mskcc / cwl-commandlinetools

Central location for CWL CommandLineTools

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Refinement of all CWL's #47

Closed rhshah closed 5 years ago

rhshah commented 5 years ago

We need to refine the following CWLS:

[x] abra2_2.17
[x] marianas_process_loop_umi_1.8.0
[x] picard_add_or_replace_read_groups_1.96
[x] picard_fix_mate_information_1.96
[x] picard_mark_duplicates_2.8.1
[x] trim_galore_0.6.2
[x] waltz_count_reads_2.0.0
[x] waltz_pileupmatrices_2.0
[x] gatk_ApplyBQSR_4.1.2.0
[x] gatk_BaseRecalibrator_4.1.2.0
[x] bedtools_genomecov_v2.28.0_cv2
[x] bedtools_merge_v2.28.0_cv2

rhshah commented 5 years ago

60