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Update command_line_tools
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@rhshah
rhshah committed Aug 21, 2021
1 parent 04bb22f commit 9396a14
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2 changes: 1 addition & 1 deletion command_line_tools
Submodule command_line_tools updated 77 files
+0 −21 abra2_2.22/README.md
+16 −34 access_utils/0.1.1/general_stats_parse.cwl
+0 −56 bedtools_genomecov_v2.28.0_cv2/README.md
+0 −57 bedtools_merge_v2.28.0_cv2/README.md
+0 −52 disambiguate_1.0.0/README.md
+71 −73 docs/SUMMARY.md
+2 −0 docs/abra2/README.md
+15 −14 docs/abra2/abra2_2.17.md
+21 −0 docs/abra2/abra2_2.22.md
+2 −0 docs/bedtools/README.md
+43 −0 docs/bedtools/bedtools_genomecov_v2.28.0_cv2.md
+43 −0 docs/bedtools/bedtools_merge_v2.28.0_cv2.md
+2 −0 docs/disambiguate/README.md
+53 −0 docs/disambiguate/disambiguate_1.0.0.md
+2 −0 docs/fgbio/README.md
+8 −8 docs/fgbio/fgbio_call_duplex_consensus_reads_1.2.0.md
+8 −7 docs/fgbio/fgbio_collect_duplex_seq_metrics_1.2.0.md
+8 −8 docs/fgbio/fgbio_fastq_to_bam_1.2.0.md
+8 −8 docs/fgbio/fgbio_filter_consensus_reads_1.2.0.md
+8 −8 docs/fgbio/fgbio_group_reads_by_umi_1.2.0.md
+8 −7 docs/fgbio/fgbio_postprocessing_simplex_filter_0.1.8.md
+2 −0 docs/gatk/README.md
+43 −0 docs/gatk/gatk_apply_bqsr_4.1.8.1.md
+43 −0 docs/gatk/gatk_applybqsr_4.1.2.0.md
+43 −0 docs/gatk/gatk_base_recalibrator_4.1.8.1.md
+43 −0 docs/gatk/gatk_baserecalibrator_4.1.2.0.md
+8 −8 docs/gatk/gatk_merge_bam_alignment_4.1.8.0.md
+8 −8 docs/gatk/gatk_merge_sam_files_4.1.8.0.md
+2 −0 docs/gatk/samtofastq-v4.1.8.0.md
+2 −0 docs/manta/README.md
+14 −13 docs/manta/manta_1.5.1.md
+2 −0 docs/marianas/README.md
+19 −0 docs/marianas/marianas_collapsing_first_pass_1.8.1.md
+19 −0 docs/marianas/marianas_collapsing_second_pass_1.8.1.md
+19 −0 docs/marianas/marianas_process_loop_umi_1.8.1.md
+33 −0 docs/marianas/marianas_separate_bams_1.8.1.md
+2 −0 docs/merge-fastq/README.md
+11 −11 docs/merge-fastq/merge_fastq_0.1.7.md
+2 −0 docs/mutect/README.md
+12 −13 docs/mutect/mutect_1.1.5.md
+2 −0 docs/picard-tools/README.md
+12 −12 docs/picard-tools/picard_add_or_replace_read_groups_1.96.md
+8 −9 docs/picard-tools/picard_add_or_replace_read_groups_2.21.2.md
+8 −9 docs/picard-tools/picard_add_or_replace_read_groups_4.1.8.1.md
+8 −8 docs/picard-tools/picard_collect_alignment_summary_metrics_2.21.2.md
+11 −11 docs/picard-tools/picard_collect_alignment_summary_metrics_2.8.1.md
+8 −8 docs/picard-tools/picard_collectmultiplemetric_2.21.2.md
+11 −11 docs/picard-tools/picard_collectmultiplemetric_2.8.1.md
+15 −14 docs/picard-tools/picard_fix_mate_information_1.96.md
+10 −10 docs/picard-tools/picard_fix_mate_information_2.21.2.md
+10 −10 docs/picard-tools/picard_fix_mate_information_4.1.8.1.md
+8 −9 docs/picard-tools/picard_hsmetrics_2.21.2.md
+26 −0 docs/picard-tools/picard_hsmetrics_2.8.1.md
+20 −0 docs/picard-tools/picard_mark_duplicates_1.96.md
+8 −8 docs/picard-tools/picard_mark_duplicates_2.21.2.md
+20 −0 docs/picard-tools/picard_mark_duplicates_2.8.1.md
+8 −8 docs/picard-tools/picard_mark_duplicates_4.1.8.1.md
+2 −0 docs/trim-galore/README.md
+15 −14 docs/trim-galore/trim_galore_0.6.2.md
+2 −0 docs/ubuntu-utilites/README.md
+26 −0 docs/ubuntu-utilites/utilities_ubuntu_18.04.md
+2 −0 docs/waltz/README.md
+12 −10 docs/waltz/waltz_count_reads_3.1.1.md
+12 −10 docs/waltz/waltz_pileupmatrices_3.1.1.md
+0 −128 gatk_ApplyBQSR_4.1.2.0/README.md
+0 −142 gatk_BaseRecalibrator_4.1.2.0/README.md
+0 −128 gatk_apply_bqsr_4.1.8.1/README.md
+0 −142 gatk_base_recalibrator_4.1.8.1/README.md
+0 −19 marianas_collapsing_first_pass_1.8.1/README.md
+0 −19 marianas_collapsing_second_pass_1.8.1/README.md
+0 −19 marianas_process_loop_umi_1.8.1/README.md
+0 −33 marianas_separate_bams_1.8.1/README.md
+12 −2 multiqc/1.10.1.7/multiqc.cwl
+0 −26 picard_hsmetrics_2.8.1/README.md
+0 −20 picard_mark_duplicates_1.96/README.md
+0 −20 picard_mark_duplicates_2.8.1/README.md
+0 −25 utilities_ubuntu_18.04/README.md

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