release 51.10 prep #226
Merged
release 51.10 prep #226
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
redirect stderr output to a log
- Add extra argument to _qc_command to support the execution of the rna_seqc qc check in seq_alignment module - Remove every trace of the execution of the rna_seqc check from npg_pipeline::archive::file::qc - Remove rna_seqc from the yaml-formatted central list and parallelisation files - Update tests to reflect changes in seq_alignment
- The attribute is not required by the check anymore. - Update test units in t/20-archive_file_generation-seq_alignment.t to reflect this change. - Remove extra argument used to create qc_report_dir in _qc_command
- remove unused libraries (update pod accordingly) - remove trailing whitespaces here and there
tests with multiple references
warn rather than croak in seq_alignemnt if multiple references for tag 0
…eads Conflicts: Changes
allow p4 stage 1 to analyse runs with different length reads
Conflicts: Changes
recalibration and olb removed
Conflicts resolved in: Changes MANIFEST lib/npg_pipeline/base.pm t/10-base.t
…into mgcam-drop_il2b Conflicts: Changes t/10-pluggable_harold_central.t
Conflicts resolved in: t/10-pluggable_harold_central.t
remove unused force_p4 attribute
remove gclp-specific code and conf. files
…litBamByChromosomes.jar for Y-split runs
…ts in our current set of human reference genomes
Ysplit fixes
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Outdated suggestions cannot be applied.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.