diff --git a/centrifuge.wdl b/centrifuge.wdl
index c88a838ed620f77753d0cfe4dc9f7f815da8c033..8aaed45ee9a101b2744ee86b1cdb5691f468907e 100644
--- a/centrifuge.wdl
+++ b/centrifuge.wdl
@@ -68,50 +68,17 @@ task Build {
}
parameter_meta {
- 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"
- }
- nameTable: {
- description: "Name table (e.g. names.dmp).",
- category: "required"
- }
- referenceFile: {
- description: "A comma-separated list of FASTA files containing the reference sequences to be aligned to.",
- category: "required"
- }
- indexBasename: {
- description: "The basename of the index files to write.",
- category: "required"
- }
- outputPrefix: {
- description: "Output directory path + output file prefix.",
- category: "required"
- }
- offrate: {
- description: "The number of rows marked by the indexer.",
- category: "common"
- }
- 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"
- }
+ 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"}
+ nameTable: {description: "Name table (e.g. names.dmp).", category: "required"}
+ referenceFile: {description: "A comma-separated list of FASTA files containing the reference sequences to be aligned to.", category: "required"}
+ indexBasename: {description: "The basename of the index files to write.", category: "required"}
+ outputPrefix: {description: "Output directory path + output file prefix.", category: "required"}
+ offrate: {description: "The number of rows marked by the indexer.", category: "common"}
+ 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"}
}
}
@@ -173,58 +140,19 @@ task Classify {
}
parameter_meta {
- 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"
- }
- indexPrefix: {
- description: "The basename of the index for the reference genomes.",
- category: "required"
- }
- read1: {
- description: "List of files containing mate 1s, or unpaired reads.",
- category: "required"
- }
- outputPrefix: {
- description: "Output directory path + output file prefix.",
- category: "required"
- }
- outputName: {
- description: "The base name of the outputPrefix.",
- category: "required"
- }
- read2: {
- description: "List of files containing mate 2s.",
- category: "common"
- }
- trim5: {
- description: "Trim <int> bases from 5' (left) end of each read before alignment.",
- category: "common"
- }
- trim3: {
- description: "Trim <int> bases from 3' (right) end of each read before alignment.",
- category: "common"
- }
- 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"
- }
+ 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"}
+ indexPrefix: {description: "The basename of the index for the reference genomes.", category: "required"}
+ read1: {description: "List of files containing mate 1s, or unpaired reads.", category: "required"}
+ outputPrefix: {description: "Output directory path + output file prefix.", category: "required"}
+ outputName: {description: "The base name of the outputPrefix.", category: "required"}
+ read2: {description: "List of files containing mate 2s.", category: "common"}
+ trim5: {description: "Trim <int> bases from 5' (left) end of each read before alignment.", category: "common"}
+ trim3: {description: "Trim <int> bases from 3' (right) end of each read before alignment.", category: "common"}
+ 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"}
}
}
@@ -264,22 +192,10 @@ task Inspect {
}
parameter_meta {
- 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"
- }
+ 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"}
}
}
diff --git a/scripts b/scripts
index a1783b5c789ebef601a8ec5849c4bbfe7dd3f87d..fc603e5d408b89b99297fb5737586c059c5f9df6 160000
--- a/scripts
+++ b/scripts
@@ -1 +1 @@
-Subproject commit a1783b5c789ebef601a8ec5849c4bbfe7dd3f87d
+Subproject commit fc603e5d408b89b99297fb5737586c059c5f9df6