T2T support

[kopardev]

Add support for T2T human assembly for CCRGB-5

• Fasta
• Annotation??

[slsevilla]

https://www.ncbi.nlm.nih.gov/assembly/GCA_009914755.4

https://ccb.jhu.edu/T2T.shtml

[kopardev]

annotation -> ftp://ftp.ccb.jhu.edu/pub/data/T2T-CHM13/chm13v2.0_RefSeq_Liftoff_v4.gff3

[kopardev]

If you open that link in Finder you get something like this:

I can see the fasta file here, but the annotations are in GFF3 format and not GTF.

[kopardev]

Check this out! This is probably what we want to use. (Fa+GTF)

[kopardev]

Just for reference the official CHM13 related download GH repo.

[slsevilla]

annotations downloaded: /data/CCBR_Pipeliner/db/PipeDB/Indices/T2T

[slsevilla]

Alignment results for HS1 are comparable with HG38 for test samples. hg38_vs_hs1.pdf

[slsevilla]

Run through annotations was deployed: 57654474

[slsevilla]

Deseq/deseq2 failed due to missing TXDB and annotation objects. Will need workaround.

[kopardev]

Tried to fix the TxDb error for hs1 ... try this branch... Let me know if it works.

[slsevilla]

combined VK and SSC merged for txdb - local run successful

Dry-run was successful .... submitting jobs to job-scheduler Running... 57716781

[slsevilla]

txdb code merger was successful. Issue with txdb required additional code fixes:

• BSgenome for hs1 requires R > 4.2. Updated R version commit 05a1e6a965a6751c0df614b45592ae7b0b93c745
• ELBOW (rules for DESEQ) and GGVEN (rules for venn) are not compatible with this new version of R. download source code. commit fd8c78f6588c9fb29f646a41674b83c65762b7b6
• HS1 has different column headers than previous output (SYMBOL is named geneId). Updated code to change col names if geneId is found. commit fd8c78f6588c9fb29f646a41674b83c65762b7b6

With these changes DESEQ/DESEQ2/VENN rules all ran to completion

[slsevilla]

homer edits for hs1:

• homer requires different command for custom genome input for findMotifsGenome; added new command and necessary params. commit fb642c61e49a68dd3c505c7c0e9ee4ce5985ea0e
• homer will create bin files to be used for future projects based on .fa name. current ref.fa naming schema for hs1 will not work. updating to hs1.fa. commit 250811e303d5651579fc55f2ba362e8dc70b12ff
• homer requires different command for custom genome input for annotatePeaks; added new command and necessary params. commit 686a49e2ea6b6266e23d206731521dcd4d787370

With these changes HOMER related rules all ran to completion.

[slsevilla]

rose edits for hs1:

• ROSE requires different command for custom genome input; added new command and necessary params. commit 5f7d1387aa6d25b4f8b989b9fba09a5de3f30748

With these changes ROSE related rules all ran to completion

[slsevilla]

Running rules with all peak callers and deduplication methods to ensure stability with new HS1 updates.

[slsevilla]

Testing is complete. Changes merged into dev branch