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Ran 09 Mar 2020 12:04PM UTC

Files 2

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Committed 09 Mar 2020 12:03PM UTC coverage: 29.577%. Remained the same

Job # 268.1

Build Type

push

travis-ci-com

Committed by

web-flow

Commit Message

Extract regions from panels (#34)

* added a snakemake file and config.json

* updated config.json

* Made changes (mostly dir structure) according to comments from HFA

* created new dir and renamed the snakefile

* created sub directory

* renamed directory

* deleted log from rule

* removed files

* created new dir

* Changed Snakefile
edited ref_vcf in rule refvcf_region_filter to local dir since it's not decided yet where to put the ref vcf
Added extra output in rule refvcf_region_filter to trim the original bed-file
Added extra code in rule refvcf_region_filter to remove header and chr from original bed-file in data_files directory
Changed the path for input in rule merge_bed_with_dbsnp

* made output files temporary

* changed script so it only collapse on the 5th col

* Added/edited explanation for the rules and changed name for output file

* For rule refvcf_region_filter added extra sed command to add 4th column with "." on it.
Changed the input value for rule merge_bed_with_dbsnp to use the bed-file in data_file directory.
Removed the sort command in rule merge_bed_with_dbsnp since the file is already sorted.

* Added rule description

* changed rule names

* changed path for reference vcf

* Added info regarding where to download ref vcf

Co-authored-by: hassanfa <hassan.foroughi@gmail.com>

Run Details

21 of 71 relevant lines covered (29.58%)

0.3 hits per line

Clinical-Genomics / target_capture_bed / 268 / 1
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master: 30%

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Clinical-Genomics / target_capture_bed / 268 / 1
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master: 30%

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