Skip to content
GitLab
Explore
Sign in
Primary navigation
Search or go to…
Project
T
tasks
Manage
Activity
Members
Labels
Plan
Issues
Issue boards
Milestones
Wiki
Code
Merge requests
Repository
Branches
Commits
Tags
Repository graph
Compare revisions
Snippets
Build
Pipelines
Jobs
Pipeline schedules
Artifacts
Deploy
Releases
Container Registry
Model registry
Operate
Environments
Monitor
Incidents
Analyze
Value stream analytics
Contributor analytics
CI/CD analytics
Repository analytics
Model experiments
Help
Help
Support
GitLab documentation
Compare GitLab plans
Community forum
Contribute to GitLab
Provide feedback
Keyboard shortcuts
?
Snippets
Groups
Projects
Show more breadcrumbs
biowdl
tasks
Commits
6e463326
Commit
6e463326
authored
5 years ago
by
Ruben Vorderman
Browse files
Options
Downloads
Patches
Plain Diff
add bedtools sort
parent
84a6521a
No related branches found
Branches containing commit
No related tags found
Tags containing commit
No related merge requests found
Changes
3
Hide whitespace changes
Inline
Side-by-side
Showing
3 changed files
LICENSE
+1
-1
1 addition, 1 deletion
LICENSE
bedtools.wdl
+58
-0
58 additions, 0 deletions
bedtools.wdl
wiseguy.wdl
+1
-1
1 addition, 1 deletion
wiseguy.wdl
with
60 additions
and
2 deletions
LICENSE
+
1
−
1
View file @
6e463326
MIT License
Copyright (c) 201
8
Leiden University Medical Center
Copyright (c) 201
7
Leiden University Medical Center
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
...
...
This diff is collapsed.
Click to expand it.
bedtools.wdl
0 → 100644
+
58
−
0
View file @
6e463326
version 1.0
# Copyright (c) 2017 Leiden University Medical Center
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
# SOFTWARE.
task sort {
input {
File inputBed
Boolean sizeA = false
Boolean sizeD = false
Boolean chrThenSizeA = false
Boolean chrThenSizeD = false
Boolean chrThenScoreD = false
File? g
File? faidx
Boolean header = false
String outputBed = "output.sorted.bed"
String dockerImage = "quay.io/biocontainers/bedtools:2.23.0--hdbcaa40_3"
}
command {
set -e
mkdir -p $(dirname ~{outputBed})
bedtools sort \
-i ~{inputBed} \
~{if sizeA then "-sizeA" else ""} \
~{if sizeD then "-sizeD" else ""} \
~{if chrThenSizeD then "-chrThenSizeD" else ""} \
> ~{outputBed}
}
output {
File bedFile = outputBed
}
runtime {
docker: dockerImage
}
}
\ No newline at end of file
This diff is collapsed.
Click to expand it.
wiseguy.wdl
+
1
−
1
View file @
6e463326
version 1.0
# Copyright (c) 201
8
Leiden University Medical Center
# Copyright (c) 201
7
Leiden University Medical Center
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
...
...
This diff is collapsed.
Click to expand it.
Preview
0%
Loading
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Save comment
Cancel
Please
register
or
sign in
to comment