Merge branch '35-workflow-job-parsing-update'
Heavily updated the yaml file parsing for two primary reasons: 1. Make it more understandable what's actually going on underneath. 2. Allow for optional arguments.
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- ChipathlonMethodParameters.xlsx 0 additions, 0 deletionsChipathlonMethodParameters.xlsx
- chipathlon/conf.py 14 additions, 9 deletionschipathlon/conf.py
- chipathlon/db.py 54 additions, 19 deletionschipathlon/db.py
- chipathlon/generators/align_generator.py 32 additions, 20 deletionschipathlon/generators/align_generator.py
- chipathlon/generators/idr_generator.py 15 additions, 5 deletionschipathlon/generators/idr_generator.py
- chipathlon/generators/module_generator.py 76 additions, 40 deletionschipathlon/generators/module_generator.py
- chipathlon/generators/peak_call_generator.py 30 additions, 28 deletionschipathlon/generators/peak_call_generator.py
- chipathlon/generators/remove_duplicates_generator.py 15 additions, 5 deletionschipathlon/generators/remove_duplicates_generator.py
- chipathlon/jobs/modules/align.yaml 103 additions, 109 deletionschipathlon/jobs/modules/align.yaml
- chipathlon/jobs/modules/idr.yaml 10 additions, 13 deletionschipathlon/jobs/modules/idr.yaml
- chipathlon/jobs/modules/peak_call.yaml 226 additions, 258 deletionschipathlon/jobs/modules/peak_call.yaml
- chipathlon/jobs/modules/remove_duplicates.yaml 27 additions, 33 deletionschipathlon/jobs/modules/remove_duplicates.yaml
- chipathlon/jobs/params/bedtools_bam_to_bed.yaml 3 additions, 4 deletionschipathlon/jobs/params/bedtools_bam_to_bed.yaml
- chipathlon/jobs/params/bowtie2_align_paired.yaml 16 additions, 26 deletionschipathlon/jobs/params/bowtie2_align_paired.yaml
- chipathlon/jobs/params/bowtie2_align_single.yaml 14 additions, 23 deletionschipathlon/jobs/params/bowtie2_align_single.yaml
- chipathlon/jobs/params/bwa_align_paired.yaml 13 additions, 20 deletionschipathlon/jobs/params/bwa_align_paired.yaml
- chipathlon/jobs/params/bwa_align_single.yaml 11 additions, 17 deletionschipathlon/jobs/params/bwa_align_single.yaml
- chipathlon/jobs/params/bwa_sai_to_sam.yaml 13 additions, 19 deletionschipathlon/jobs/params/bwa_sai_to_sam.yaml
- chipathlon/jobs/params/cat_awk_sort_peaks.yaml 4 additions, 5 deletionschipathlon/jobs/params/cat_awk_sort_peaks.yaml
- chipathlon/jobs/params/ccat_callpeak.yaml 15 additions, 26 deletionschipathlon/jobs/params/ccat_callpeak.yaml
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