Commit cfab797
Submodule command_line_tools updated 94 files
- abra2_2.22/abra2_2.22.cwl+7-5
- access_utils/0.1.1/general_stats_parse.cwl+4-1
- athena/1.4.2/annotate_bed/annotate_bed.cwl+2-2
- athena/1.4.2/coverage_report_single/coverage_report_single.cwl+3-3
- athena/1.4.2/coverage_stats_single/coverage_stats_single.cwl+3-3
- bcftools_1.15.1/bcftools_bgzip_1.15.1.cwl+14-14
- bcftools_1.15.1/bcftools_concat_1.15.1.cwl+3-3
- bcftools_1.15.1/bcftools_norm_1.15.1.cwl+6-6
- bcftools_1.15.1/bcftools_sort._1.15.1.cwl+6-6
- bcftools_1.15.1/bcftools_tabix_1.15.1.cwl+2-2
- bcftools_1.6/bcftools_concat_1.6.cwl+4-4
- bedtools_genomecov_v2.28.0_cv2/bedtools_genomecov_v2.28.0_cv2.cwl+2-2
- bedtools_merge_v2.28.0_cv2/bedtools_merge_v2.28.0_cv2.cwl+2-2
- bedtools_sortBed_v2.28.0_cv2/bedtools_sortBed_v2.28.0_cv2.cwl+6-6
- biometrics_extract/0.2.15/biometrics_extract.cwl+2-2
- biometrics_genotype/0.2.15/biometrics_genotype.cwl+2-2
- biometrics_major/0.2.15/biometrics_major.cwl+2-2
- biometrics_minor/0.2.15/biometrics_minor.cwl+2-2
- biometrics_sexmismatch/0.2.15/biometrics_sexmismatch.cwl+2-2
- bwa_mem_0.7.12/bwa_mem_0.7.12.cwl+3-3
- bwa_mem_0.7.17/bwa_mem_0.7.17.cwl+3-3
- bwa_mem_0.7.5a/bwa_mem_0.7.5a.cwl+3-3
- cci_utils/0.3.1/general_stats_parse.cwl+3
- cci_utils/0.3.2/general_stats_parse.cwl+3
- delly_0.9.1/delly_0.9.1.cwl+2-2
- delly_1.0.3/delly_1.0.3.cwl+3-3
- facets_1.5.6/facets.doFacets-1.5.6.cwl+4-4
- fastp_0.20.1/fastp_0.20.1.cwl+5-5
- fgbio_call_duplex_consensus_reads_1.2.0/fgbio_call_duplex_consensus_reads_1.2.0.cwl+5-5
- fgbio_collect_duplex_seq_metrics_1.2.0/fgbio_collect_duplex_seq_metrics_1.2.0.cwl+4-4
- fgbio_fastq_to_bam_1.2.0/fgbio_fastq_to_bam_1.2.0.cwl+4-4
- fgbio_filter_consensus_reads_1.2.0/fgbio_filter_consensus_reads_1.2.0.cwl+4-4
- fgbio_group_reads_by_umi_1.2.0/fgbio_group_reads_by_umi_1.2.0.cwl+4-4
- fgbio_postprocessing_simplex_filter_0.1.8/fgbio_postprocessing_simplex_filter_0.1.8.cwl+2-2
- gatk_ApplyBQSR_4.1.2.0/gatk_ApplyBQSR_4.1.2.0.cwl+2-2
- gatk_BaseRecalibrator_4.1.2.0/gatk_baserecalibrator_4.1.2.0.cwl+3-3
- gatk_apply_bqsr_4.1.0.0/gatk_apply_bqsr_4.1.0.0.cwl+2-2
- gatk_apply_bqsr_4.1.8.1/gatk_apply_bqsr_4.1.8.1.cwl+4-4
- gatk_base_recalibrator_4.1.0.0/gatk_base_recalibrator_4.1.0.0.cwl+2-2
- gatk_base_recalibrator_4.1.8.1/gatk_base_recalibrator_4.1.8.1.cwl+4-4
- gatk_collect_alignment_summary_metrics_4.1.8.0/gatk_collect_alignment_summary_metrics_4.1.8.0.cwl+8-8
- gatk_collect_hs_metrics_4.1.8.0/gatk_collect_hs_metrics_4.1.8.0.cwl+6-6
- gatk_downsamplesam_4.1.8.1/gatk_downsamplesam_4.1.8.1.cwl+4-4
- gatk_mark_duplicates_4.1.0.0/gatk_mark_duplicates_4.1.0.0.cwl+2-2
- gatk_mean_quality_by_cycle/4.1.8.0/gatk_mean_quality_by_cycle_4.1.8.0.cwl+4-4
- gatk_merge_bam_alignment_4.1.8.0/gatk_merge_bam_alignment_4.1.8.0.cwl+10-10
- gatk_merge_sam_files_4.1.8.0/gatk_merge_sam_files_4.1.8.0.cwl+6-6
- gatk_revert_sam/4.1.8.0/gatk_revert_sam_4.1.8.0.cwl+4-4
- gatk_sam_to_fastq_4.1.8.0/gatk_sam_to_fastq_4.1.8.0.cwl+13-13
- getbasecountsmultisample/1.2.5/getbasecountsmultisample_1.2.5.cwl+2-2
- manta_1.5.1/manta_1.5.1.cwl+3-3
- merge_fastq_0.1.7/merge_fastq_0.1.7.cwl+4-4
- mosdepth_0.3.3/mosdepth_0.3.3.cwl+3-3
- multiqc/1.10.1.7/multiqc.cwl+2-2
- multiqc/1.12/multiqc_1.12.cwl+2-2
- mutect_1.1.5/mutect_1.1.5.cwl+4-4
- octopus/0.7.4/octopus_0-7-4.cwl+4-4
- picard_add_or_replace_read_groups_1.96/picard_add_or_replace_read_groups_1.96.cwl+6-6
- picard_add_or_replace_read_groups_2.21.2/picard_add_or_replace_read_groups_2.21.2.cwl+6-6
- picard_add_or_replace_read_groups_4.1.8.1/picard_add_or_replace_read_groups_4.1.8.1.cwl+4-4
- picard_collect_alignment_summary_metrics_2.21.2/picard_collect_alignment_summary_metrics_2.21.2.cwl+5-5
- picard_collect_alignment_summary_metrics_2.8.1/picard_collect_alignment_summary_metrics_2.8.1.cwl+5-5
- picard_collectmultiplemetric_2.21.2/picard_collectmultiplemetrics_2.21.2.cwl+4-4
- picard_collectmultiplemetric_2.8.1/picard_collectmultiplemetrics_2-8-1.cwl+4-4
- picard_fix_mate_information_1.96/picard_fix_mate_information_1.96.cwl+7-7
- picard_fix_mate_information_2.21.2/picard_fix_mate_information_2.21.2.cwl+7-7
- picard_fix_mate_information_2.9.0/picard_fix_mate_information_2.9.0.cwl+4-4
- picard_fix_mate_information_4.1.8.1/picard_fix_mate_information_4.1.8.1.cwl+4-4
- picard_hsmetrics_2.21.2/picard_hsmetrics_2.21.2.cwl+2-2
- picard_hsmetrics_2.8.1/picard_hsmetrics_2.8.1.cwl+2-2
- picard_mark_duplicates_2.21.2/picard_mark_duplicates_2.21.2.cwl+6-6
- picard_mark_duplicates_2.8.1/picard_mark_duplicates_2.8.1.cwl+6-6
- picard_mark_duplicates_2.9.0/picard_mark_duplicates_2.9.0.cwl+4-4
- picard_mark_duplicates_4.1.8.1/picard_mark_duplicates_4.1.8.1.cwl+4-4
- postprocessing_variant_calls/0.2.2/maf_annotated_by_bed/maf_annotated_by_bed.cwl+8-8
- postprocessing_variant_calls/0.2.3/maf_annotated_by_bed/maf_annotated_by_bed.cwl+8-8
- postprocessing_variant_calls/0.2.3/maf_annotated_by_tsv/maf_annotated_by_tsv.cwl+14-14
- postprocessing_variant_calls/0.2.3/maf_filter_cmoch/maf_filter_cmoch.cwl+14-14
- postprocessing_variant_calls/0.2.3/maf_tag_cmoch/maf_tag_cmoch.cwl+14-14
- samtools-merge_1.9/samtools-merge_1.9.cwl+2-2
- samtools_sort_1.3.1/samtools_sort_1.3.1.cwl+3-3
- samtools_view_1.3.1/samtools_view_1.3.1.cwl+3-3
- sequence_qc/0.2.4/sequence_qc_0.2.4.cwl+2-2
- snp-pileup_0.1.1/htstools-0.1.1.cwl+3-3
- snpsift_annotate_5.0/snpsift_annotate_5-0.cwl+8-8
- trim_galore_0.6.2/trim_galore_0.6.2.cwl+2-2
- utilities_ubuntu_18.04/gzip.cwl+1-1
- utilities_ubuntu_18.04/mv.cwl+2-2
- utilities_ubuntu_18.04/sort.cwl+6-6
- vardictjava/v1.8.2/teststrandbias.cwl+2-2
- vardictjava/v1.8.2/var_to_vcf.cwl+6-6
- vardictjava/v1.8.2/vardict_app.cwl+4-4
- vcf2maf_1.6.17/vcf2maf_1.6.17.cwl+4-4
- vcf2maf_1.6.21/vcf2maf_1.6.21.cwl+12-12
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