Tumor-only mode for Mutect2 and MSIsensor #354
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
Merge from base
maxulysse
reviewed
Mar 2, 2021
main.nf
Outdated
| @@ -564,7 +564,7 @@ process get_software_versions { | |||
| freebayes --version &> v_freebayes.txt 2>&1 || true | |||
| freec &> v_controlfreec.txt 2>&1 || true | |||
| gatk ApplyBQSR --help &> v_gatk.txt 2>&1 || true | |||
| msisensor &> v_msisensor.txt 2>&1 || true | |||
| msisensor-pro &> v_msisensor.txt 2>&1 || true | |||
There was a problem hiding this comment.
let's keep msisensor here, msisensor-pro is not in the main container, but just used for the msi processes
There was a problem hiding this comment.
Thought you wanted to keep msisensor there instead of msisensor-pro
There was a problem hiding this comment.
got spot, I forgot again about that...
maxulysse
approved these changes
Mar 9, 2021
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Outdated suggestions cannot be applied.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.
Currently the tumor samples are processed with Strelka (if included in --tools) which is not really designed
to process tumor samples. Changes have been made so to process tumor samples with
Mutect2 in tumor-only mode. The same has been done to MSIsensor to be able to compute
MSI scores for tumor samples in tumor-only mode (this required an upgrade to msisensor-pro).
Notes:
correct behaviour would be to process only the tumor-only samples with Mutect2 and the germline (normal)
samples with Strelka (if there are any of course and if these tools are included in the --tools option).
the next release (dsl2).
PR checklist
scrape_software_versions.pynf-core lint .).nextflow run . -profile test,docker).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).