Shortreads bbcms #18 #19
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
aclum
reviewed
Jun 5, 2024
aclum
reviewed
Jun 5, 2024
aclum
reviewed
Jun 5, 2024
shortReads_assembly.wdl
Outdated
| @@ -214,6 +217,7 @@ task finish_asm { | |||
| cat ~{scaffold} | sed ~{sed} > ~{prefix}_scaffolds.fna | |||
| cat ~{covstats} | sed ~{sed} > ~{prefix}_covstats.txt | |||
| cat ~{agp} | sed ~{sed} > ~{prefix}_assembly.agp | |||
| cat ~{bbcms_fastq} | sed ~{sed} > ~{prefix}_bbcms.fastq.gz | |||
There was a problem hiding this comment.
This file doesn't need to go through a sed command Ie the headers don't need to change, the file itself just needs to be changed.
…nks in shortReads_assembly.wdl
aclum
approved these changes
Jun 11, 2024
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Updated shortReads_assembly.wdl and jgi_assembly.wdl so that these bbcms task output files are also getting passed as outputs to the workflow. Created new input.json that works with Condor. Added labels.json and submit_curl.sh in order to test using Condor.