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Updating cores and mem
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@rhshah
rhshah committed Aug 27, 2024
1 parent 275a628 commit cfab797
Showing 1 changed file with 1 addition and 1 deletion.
2 changes: 1 addition & 1 deletion command_line_tools
Submodule command_line_tools updated 94 files
+7 −5 abra2_2.22/abra2_2.22.cwl
+4 −1 access_utils/0.1.1/general_stats_parse.cwl
+2 −2 athena/1.4.2/annotate_bed/annotate_bed.cwl
+3 −3 athena/1.4.2/coverage_report_single/coverage_report_single.cwl
+3 −3 athena/1.4.2/coverage_stats_single/coverage_stats_single.cwl
+14 −14 bcftools_1.15.1/bcftools_bgzip_1.15.1.cwl
+3 −3 bcftools_1.15.1/bcftools_concat_1.15.1.cwl
+6 −6 bcftools_1.15.1/bcftools_norm_1.15.1.cwl
+6 −6 bcftools_1.15.1/bcftools_sort._1.15.1.cwl
+2 −2 bcftools_1.15.1/bcftools_tabix_1.15.1.cwl
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+2 −2 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
+6 −6 bedtools_sortBed_v2.28.0_cv2/bedtools_sortBed_v2.28.0_cv2.cwl
+2 −2 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
+3 −3 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 −0 cci_utils/0.3.1/general_stats_parse.cwl
+3 −0 cci_utils/0.3.2/general_stats_parse.cwl
+2 −2 delly_0.9.1/delly_0.9.1.cwl
+3 −3 delly_1.0.3/delly_1.0.3.cwl
+4 −4 facets_1.5.6/facets.doFacets-1.5.6.cwl
+5 −5 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
+4 −4 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
+2 −2 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
+3 −3 gatk_BaseRecalibrator_4.1.2.0/gatk_baserecalibrator_4.1.2.0.cwl
+2 −2 gatk_apply_bqsr_4.1.0.0/gatk_apply_bqsr_4.1.0.0.cwl
+4 −4 gatk_apply_bqsr_4.1.8.1/gatk_apply_bqsr_4.1.8.1.cwl
+2 −2 gatk_base_recalibrator_4.1.0.0/gatk_base_recalibrator_4.1.0.0.cwl
+4 −4 gatk_base_recalibrator_4.1.8.1/gatk_base_recalibrator_4.1.8.1.cwl
+8 −8 gatk_collect_alignment_summary_metrics_4.1.8.0/gatk_collect_alignment_summary_metrics_4.1.8.0.cwl
+6 −6 gatk_collect_hs_metrics_4.1.8.0/gatk_collect_hs_metrics_4.1.8.0.cwl
+4 −4 gatk_downsamplesam_4.1.8.1/gatk_downsamplesam_4.1.8.1.cwl
+2 −2 gatk_mark_duplicates_4.1.0.0/gatk_mark_duplicates_4.1.0.0.cwl
+4 −4 gatk_mean_quality_by_cycle/4.1.8.0/gatk_mean_quality_by_cycle_4.1.8.0.cwl
+10 −10 gatk_merge_bam_alignment_4.1.8.0/gatk_merge_bam_alignment_4.1.8.0.cwl
+6 −6 gatk_merge_sam_files_4.1.8.0/gatk_merge_sam_files_4.1.8.0.cwl
+4 −4 gatk_revert_sam/4.1.8.0/gatk_revert_sam_4.1.8.0.cwl
+13 −13 gatk_sam_to_fastq_4.1.8.0/gatk_sam_to_fastq_4.1.8.0.cwl
+2 −2 getbasecountsmultisample/1.2.5/getbasecountsmultisample_1.2.5.cwl
+3 −3 manta_1.5.1/manta_1.5.1.cwl
+4 −4 merge_fastq_0.1.7/merge_fastq_0.1.7.cwl
+3 −3 mosdepth_0.3.3/mosdepth_0.3.3.cwl
+2 −2 multiqc/1.10.1.7/multiqc.cwl
+2 −2 multiqc/1.12/multiqc_1.12.cwl
+4 −4 mutect_1.1.5/mutect_1.1.5.cwl
+4 −4 octopus/0.7.4/octopus_0-7-4.cwl
+6 −6 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
+4 −4 picard_add_or_replace_read_groups_4.1.8.1/picard_add_or_replace_read_groups_4.1.8.1.cwl
+5 −5 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
+4 −4 picard_collectmultiplemetric_2.21.2/picard_collectmultiplemetrics_2.21.2.cwl
+4 −4 picard_collectmultiplemetric_2.8.1/picard_collectmultiplemetrics_2-8-1.cwl
+7 −7 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
+4 −4 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
+2 −2 picard_hsmetrics_2.21.2/picard_hsmetrics_2.21.2.cwl
+2 −2 picard_hsmetrics_2.8.1/picard_hsmetrics_2.8.1.cwl
+6 −6 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
+4 −4 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
+8 −8 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
+14 −14 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
+2 −2 samtools-merge_1.9/samtools-merge_1.9.cwl
+3 −3 samtools_sort_1.3.1/samtools_sort_1.3.1.cwl
+3 −3 samtools_view_1.3.1/samtools_view_1.3.1.cwl
+2 −2 sequence_qc/0.2.4/sequence_qc_0.2.4.cwl
+3 −3 snp-pileup_0.1.1/htstools-0.1.1.cwl
+8 −8 snpsift_annotate_5.0/snpsift_annotate_5-0.cwl
+2 −2 trim_galore_0.6.2/trim_galore_0.6.2.cwl
+1 −1 utilities_ubuntu_18.04/gzip.cwl
+2 −2 utilities_ubuntu_18.04/mv.cwl
+6 −6 utilities_ubuntu_18.04/sort.cwl
+2 −2 vardictjava/v1.8.2/teststrandbias.cwl
+6 −6 vardictjava/v1.8.2/var_to_vcf.cwl
+4 −4 vardictjava/v1.8.2/vardict_app.cwl
+4 −4 vcf2maf_1.6.17/vcf2maf_1.6.17.cwl
+12 −12 vcf2maf_1.6.21/vcf2maf_1.6.21.cwl

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