AH - update mitochondria wdl for new pipeline #6597
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
meganshand
reviewed
May 12, 2020
| @@ -523,6 +527,7 @@ task Filter { | |||
| Boolean compress | |||
| Float? vaf_cutoff | |||
| String sample_name | |||
There was a problem hiding this comment.
Since you're switching to base_name can you delete sample_name from the whole pipeline? Does it get used anywhere? I didn't see it in this task.
| @@ -1,8 +1,11 @@ | |||
| { | |||
| "MitochondriaPipeline.wgs_aligned_input_bam_or_cram": "input_bam_here", | |||
| "MitochondriaPipeline.wgs_aligned_input_bam_or_cram_index": "input_bam_index_here", | |||
| "MitochondriaPipeline.autosomal_coverage": autosomal_median_coverage_here, | |||
| "MitochondriaPipeline.autosomal_coverage": "autosomal_median_coverage_here", | |||
There was a problem hiding this comment.
I think we left the quotes off in this example to indicate that this was an Int instead of a String. Do you think it would be clearer to put an actual example here like 30?
jonn-smith
pushed a commit
that referenced
this pull request
Jul 14, 2020
* change sample name to base filename * add base name to final split vcf * add --read-index option * remove sample_name * remove sample_name from json in m2_cromwell_tests
mwalker174
pushed a commit
that referenced
this pull request
Nov 3, 2020
* change sample name to base filename * add base name to final split vcf * add --read-index option * remove sample_name * remove sample_name from json in m2_cromwell_tests
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Outdated suggestions cannot be applied.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.
No description provided.