Seperate ends

[rroutsong]

Separate rule hierarchy for paired and single end, incorporating cfCHiP in as another hierarchical import in Snakemake

[rroutsong]

Waiting for test data sets to finish running before review, all data stored at /data/OpenOmics/dev/datasets/outputs

[rroutsong]

Using the command

tree -I 'logfiles|resources|workflow|bin|config|config.json|failed_jobs_*|job_information_*|*.R*.fastq.gz|*.krona.html.files|*.sh|COMPLETED' $DIRONE > $DIRONE.tree
tree -I 'logfiles|resources|workflow|bin|config|config.json|failed_jobs_*|job_information_*|*.R*.fastq.gz|*.krona.html.files|*.sh|COMPLETED' $DIRTWO > $DIRTWO.tree
diff $DIRONE.tree $DIRTWO.tree

I identified that some insert size files are missing in the wo_blocking and w_blocking toy data sets.

1c1
< wo_blocking
---
> wo_blocking_PREV
237a238,239
> │   ├── 27_IFN0h_1_Sp100_S15.Q5DD.insert_size_histogram.pdf
> │   ├── 27_IFN0h_1_Sp100_S15.Q5DD.insert_size_metrics.txt
242a245,246
> │   ├── 35_IFN24h_1_Sp100_S6.Q5DD.insert_size_histogram.pdf
> │   ├── 35_IFN24h_1_Sp100_S6.Q5DD.insert_size_metrics.txt
247a252,253
> │   ├── 39_IFN0h_2_Sp100_S46.Q5DD.insert_size_histogram.pdf
> │   ├── 39_IFN0h_2_Sp100_S46.Q5DD.insert_size_metrics.txt
252a259,260
> │   ├── 47_IFN24h_2_Sp100_S43.Q5DD.insert_size_histogram.pdf
> │   ├── 47_IFN24h_2_Sp100_S43.Q5DD.insert_size_metrics.txt
417c425

< w_blocking
---
> w_blocking_PREV
245a246,247
> │   ├── 27_IFN0h_1_Sp100_S15.Q5DD.insert_size_histogram.pdf
> │   ├── 27_IFN0h_1_Sp100_S15.Q5DD.insert_size_metrics.txt
250a253,254
> │   ├── 35_IFN24h_1_Sp100_S6.Q5DD.insert_size_histogram.pdf
> │   ├── 35_IFN24h_1_Sp100_S6.Q5DD.insert_size_metrics.txt
255a260,261
> │   ├── 39_IFN0h_2_Sp100_S46.Q5DD.insert_size_histogram.pdf
> │   ├── 39_IFN0h_2_Sp100_S46.Q5DD.insert_size_metrics.txt
260a267,268
> │   ├── 47_IFN24h_2_Sp100_S43.Q5DD.insert_size_histogram.pdf
> │   ├── 47_IFN24h_2_Sp100_S43.Q5DD.insert_size_metrics.txt
425c433

[rroutsong]

tree -I 'logfiles|resources|workflow|bin|config|config.json|failed_jobs_*|job_information_*|*.R*.fastq.gz|*.krona.html.files|*.sh|COMPLETED'

Commit 27709bd fixes insert size metric diff problem

1c1
< w_blocking
---
> w_blocking_PREV

[tovahmarkowitz]

Hey, I just looked through your changes in the PE-specific rules as your current test runs shouldn't affect them. I noticed a few small things that I would like addressed. Thanks for all the hard work.
Tovah