Staging removed

Minor changes:

• Data are no longer staged to Projects
• Archiving jobs are prevented to start on Irma

Ignore index fastqs when creating aeacus report

Merge pull request #153 from MatildaAslin/ignore_index_fastqs

Skip index fastqs in aeacus scripts

Extended amount of cores for aeacus-stats.pl

Minor update. FF-jobs terminated with a non-zero exit code due to memory limit hit. Aeacus-stats.pl updated with more cores.

GNUplot fix

Minor change:

• gnuplot version is now specified when loaded via the module system on Uppmax. Last update only applied to Summary reports, this applies to Project reports too.

Gnuplot hotfix

Minor change:

• gnuplot version is now specified when loaded via the module system on Uppmax

New README and bcl2fastq version written in report

Only minor changes:

• Updates to config:

  1. Default setting is now to ignore missing FASTQs, when creating the QuickReport
  2. Uppmax project is updated
  3. The qos flag has been turned into a comment, since it is not used on Irma

• Bcl2fastq version will now be written i aeacus-reports

• QC config updated acccording to new version of INS-0123

• Användarmanual Sisyphus has been added to the README

Updated QC-config and fixed "toolongtoprint" PDL-bug

In this release, the QC-config was updated to correspond to the threshold values for quality parameters stated in INS-0123. The variable "toolongtoprint" used in the PDL-package is set to handle runs with more than 500 cycles.

Updated index check

Minor update of script checkIndices.pl. Script will now print the percentage of a significant undetermined index in a lane.

No Swestore sync on Irma

• Unzipping of config will only be performed if unzipped config does not already exist
• Swestore sync is now based on host rather than machine type. Sisyphus is now hard coded to perform swestore sync on milou(-b) but not on irma.
• Some slurm jobs performing statistics were given more resources.

HiSeqX runs are no longer uploaded to SweStore

Major changes:

• HiSeqX runs are no longer uploaded to SweStore

Minor Changes:

• Sisyphus no longer waits for config file (terminates instead)
• If indexcheck fails, pipeline will not be terminated until after QC check.
• IndeckCheck: prints have been improved and regex bug has been fixed