add optional stage1 methods to allow analysis using product crams as input (instead of default BCL) #331
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
add test for this
…te method; select between i2b or reanalysis from product crams using i2b_switch parameter, or select an arbitrary VTFILE template using the s1_produce_init_bam_method parameter incorporates required vtfp fix for parameter value inheritance bug
add --reject-PG flag to reset step
remove unneeded warn from test
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Outdated suggestions cannot be applied.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.
allow initial input bam to be produced by "bambi i2b" or some alternate method; select between i2b or reanalysis from product crams using i2b_switch parameter, or select an arbitrary VTFILE template using the s1_produce_init_bam_method parameter
incorporates required vtfp fix for parameter value inheritance bug