From ccc38727ddf49a3cebb566fadf7145675b0eafa2 Mon Sep 17 00:00:00 2001
From: JasperBoom <jboom@infernum.nl>
Date: Wed, 11 Nov 2020 17:19:50 +0100
Subject: [PATCH] Update samtools.
---
samtools.wdl | 34 +++++++++++++++++-----------------
1 file changed, 17 insertions(+), 17 deletions(-)
diff --git a/samtools.wdl b/samtools.wdl
index fcd996c..0aecf4e 100644
--- a/samtools.wdl
+++ b/samtools.wdl
@@ -58,8 +58,8 @@ task BgzipAndIndex {
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
- compressed: {description: ""}
- index: {description: ""}
+ compressed: {description: "Compressed input file."}
+ index: {description: "Index of the compressed input file."}
}
}
@@ -167,9 +167,9 @@ task Fastq {
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
- read1: {description: ""}
- read2: {description: ""}
- read0: {description: ""}
+ read1: {description: "Reads with the READ1 FLAG set."}
+ read2: {description: "Reads with the READ2 FLAG set."}
+ read0: {description: "Reads with either READ1 FLAG or READ2 flag set."}
}
}
@@ -214,8 +214,8 @@ task FilterShortReadsBam {
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
- filteredBam: {description: ""}
- filteredBamIndex: {description: ""}
+ filteredBam: {description: "BAM file filtered for short reads."}
+ filteredBamIndex: {description: "Index of filtered BAM file."}
}
}
@@ -254,7 +254,7 @@ task Flagstat {
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
- flagstat: {description: ""}
+ flagstat: {description: "The number of alignments for each FLAG type."}
}
}
@@ -306,8 +306,8 @@ task Index {
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
- indexedBam: {description: ""}
- index: {description: ""}
+ indexedBam: {description: "BAM file that was indexed."}
+ index: {description: "Index of the input BAM file."}
}
}
@@ -343,7 +343,7 @@ task Markdup {
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
- outputBam: {description: ""}
+ outputBam: {description: "BAM file with duplicate alignments marked."}
}
}
@@ -395,8 +395,8 @@ task Merge {
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
- outputBam: {description: ""}
- outputBamIndex: {description: ""}
+ outputBam: {description: "Multiple BAM files merged into one."}
+ outputBamIndex: {description: "Index of the merged BAM file."}
}
}
@@ -503,8 +503,8 @@ task Tabix {
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
- indexedFile: {description: ""}
- index: {description: ""}
+ indexedFile: {description: "Indexed input file."}
+ index: {description: "Index of the input file."}
}
}
@@ -573,7 +573,7 @@ task View {
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
- outputBam: {description: ""}
- outputBamIndex: {description: ""}
+ outputBam: {description: "Processed input file."}
+ outputBamIndex: {description: "Index of the processed input file."}
}
}
--
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