CARLISLE 2.6.1

• Load the module for snakemake v7, but do not specify the minor and patch versions. (#149, @kelly-sovacool)

CARLISLE 2.6.0

Bug fixes

• Bug fixes for DESeq (#127, @epehrsson)
  • Removes single-sample group check for DESeq.
  • Increases memory for DESeq.
  • Ensures control replicate number is an integer.
  • Fixes FDR cutoff misassigned to log2FC cutoff.
  • Fixes no_dedup variable names in library normalization scripts.
• Fig bug that added nonexistent directories to the singularity bind paths. (#135, @kelly-sovacool)
  • Containerize rules that require R (deseq, go_enrichment, and spikein_assessment) to fix installation issues with common R library path. (#129, @kelly-sovacool)
    • The Rlib_dir and Rpkg_config config options have been removed as they are no longer needed.

New features

• New visualizations: (#132, @epehrsson)
  • New rules cov_correlation, homer_enrich, combine_homer, count_peaks
  • Add peak caller to MACS2 peak xls filename
• New parameters in the config file to make certain rules optional: (#133, @kelly-sovacool)
  • GO enrichment is controlled by run_go_enrichment (default: false)
  • ROSE is controlled by run_rose (default: false)
• New --singcache argument to provide a singularity cache dir location. The singularity cache dir is automatically set inside /data/$USER/ or $WORKDIR/ if --singcache is not provided. (#143, @kelly-sovacool)

Misc

• The singularity version is no longer specified, per request of the biowulf admins. (#139, @kelly-sovacool)
• Minor documentation updates. (#146, @kelly-sovacool)

CARLISLE 2.5.0

What's Changed

• Citation updates by @kelly-sovacool in #111
• Adds a --force flag to allow for re-initialization of a workdir @slsevilla, #97
• Fixes error with testrun in DESEQ2 @slsevilla, #113
• Decreases the number of samples being run with testrun, essentially running tinytest as default and removing tinytest as an option @slsevilla, #115
• Reads version from VERSION file instead of github repo link @slsevilla, #96 and #112
• Added a CHANGELOG @slsevilla, #116
• Refactor R library handling @slsevilla, #117
• Adds missing mm10 parameters @slsevilla, #121
• Removes some testing from annotation report gopeaks due to latency @slsevilla, #125

Full Changelog: v2.4.1...v.2.5.0

v2.4.1

What's Changed

• Add GitHub Action to add issues/PRs to personal project boards by @kelly-sovacool in #95
• Create install script by @kelly-sovacool in #93
• feat: use summits bed for homer input; save temporary files; fix deseq2 bug by @slsevilla in #108
• docs: adding citation and DOI to pipeline by @slsevilla in #107
• Test a dryrun with GitHub Actions by @kelly-sovacool in #94
• version 2.4.1 updates by @slsevilla in #110

New Contributors

• @kelly-sovacool made their first contribution in #95

Full Changelog: v2.4.0...v2.4.1

v2.4.0

• Feature- Merged Yue's fork, adding DEEPTOOLS by @slsevilla in #85
• Feature- Added tracking features from SPOOK by @slsevilla in #88
• Feature - Dev test run completed by @slsevilla in #89
• Bug - Fixed bugs related to Biowulf transition

v2.3.0

features added:

• created partition specific module information
• added flags to check for, and set up, config files based on partitions

v2.1.0

enhancement

• update gopeaks resources
• change SEACR to run "norm" without spikein controls, "non" with spikein controls
• update docs for changes; provide extra troubleshooting guidance

bug

• fix GoEnrich bug for failed plots

v2.0.1

bug

• fix error when contrasts set to "N"

enhancement

• adjust goenrich resources to be more efficient

version 2.0.0

• new features
  • Add a MAPQ filter to samtools (rule align)
  • Add GoPeaks MultiQC module
  • Allow for library normalization to occur during first pass
  • Add --broad-cutoff to MACS2 broad peak calling for MACS2
  • Create a spike in QC report
• enhancements
  • Reorganize file structure to help with qthreshold folder
  • Update variable names of all peak caller
  • Merge rules with input/output/wildcard congruency
  • Convert the "spiked" variable to "norm_method
  • Add name of control used to MACS2 peaks
• bugs fixed
  • Running extra control:sample comparisons that are not needed
• improved resource allocation
  • test data originally included 1475 jobs, this version includes 1087 jobs (reduction of 25%) despite including additional features
  • moved ~12% of all jobs to local deployment (within SLURM submission)

Output dir

├── alignment_stats
├── bam
├── bedgraph
├── bigwig
├── fragments
├── peaks
│   ├── 0.05
│   │   ├── contrasts
│   │   │   ├── contrast_id1.dedup_status
│   │   │   └── contrast_id2.dedup_status
│   │   ├── gopeaks
│   │   │   ├── annotation
│   │   │   │   ├── go_enrichment
│   │   │   │   │   ├── contrast_id1.dedup_status.go_enrichment_files
│   │   │   │   │   └── contrast_id2.dedup_status.go_enrichment_files
│   │   │   │   ├── homer
│   │   │   │   │   ├── replicate_id1_vs_control_id.dedup_status.gopeaks_broad.motifs
│   │   │   │   │   │   ├── homerResults
│   │   │   │   │   │   └── knownResults
│   │   │   │   │   ├── replicate_id1_vs_control_id.dedup_status.gopeaks_narrow.motifs
│   │   │   │   │   │   ├── homerResults
│   │   │   │   │   │   └── knownResults
│   │   │   │   │   ├── replicate_id2_vs_control_id.dedup_status.gopeaks_broad.motifs
│   │   │   │   │   │   ├── homerResults
│   │   │   │   │   │   └── knownResults
│   │   │   │   │   ├── replicate_id2_vs_control_id.dedup_status.gopeaks_narrow.motifs
│   │   │   │   │   │   ├── homerResults
│   │   │   │   │   │   └── knownResults
│   │   │   │   └── rose
│   │   │   │       ├── replicate_id1_vs_control_id.dedup_status.gopeaks_broad.12500
│   │   │   │       ├── replicate_id1_vs_control_id.dedup_status.gopeaks_narrow.12500
│   │   │   │       ├── replicate_id2_vs_control_id.dedup_status.dedup.gopeaks_broad.12500
│   │   │   │       ├── replicate_id2_vs_control_id.dedup_status.dedup.gopeaks_narrow.12500
│   │   │   └── peak_output
│   │   ├── macs2
│   │   │   ├── annotation
│   │   │   │   ├── go_enrichment
│   │   │   │   │   ├── contrast_id1.dedup_status.go_enrichment_files
│   │   │   │   │   └── contrast_id2.dedup_status.go_enrichment_files
│   │   │   │   ├── homer
│   │   │   │   │   ├── replicate_id1_vs_control_id.dedup_status.macs2_narrow.motifs
│   │   │   │   │   │   ├── homerResults
│   │   │   │   │   │   └── knownResults
│   │   │   │   │   ├── replicate_id1_vs_control_id.dedup_status.macs2_broad.motifs
│   │   │   │   │   │   ├── homerResults
│   │   │   │   │   │   └── knownResults
│   │   │   │   │   ├── replicate_id2_vs_control_id.dedup_status.macs2_narrow.motifs
│   │   │   │   │   │   ├── homerResults
│   │   │   │   │   │   └── knownResults
│   │   │   │   │   ├── replicate_id2_vs_control_id.dedup_status.macs2_broad.motifs
│   │   │   │   │   │   ├── homerResults
│   │   │   │   │   │   └── knownResults
│   │   │   │   └── rose
│   │   │   │       ├── replicate_id1_vs_control_id.dedup_status.macs2_broad.12500
│   │   │   │       ├── replicate_id1_vs_control_id.dedup_status.macs2_narrow.12500
│   │   │   │       ├── replicate_id2_vs_control_id.dedup_status.macs2_broad.12500
│   │   │   │       ├── replicate_id2_vs_control_id.dedup_status.macs2_narrow.12500
│   │   │   └── peak_output
│   │   └── seacr
│   │   │   ├── annotation
│   │   │   │   ├── go_enrichment
│   │   │   │   │   ├── contrast_id1.dedup_status.go_enrichment_files
│   │   │   │   │   └── contrast_id2.dedup_status.go_enrichment_files
│   │   │   │   ├── homer
│   │   │   │   │   ├── replicate_id1_vs_control_id.dedup_status.seacr_non_relaxed.motifs
│   │   │   │   │   │   ├── homerResults
│   │   │   │   │   │   └── knownResults
│   │   │   │   │   ├── replicate_id1_vs_control_id.dedup_status.seacr_non_stringent.motifs
│   │   │   │   │   │   ├── homerResults
│   │   │   │   │   │   └── knownResults
│   │   │   │   │   ├── replicate_id1_vs_control_id.dedup_status.seacr_norm_relaxed.motifs
│   │   │   │   │   │   ├── homerResults
│   │   │   │   │   │   └── knownResults
│   │   │   │   │   ├── replicate_id1_vs_control_id.dedup_status.seacr_norm_stringent.motifs
│   │   │   │   │   │   ├── homerResults
│   │   │   │   │   │   └── knownResults
│   │   │   │   │   ├── replicate_id2_vs_control_id.dedup_status.seacr_non_relaxed.motifs
│   │   │   │   │   │   ├── homerResults
│   │   │   │   │   │   └── knownResults
│   │   │   │   │   ├── replicate_id2_vs_control_id.dedup_status.seacr_non_stringent.motifs
│   │   │   │   │   │   ├── homerResults
│   │   │   │   │   │   └── knownResults
│   │   │   │   │   ├── replicate_id2_vs_control_id.dedup_status.seacr_norm_relaxed.motifs
│   │   │   │   │   │   ├── homerResults
│   │   │   │   │   │   └── knownResults
│   │   │   │   │   ├── replicate_id2_vs_control_id.dedup_status.seacr_norm_stringent.motifs
│   │   │   │   │   │   ├── homerResults
│   │   │   │   │   │   └── knownResults
│   │   │   │   └── rose
│   │   │   │       ├── replicate_id1_vs_control_id.dedup_status.seacr_non_relaxed.12500
│   │   │   │       ├── replicate_id1_vs_control_id.dedup_status.seacr_non_stringent.12500
│   │   │   │       ├── replicate_id1_vs_control_id.dedup_status.seacr_norm_relaxed.12500
│   │   │   │       ├── replicate_id1_vs_control_id.dedup_status.seacr_norm_stringent.12500
│   │   │   │       ├── replicate_id2_vs_control_id.dedup_status.seacr_non_relaxed.12500
│   │   │   │       ├── replicate_id2_vs_control_id.dedup_status.seacr_non_stringent.12500
│   │   │   │       ├── replicate_id2_vs_control_id.dedup_status.seacr_norm_relaxed.12500
│   │   │   │       ├── replicate_id2_vs_control_id.dedup_status.seacr_norm_stringent.12500
│   │       └── peak_output
└── qc
    ├── fastqc_raw
    └── fqscreen_raw

version1.2.0

merge increases to resources; update workflow img, contributions