argument --region in ./gkno pipe fastq-short-variants

[S-ES]

Hi,

I would like to report the following issue, when trying to run pipe fastq-short-variants by this command line for example:

./gkno pipe fastq-short-variants \ --fasta-reference resources/tutorial/current/chr20_fragment.fa \ --fastq resources/tutorial/current/mutated_genome_set2_1.fq \ --fastq2 resources/tutorial/current/mutated_genome_set2_2.fq \ --ann-single-end resources/tutorial/current/se.100.005.ann \ --ann-paired-end resources/tutorial/current/pe.100.01.ann \ --special-reference-hashes [0] \ --sequencing-technology [illumina] \ --hash-size [4] \ --output-path /Users/apple/gkno_launcher/NGS

I am receiving this error msg: ERROR: A required command line argument is missing.

DETAILS: The task 'call-short-variants' requires the argument '--region (-r)' to be set, but it has not been specified on the command line. This argument cannot be set using a pipeline argument and consequently must be set using the syntax:

     ./gkno pipe <pipeline name> --call-short-variants [--region <value>] [options]

     This argument is described as the following: <chrom>:<start_position>..<end_position>.
     Limit analysis to the specified region, 0-base coordinates, end_position not included
     (same as BED format).

However, --region is not listed among the required arguments.. is there any mistake in my command line so I am recieving this error ?

P.S: when I write ./gkno pipe fastq-short-variants --help, I am getting this erorr msg at the end: The following tasks can have parameters modified: Traceback (most recent call last): File "/Users/apple/gkno_launcher/src/gkno.py", line 484, in main() File "/Users/apple/gkno_launcher/src/gkno.py", line 231, in main gknoHelp.specificPipelineUsage(pipelineGraph, config, gknoConfig, runName, toolConfigurationFilesPath, instanceName) File "/Users/apple/gkno_launcher/src/gkno/helpClass.py", line 571, in specificPipelineUsage isHidden = self.availableTools[associatedTool][1] KeyError: u'mosaik-aligner-special'

Best regards,

Kiz

[AlistairNWard]

Fixed and pushed. The region is not required, but is an option. In addition, the pipeline has been extended to allow a list of regions to be provided using the arguments --region-list-single and --region-list-multiple. The former command will produce a single makefile with multiple calls to the variant caller; each call with a different region. The latter case produces a makefile for each region allowing them to be executed in parallel on a cluster.

[S-ES]

As we say in French : ça marche nickel !

Thx again