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CGATOxford / cgat

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mergeBAMfiles in pipeline_mapping #131

Closed csandorfr closed 9 years ago

csandorfr commented 9 years ago

I was wondering why the function mergeBAMfiles was removed in pipeline_mapping

python /net/isi-scratch/cynthia/CGAT-DEPS/cgat/CGATPipelines/pipeline_mapping.py -v5 --local make mergeBAMFiles

Target task 'mergeBAMFiles' is not a pipelined task in Ruffus. Have you mis-spelt the function name?

AndreasHeger commented 9 years ago

mergeBAMfiles is only visible if the regular expresssion telling which files should be merged are set:

if "merge_pattern_input" in PARAMS and PARAMS["merge_pattern_input"]:

Could this be the reason?

Best wishes, Andreas

On 02/09/15 13:32, csandorfr wrote:

I was wondering why the function mergeBAMfiles was removed in pipeline_mapping

python /net/isi-scratch/cynthia/CGAT-DEPS/cgat/CGATPipelines/pipeline_mapping.py -v5 --local make mergeBAMFiles

Target task 'mergeBAMFiles' is not a pipelined task in Ruffus. Have you mis-spelt the function name?

— Reply to this email directly or view it on GitHub https://github.com/CGATOxford/cgat/issues/131.

csandorfr commented 9 years ago

Hi Andreas,

OK I should fill in pipeline.ini:

pattern_input= pattern_output=

However I was wondering what function I have run with pipeline_mapping to just merge bam file and avoid to re-align my fasq file

Thanks

Cynthia

csandorfr commented 9 years ago

Thanks

it works...

I added the parameters in my parameters.ini and I ran mergeBAMFiles