From 2fe5710c5ba5a8968cf0e9c514939307287b7e04 Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Thu, 31 Oct 2019 13:30:34 +0100
Subject: [PATCH] add parameter_meta to fastqc
---
bwa.wdl | 4 +--
collect-columns.wdl | 2 +-
cutadapt.wdl | 4 +--
fastqc.wdl | 80 +++++++++++++++++++++++++++++++++++++++++++++
htseq.wdl | 2 +-
stringtie.wdl | 4 +--
6 files changed, 88 insertions(+), 8 deletions(-)
diff --git a/bwa.wdl b/bwa.wdl
index f821b91..6623899 100644
--- a/bwa.wdl
+++ b/bwa.wdl
@@ -104,7 +104,7 @@ task Kit {
category: "required"
}
outputPrefix: {
- description: "The prefix of the output files, including any parent directories",
+ description: "The prefix of the output files, including any parent directories.",
category: "required"
}
readgroup: {
@@ -128,7 +128,7 @@ task Kit {
category: "advanced"
}
dockerImage: {
- description: "The docker image used for this task. Changing this may result in errors which the developers may chose not to address.",
+ 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/collect-columns.wdl b/collect-columns.wdl
index 8ed7232..914c785 100644
--- a/collect-columns.wdl
+++ b/collect-columns.wdl
@@ -85,7 +85,7 @@ task CollectColumns {
category: "advanced"
}
dockerImage: {
- description: "The docker image used for this task. Changing this may result in errors which the developers may chose not to address.",
+ 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 f663071..9c869c2 100644
--- a/cutadapt.wdl
+++ b/cutadapt.wdl
@@ -374,7 +374,7 @@ task Cutadapt {
catgeory: "advanced"
}
cores: {
- description: "The number of cores to use",
+ description: "The number of cores to use.",
catgeory: "advanced"
}
memory: {
@@ -382,7 +382,7 @@ task Cutadapt {
category: "advanced"
}
dockerImage: {
- description: "The docker image used for this task. Changing this may result in errors which the developers may chose not to address.",
+ 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 4c68cd2..a50a1c2 100644
--- a/fastqc.wdl
+++ b/fastqc.wdl
@@ -63,6 +63,79 @@ task Fastqc {
cpu: threads
docker: dockerImage
}
+
+ parameter_meta {
+ seqFile: {
+ description: "A FastQ file.",
+ category: "required"
+ }
+ outdirPath: {
+ description: "The path to write the output to",
+ catgory: "required"
+ }
+ casava: {
+ description: "Equivalent to fastqc's --casava flag.",
+ catgeory: "advanced"
+ }
+ nano: {
+ description: "Equivalent to fastqc's --nano flag.",
+ catgeory: "advanced"
+ }
+ noFilter: {
+ description: "Equivalent to fastqc's --nofilter flag.",
+ catgeory: "advanced"
+ }
+ extract: {
+ description: "Equivalent to fastqc's --extract flag.",
+ catgeory: "advanced"
+ }
+ nogroup: {
+ description: "Equivalent to fastqc's --nogroup flag.",
+ catgeory: "advanced"
+ }
+ minLength: {
+ description: "Equivalent to fastqc's --min_length option.",
+ catgeory: "advanced"
+ }
+ format: {
+ description: "Equivalent to fastqc's --format option.",
+ catgeory: "advanced"
+ }
+ contaminants: {
+ description: "Equivalent to fastqc's --contaminants option.",
+ catgeory: "advanced"
+ }
+ adapters: {
+ description: "Equivalent to fastqc's --adapters option.",
+ catgeory: "advanced"
+ }
+ limits: {
+ description: "Equivalent to fastqc's --limits option.",
+ catgeory: "advanced"
+ }
+ kmers: {
+ description: "Equivalent to fastqc's --kmers option.",
+ catgeory: "advanced"
+ }
+ dir: {
+ description: "Equivalent to fastqc's --dir option.",
+ catgeory: "advanced"
+ }
+ threads: {
+ description: "The number of cores to use.",
+ catgeory: "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"
+ }
+ }
+
+ meta {
+ WDL_AID: {
+ exclude: ["NoneFile", "NoneArray"]
+ }
+ }
}
task GetConfiguration {
@@ -89,4 +162,11 @@ task GetConfiguration {
memory: "2G" # Needs more than 1 to pull the docker image
docker: dockerImage
}
+
+ parameter_meta {
+ 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 ad83ac3..645396e 100644
--- a/htseq.wdl
+++ b/htseq.wdl
@@ -82,7 +82,7 @@ task HTSeqCount {
category: "advanced"
}
dockerImage: {
- description: "The docker image used for this task. Changing this may result in errors which the developers may chose not to address.",
+ 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 f026298..b9bfade 100644
--- a/stringtie.wdl
+++ b/stringtie.wdl
@@ -83,7 +83,7 @@ task Stringtie {
category: "advanced"
}
dockerImage: {
- description: "The docker image used for this task. Changing this may result in errors which the developers may chose not to address.",
+ description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"
}
}
@@ -177,7 +177,7 @@ task Merge {
category: "advanced"
}
dockerImage: {
- description: "The docker image used for this task. Changing this may result in errors which the developers may chose not to address.",
+ description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"
}
}
--
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