A submission of a job (Aligner, Alignment Analysis or Task) returns the tag assigned to the job. Starting from version 2.2, such tag can be used to access to the results pushed by the job in the FileSet area. Do note that the access is limited to a local FileSet area. If a remote FileSet are was used at job submission time, the plugins SDK has to be installed on the remote node and the area has to be accessed locally.

The following example shows how to access to the results of a job with tag KCVWVHS:

plugins-list-fileset \
--fileset-area /zenodotus/dat01/campagne_lab_store/gobyweb_dat/GOBYWEB_TRIAL/FILESETS_AREA/ \
--output-format table \
--filter-attribute GENERATED_BY=KCVWVHS

The command prints out a table. The first row is a header explaining the information reported in each column. Then, the following rows report information about each fileset instance published by the job. Here is an example for an alignment analysis that produced 6 fileset instances:

TAG    	INSTANCE OF                   	BASENAME                                                    	SIZE (in bytes)     	ATTRIBUTES
JDHNBBX	TSV                           	KCVWVHS-contaminants                                        	21073               	GENOME_REFERENCE_ID=1000GENOMES.37,ORGANISM=homo_sapiens,BASENAME=KCVWVHS-contaminants,GENERATED_BY=KCVWVHS
VGEUSKL	TSV                           	KCVWVHS-realigned                                           	46                  	GENOME_REFERENCE_ID=1000GENOMES.37,ORGANISM=homo_sapiens,BASENAME=KCVWVHS-realigned,GENERATED_BY=KCVWVHS
LRJDURK	TSV                           	KCVWVHS-summary                                             	203                 	GENOME_REFERENCE_ID=1000GENOMES.37,ORGANISM=homo_sapiens,BASENAME=KCVWVHS-summary,GENERATED_BY=KCVWVHS
VPCIRSY	LUCENE_INDEX                  	KCVWVHS-contaminants                                        	43122               	GENOME_REFERENCE_ID=1000GENOMES.37,ORGANISM=homo_sapiens,TABLENAME=contaminants,BASENAME=KCVWVHS-contaminants,GENERATED_BY=KCVWVHS
GBNCPFE	LUCENE_INDEX                  	KCVWVHS-realigned                                           	423                 	GENOME_REFERENCE_ID=1000GENOMES.37,ORGANISM=homo_sapiens,TABLENAME=realigned,BASENAME=KCVWVHS-realigned,GENERATED_BY=KCVWVHS
TUVNVAD	LUCENE_INDEX                  	KCVWVHS-summary                                             	1526                	GENOME_REFERENCE_ID=1000GENOMES.37,ORGANISM=homo_sapiens,TABLENAME=summary,BASENAME=KCVWVHS-summary,GENERATED_BY=KCVWVHS

Only-tags format

If we are interested only in the tags of the fileset instances (for example, to copy and paste them as input for another job), we can use as value of the output-format option the value only-tags:

plugins-list-fileset \
--fileset-area /zenodotus/dat01/campagne_lab_store/gobyweb_dat/GOBYWEB_TRIAL/FILESETS_AREA/ \
--output-format only-tags \
--filter-attribute GENERATED_BY=KCVWVHS

and this prints out only the list of tags assigned to the fileset instances published by the job:

JDHNBBX	VGEUSKL	LRJDURK	VPCIRSY	GBNCPFE	TUVNVAD

By default, the elements in the list are tab-separated. If we want to separate them differently, we can use the separator option. In the following example, we request a list separated by commas:

plugins-list-fileset \
--fileset-area /zenodotus/dat01/campagne_lab_store/gobyweb_dat/GOBYWEB_TRIAL/FILESETS_AREA/ \
--output-format only-tags \
--separator , \
--filter-attribute GENERATED_BY=KCVWVHS

and this is what it is printed out:

JDHNBBX,VGEUSKL,LRJDURK,VPCIRSY,GBNCPFE,TUVNVAD

Further filtering

It is possible to restrict the results returned by adding further filters to the command. For instance, if in the previous example we want to access to only the summary table, we re-execute the command as follows:

plugins-list-fileset \
--fileset-area /zenodotus/dat01/campagne_lab_store/gobyweb_dat/GOBYWEB_TRIAL/FILESETS_AREA/ \
--output-format table \
--filter-attribute GENERATED_BY=KCVWVHS \
--filter-attribute TABLENAME=summary

and this prints out the following table:

TAG    	INSTANCE OF                   	BASENAME                                                    	SIZE (in bytes)     	ATTRIBUTES
TUVNVAD	LUCENE_INDEX                  	KCVWVHS-summary                                             	1526                	GENOME_REFERENCE_ID=1000GENOMES.37,ORGANISM=homo_sapiens,TABLENAME=summary,BASENAME=KCVWVHS-summary,GENERATED_BY=KCVWVHS