added sneaky garbage removal in fetch_input
now passes fastq files instead of bam files to enable defered clean up in merge
now optionally takes fastq file input and removes them. also passes bam_files as garbage to next analysis to prevent job failure on retry
no evals PeakCaller run so it can throw_no_retry
now takes and passes on debug param
now takes and passes on debug param. also sets is_half_open for known formats
added debug output. Moved clean up to end, so we maintain intermediate files in case of failure. Fixed bam deletion
added debug output. moved is_half_open setting to PeakCaller. Now uses run_system_cmd
updated constructor to take sam_ref_fai and includes that in the output bam
now validate sam_header path
merge_bams and validate_sam_header now fixed
now passes debug to PeakCaller wrapper
fixed bam_file deletion bug, always passes swam_header to merge_bams for validation
added some debug output. Now passes aligner specific default params based on aligner_param_methods
Killed fastq overwrite bug which was cause by the parent set name being used instead of the replicte set name
constructor now returns something...doh!
comments and minor typos, move along
update to use new validate_sam_header method name
added a 10gb resource and some notes about a potential no_tidy mode
added checksum_optional to batch params, also added control_feature_types to pipelinewide, but can probably drop these?