0.4.0

Modifying bwa, arrg and other tools based on access workflows

include readme's and example inputs (#55)

Return disambiguate files instead of directory

Merge pull request #59 from mskcc/feature/add_pu_bwa_mem_0.7.12 …

Merge pull request #62 from mskcc/roslin_integration_changes …

Ij/bwa arrg md output changes (#60)

0.3.0

Changelog

• abra2_2.17
• alfred_0.1.17
• bedtools_genomecov_v2.28.0_cv2
• bedtools_merge_v2.28.0_cv2
• disambiguate_1.0.0
• gatk_ApplyBQSR_4.1.2.0
• gatk_BaseRecalibrator_4.1.2.0
• marianas_collapsing_first_pass_1.8.1
• marianas_collapsing_second_pass_1.8.1
• marianas_process_loop_umi_1.8.1
• picard_add_or_replace_read_groups_1.96
• picard_fix_mate_information_1.96
• trim_galore_0.6.2
• waltz_count_reads_3.1.1
• waltz_pileupmatrices_3.1.1

0.2.0

Added the following files:

abra2_2.17/README.md
abra2_2.17/abra2_2.17.cwl
abra2_2.17/container/Dockerfile
abra2_2.17/example_inputs.yaml
abra2_2.19/README.md
abra2_2.19/abra2_2.19.cwl
abra2_2.19/container/Dockerfile
abra2_2.19/example_inputs.yaml
bedtools_genomecov_v2.28.0_cv2/bedtools_genomecov.cwl
bedtools_genomecov_v2.28.0_cv2/example_inputs.yml
bedtools_merge_v2.28.0_cv2/bedtools_merge.cwl
bedtools_merge_v2.28.0_cv2/example_inputs.yml
gatk_ApplyBQSR_4.1.2.0/example_inputs.yml
gatk_ApplyBQSR_4.1.2.0/gatk_ApplyBQSR.cwl
gatk_BaseRecalibrator_4.1.2.0/example_inputs.yml
gatk_BaseRecalibrator_4.1.2.0/gatk_baserecalibrator.cwl
marianas_collapsing_first_pass_1.8.1/marianas_first_pass.cwl
marianas_collapsing_first_pass_1.8.1/test_inputs_first_pass.yaml
marianas_collapsing_second_pass_1.8.1/marianas_second_pass.cwl
marianas_collapsing_second_pass_1.8.1/test_inputs_second_pass.yaml
marianas_process_loop_umi_1.8.1/container/Dockerfile
marianas_process_loop_umi_1.8.1/marianas_process_loop_umi.cwl
utilities_ubuntu_18.04/README.md
utilities_ubuntu_18.04/example_inputs_gzip.yaml
utilities_ubuntu_18.04/example_inputs_sort.yaml
utilities_ubuntu_18.04/gzip.cwl
utilities_ubuntu_18.04/sort.cwl
waltz_count_reads_3.1.1/container/Dockerfile
waltz_count_reads_3.1.1/example_inputs.yml
waltz_count_reads_3.1.1/waltz_count_reads_3.1.1.cwl
waltz_pileupmatrices_3.1.1/example_inputs.yml
waltz_pileupmatrices_3.1.1/waltz_pileupmatrices_3.1.1.cwl

0.1.0

Changelog:

Added CommandLineTools:
bwa_mem_0.7.12
bwa_mem_0.7.5a
facets_1.5.6
gatk_mark_duplicates_4.1.0.0
msisensor_0.2
msisensor_0.6
mutect2_4.1.0.0
samtools-merge_1.9
samtools_sort_1.3.1
samtools_view_1.3.1
scatterintervals_4.1.0.0
snp-pileup_0.1.1