: "advanced"}
datasetsFile: {description: "A file indicating which datasets should be included.", category: "advanced"}
memory: {description: "The amount of memory available to the job.", 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"}
+ 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"}
# outputs
outputAbundanceFile: {description: "Abundance for each transcript in the TALON database across datasets."}
@@ -120,8 +119,7 @@ task CreateGtfFromDatabase {
whitelistFile: {description: "Whitelist file of transcripts to include in the output.", category: "advanced"}
datasetFile: {description: "A file indicating which datasets should be included.", category: "advanced"}
memory: {description: "The amount of memory available to the job.", 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"}
+ 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"}
# outputs
outputGTFfile: {description: "The genes, transcripts, and exons stored a TALON database in GTF format."}
@@ -160,13 +158,16 @@ task FilterTalonTranscripts {
}
parameter_meta {
+ # inputs
databaseFile: {description: "TALON database.", category: "required"}
annotationVersion: {description: "Which annotation version to use.", category: "required"}
outputPrefix: {description: "Output directory path + output file prefix.", category: "required"}
pairingsFile: {description: "A file indicating which datasets should be considered together.", category: "advanced"}
memory: {description: "The amount of memory available to the job.", 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"}
+ 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"}
+
+ # outputs
+ outputTranscriptWhitelist: {description: "A transcript whitelist produced from the TALON database."}
}
}
@@ -208,8 +209,7 @@ task GetReadAnnotations {
outputPrefix: {description: "Output directory path + output file prefix.", category: "required"}
datasetFile: {description: "A file indicating which datasets should be included.", category: "advanced"}
memory: {description: "The amount of memory available to the job.", 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"}
+ 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"}
# outputs
outputAnnotation: {description: "Read-specific annotation information from a TALON database."}
@@ -265,8 +265,7 @@ task InitializeTalonDatabase {
cutoff3p: {description: "Maximum allowable distance (bp) at the 3' end during annotation.", category: "advanced"}
outputPrefix: {description: "Output directory path + output file prefix.", category: "required"}
memory: {description: "The amount of memory available to the job.", 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"}
+ 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"}
# outputs
outputDatabase: {description: "TALON database."}
@@ -297,10 +296,13 @@ task ReformatGtf {
}
parameter_meta {
+ # inputs
GTFfile: {description: "GTF annotation containing genes, transcripts, and edges.", category: "required"}
memory: {description: "The amount of memory available to the job.", 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"}
+ 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"}
+
+ # outputs
+ outputReformattedGTF: {description: "Reformatted GTF file."}
}
}
@@ -342,8 +344,7 @@ task SummarizeDatasets {
outputPrefix: {description: "Output directory path + output file prefix.", category: "required"}
datasetGroupsCSV: {description: "File of comma-delimited dataset groups to process together.", category: "advanced"}
memory: {description: "The amount of memory available to the job.", 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"}
+ 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"}
# outputs
outputSummaryFile: {description: "Tab-delimited file of gene and transcript counts for each dataset."}
@@ -413,8 +414,7 @@ task Talon {
outputPrefix: {description: "Output directory path + output file prefix.", category: "required"}
cores: {description: "The number of cores to be used.", category: "advanced"}
memory: {description: "The amount of memory available to the job.", 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"}
+ 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"}
# outputs
outputUpdatedDatabase: {description: "Updated TALON database."}
--
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