From e76c0c02f410eb8b8f9b09b9cbccb125930d4c35 Mon Sep 17 00:00:00 2001
From: JasperBoom <jboom@infernum.nl>
Date: Fri, 6 Nov 2020 13:50:40 +0100
Subject: [PATCH] Upload more tasks.
---
cutadapt.wdl | 24 ++++++++++++------------
deepvariant.wdl | 7 +++++++
delly.wdl | 3 +++
fastqc.wdl | 12 ++++++++++++
4 files changed, 34 insertions(+), 12 deletions(-)
diff --git a/cutadapt.wdl b/cutadapt.wdl
index 8d409c3..b2dbdec 100644
--- a/cutadapt.wdl
+++ b/cutadapt.wdl
@@ -237,17 +237,17 @@ task Cutadapt {
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
- cutRead1: {description: ""}
- report: {description: ""}
- cutRead2: {description: ""}
- tooLongOutput: {description: ""}
- tooShortOutput: {description: ""}
- untrimmedOutput: {description: ""}
- tooLongPairedOutput: {description: ""}
- tooShortPairedOutput: {description: ""}
- untrimmedPairedOutput: {description: ""}
- infoFile: {description: ""}
- restFile: {description: ""}
- wildcardFile: {description: ""}
+ cutRead1: {description: "Trimmed read one."}
+ report: {description: "Per-adapter statistics file."}
+ cutRead2: {description: "Trimmed read two in pair."}
+ tooLongOutput: {description: "Reads that are too long according to -M."}
+ tooShortOutput: {description: "Reads that are too short according to -m."}
+ untrimmedOutput: {description: "All reads without adapters (instead of the regular output file)."}
+ tooLongPairedOutput: {description: "Second reads in a pair."}
+ tooShortPairedOutput: {description: "Second reads in a pair."}
+ untrimmedPairedOutput: {description: "The second reads in a pair that were not trimmed."}
+ infoFile: {description: "Detailed information about where adapters were found in each read."}
+ restFile: {description: "The rest file."}
+ wildcardFile: {description: "The wildcard file."}
}
}
diff --git a/deepvariant.wdl b/deepvariant.wdl
index 8b08e11..f71a1c8 100644
--- a/deepvariant.wdl
+++ b/deepvariant.wdl
@@ -90,5 +90,12 @@ task RunDeepVariant {
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"}
+
+ # outputs
+ outputVCF: {description: "Output VCF file."}
+ outputVCFIndex: {description: "Index of output VCF file."}
+ outputVCFStatsReport: {description: "Statistics file."}
+ outputGVCF: {description: "GVCF version of VCF file(s)."}
+ outputGVCFIndex: {description: "Index of GVCF file(s)."}
}
}
diff --git a/delly.wdl b/delly.wdl
index ffe9023..bf00ed3 100644
--- a/delly.wdl
+++ b/delly.wdl
@@ -62,5 +62,8 @@ task CallSV {
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"}
+
+ # outputs
+ dellyBcf: {description: "File containing structural variants."}
}
}
diff --git a/fastqc.wdl b/fastqc.wdl
index feeeaae..7ca0baa 100644
--- a/fastqc.wdl
+++ b/fastqc.wdl
@@ -125,6 +125,13 @@ task Fastqc {
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"}
+
+ # outputs
+ htmlReport: {description: ""}
+ reportZip: {description: ""}
+ summary: {description: ""}
+ rawReport: {description: ""}
+ images: {description: ""}
}
meta {
@@ -167,5 +174,10 @@ task GetConfiguration {
# inputs
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"}
+
+ # outputs
+ adapterList: {description: ""}
+ contaminantList: {description: ""}
+ limits: {description: ""}
}
}
--
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