Updated to workflow 1.5 task xml schema; now can take multiple fastq
input files.
Updated to use workflow 1.5 task xml schema.
Task definition for new dataset iterator Java task.
New task class for iterating over the datasets specified in a sample
sheet, setting the id and file names (or patterns) for each as variables
for to be used in subtasks within the workflow.
Sample sheet variable is no longer optional, no longer checking for
specialisations since these now replaced by dataset iterator.
Updated to workflow 1.5 task xml schema; added new output file prefix
argument.
Now carries out the XSLT transform and embeds the base64-encoded image
inside the html report; the output report file argument replaced by an
output file prefix argument.
Updated to support embedding of base64-encoded images in html report.
Rename fastqFile input name to fastqFiles reflecting possibility of
multiple input files.
Fix warning about ZipInputStream not being closed.
Fixed problem with initialization of output file prefix; fixed issue
with reference genomes for which no alignments were made not appearing
in the report.
Updates for use of new DatasetIterator Java task in place of
specialisations; updated names for fastq input files for countFastq and
sampleFastq tasks; updated with changes to createReport task, e.g.
specifying output file prefix.
Added line break after image.
Updated to use new DatasetIteratorTask class instead of inbuilt
specialisation mechanism.
Updated to workflow version 1.5, added commons-codec dependency used in
embedding images into the report, added json.org dependency to be used
for BaseSpace integration, renamed create-config-from-samplesheet
generated script to prepare-pipeline, updated local maven repository
information.
No longer creates specialisations for each dataset as these no longer in
use, added configuration of bowtie and exonerate executable paths,
option to specify generation of separate reports for each dataset, fixed
configuration of output directory for LSF log files, added check for
existence of files specified in sample sheet.
Added configuration of output directory for log files in local mode,
reordered some of the variables.
Updates to versions of software used by MGA at CRUK-CI, updated
information on configuring the pipeline and use of wildcards and
delimiter character to specify multiple files for each dataset.
Renamed output directories for local and lsf modes.
Added additional TruSeq adapter sequences.