Create an 'ercc' option to fab process which runs an ercc-aware pipeline.
General Changes
The Makefile has a "regex" which locates the input FASTQ files. This regex has been updated.
Previously it would only find samples with R1 or R2 followed by no numbers at all.
Now, it also can find samples that end in R1_001 and R2_001.
Removed TOIL's 'debug' output spam from the expression step
_STARtmp directories will never be downloaded in the case of a fusions crash
At the end of the log it will print out a list of all sample IDs which failed the fusion step, if any
Fusion now runs before jfkm instead of after.
Added some troubleshooting guidance to the treeshop page
Changes to text in:
Treeshop's list of output files
expression step of makefile
error message in _setup()
README
ERCC-aware pipeline
New ercc.md page documenting how to use the ERCC pipeline
Makefile:
new reference_ercc option
new expression_ercc option
new qc_ercc option
Fabfile:
new reference_ercc() method
pipeline steps now have an "ercc" bool parameter to change output dir if ercc-aware pipeline is run
fab process() is ercc-aware when run with ercc=True. ERCC will not run pizzly, fusions, jfkm, variants.
Implements changes per https://github.com/UCSC-Treehouse/operations/issues/466.
Create an 'ercc' option to fab process which runs an ercc-aware pipeline.
General Changes
The Makefile has a "regex" which locates the input FASTQ files. This regex has been updated. Previously it would only find samples with R1 or R2 followed by no numbers at all. Now, it also can find samples that end in R1_001 and R2_001.
Removed TOIL's 'debug' output spam from the expression step
_STARtmp directories will never be downloaded in the case of a fusions crash
At the end of the log it will print out a list of all sample IDs which failed the fusion step, if any
Fusion now runs before jfkm instead of after.
Added some troubleshooting guidance to the treeshop page
Changes to text in:
ERCC-aware pipeline
New ercc.md page documenting how to use the ERCC pipeline
Makefile:
Fabfile: