Merge branch 'release/0.139' into develop
clean up tests for rna-seq pipelines
Merge branch 'develop' of /software/vertres/git/origin/vr-pipe into develop
force full triggers if there are fewer incomplete subs than incomplete elements
updated bamcheck parser for compatability with latest SN lines
now --retries allows that number or more, instead of exactly that number, and meaning of 0 is explained
changed archive_files step so that it no longer advertises that it outputs any files - this prevents chaining but also avoids risks when resetting failed subs, avoiding loss of files
fix step to be acted on when cleaning up snp_calling_gatk_haplotype_caller pipeline
apply_recalibration_mode option should not flow through to the frontend
Merge branch 'develop' of /software/vertres/git/origin/vr-pipe into develop
add general vqsr pipeline and fix description of vqsr_for_snps pipeline
platform field in bam headers should be one of ILLUMINA,LS454,ABI_SOLID
steps that need their bams indexed now specify the bai an in input; pipelines that use bam_index step now pass the bai to the step that needs it: this lets auto-resets work properly
Merge branch 'develop' of /software/vertres/git/origin/vr-pipe into develop
adding fofnwmd for newly altered gatk_reduce_reads.t
corrected error message when files do not exist
debug now outputs the time and pid
instead of calling debug() when start_over is called, we warn to get a stackstrace
trigger() now redos the estate loop on encountering issues, and does so as many times as there are steps, to reset back to step 1 if necessary; we also last out immediately under normal circumstances; added lots of debug() calls
added --debug option and lots of debug() calls