This repository has been archived by the owner on Oct 23, 2023. It is now read-only.
Merge activeDev 4.0.6 into master #483
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
Bug Fix in integrateBatches.R URD call
* improving estimated fragment length * est fraglen; diffbind * DiffBind and cleanup * ppqt changes * ppqt improvements and a few other details * scRNASeq changes Feb 2020 (#438) * scRNASeq changes Feb 2020 * March updates * Merging activeDev for v4.0.1 release (#444) * Fix sequenza error * Scrnaseq (#437) Scrnaseq: miRNA-seq changes and scRNA-seq changes * Symlink counts matrix if "counts/" exists in users rawdata directory * Dectect if users is starting from a raw counts matrix * Updating pop-up box dialogue after detection of new counts matrix filetype * Find differential expression metadata in "/path/to/rawdata/counts/" * Readability: checking for counts matrix outside conditional statement * Adding "--alignEndsProtrude 10 ConcordantPair --peOverlapNbasesMin 10" to the first and second pass of STAR * Explicitly loading 'python/2.7': default version of python changing to '3.7' Co-authored-by: Mayank Tandon <mtandon09@gmail.com> Co-authored-by: wong-nw <38703762+wong-nw@users.noreply.github.com> Co-authored-by: jlac <justin.lack@nih.gov> Co-authored-by: Skyler Kuhn <kuhnsa2@mymail.vcu.edu> Co-authored-by: Mayank Tandon <mtandon09@gmail.com> Co-authored-by: jlac <justin.lack@nih.gov> Co-authored-by: skchronicles <kuhnsa2@vcu.edu> * improving ppqt, diffbind, frip, and jaccard * fixed the InitialChIPseqQC.snakefile conflict * fastqc bug fixed * more memory for BWA in ChIP-seq pipeline * reverting ngsqc_plot to a version that functions Co-authored-by: wong-nw <38703762+wong-nw@users.noreply.github.com> Co-authored-by: Skyler Kuhn <kuhnsa2@mymail.vcu.edu> Co-authored-by: Mayank Tandon <mtandon09@gmail.com> Co-authored-by: jlac <justin.lack@nih.gov> Co-authored-by: skchronicles <kuhnsa2@vcu.edu>
* Improved QC Reports - June 2020 (NW) * BUG FIX IN H5 FILE IMPORT * scrnaQC.Rmd typo correction * miRSeq mirdeep_config file automation * bug fixes * bug follow * integration bugs * integration_bug * integration_bug * integrate_batches_should_now_run
* improving estimated fragment length * est fraglen; diffbind * DiffBind and cleanup * ppqt changes * ppqt improvements and a few other details * scRNASeq changes Feb 2020 (#438) * scRNASeq changes Feb 2020 * March updates * Merging activeDev for v4.0.1 release (#444) * Fix sequenza error * Scrnaseq (#437) Scrnaseq: miRNA-seq changes and scRNA-seq changes * Symlink counts matrix if "counts/" exists in users rawdata directory * Dectect if users is starting from a raw counts matrix * Updating pop-up box dialogue after detection of new counts matrix filetype * Find differential expression metadata in "/path/to/rawdata/counts/" * Readability: checking for counts matrix outside conditional statement * Adding "--alignEndsProtrude 10 ConcordantPair --peOverlapNbasesMin 10" to the first and second pass of STAR * Explicitly loading 'python/2.7': default version of python changing to '3.7' Co-authored-by: Mayank Tandon <mtandon09@gmail.com> Co-authored-by: wong-nw <38703762+wong-nw@users.noreply.github.com> Co-authored-by: jlac <justin.lack@nih.gov> Co-authored-by: Skyler Kuhn <kuhnsa2@mymail.vcu.edu> Co-authored-by: Mayank Tandon <mtandon09@gmail.com> Co-authored-by: jlac <justin.lack@nih.gov> Co-authored-by: skchronicles <kuhnsa2@vcu.edu> * improving ppqt, diffbind, frip, and jaccard * fixed the InitialChIPseqQC.snakefile conflict * fastqc bug fixed * more memory for BWA in ChIP-seq pipeline * reverting ngsqc_plot to a version that functions * fixing FRiP * improved ChIP-seq PE and bug fixes Co-authored-by: wong-nw <38703762+wong-nw@users.noreply.github.com> Co-authored-by: Skyler Kuhn <kuhnsa2@mymail.vcu.edu> Co-authored-by: Mayank Tandon <mtandon09@gmail.com> Co-authored-by: jlac <justin.lack@nih.gov> Co-authored-by: skchronicles <kuhnsa2@vcu.edu>
scRNA QC and integration fixes
…RNA variant calling pipeline, see issue #464
Changing uropa query0 conditions for TSSprot and TSSgenes to allow more flexibility downstream of TSS starts (more peaks will be annotated with query0)
* Removing reference to /scratch * Adding more lscratch space for sorting * Fix indentation * Fixing cluster.json by re-syncing to activeDev
Path resolves KeyError with FREEC reference file with mm10 genome option.
…ed uropa conditions
…quested by Yu, Qi (NIH/CIT) <yuq3@hpc.nih.gov>
…n.json_ and not "bin" or standard_bin block.
…reads based on HPC staff benchmarking
ChIP-seq pipeline improvements; Merge never actually happened... Pushing through now
Sign up for free
to subscribe to this conversation on GitHub.
Already have an account?
Sign in.
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.
Merging tagged 4.0.6 version on Biowulf into master branch. This will allow us to start following proper tagging / versioning / development workflow + prepare for Biowulf8 transition.