From 776c359e8a5bc278be8aad840104591ae1979387 Mon Sep 17 00:00:00 2001 From: Ronak Shah Date: Thu, 7 Nov 2024 09:28:56 -0500 Subject: [PATCH 1/6] Update subworkflows --- subworkflows | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows b/subworkflows index aeb7fec..5d99719 160000 --- a/subworkflows +++ b/subworkflows @@ -1 +1 @@ -Subproject commit aeb7fec838db8abdfbdae7fbc617e2dd6bc5ae9c +Subproject commit 5d99719d1daad2e62b78eb1d4aa0708f80958ffc From 8e270032593d7d32e14e76f6043e84610092bacd Mon Sep 17 00:00:00 2001 From: Ronak Shah Date: Thu, 7 Nov 2024 09:45:25 -0500 Subject: [PATCH 2/6] Update uncollapsed_bam_generation.cwl --- uncollapsed_bam_generation.cwl | 271 ++++++++++++++++----------------- 1 file changed, 131 insertions(+), 140 deletions(-) diff --git a/uncollapsed_bam_generation.cwl b/uncollapsed_bam_generation.cwl index 9d61ff0..1278aad 100644 --- a/uncollapsed_bam_generation.cwl +++ b/uncollapsed_bam_generation.cwl @@ -18,85 +18,85 @@ inputs: type: string? doc: 'Fgbio FastqToBam: Tag in which to store molecular barcodes/UMIs.' 'sbg:x': 0 - 'sbg:y': 2776.71875 + 'sbg:y': 2666.828125 - id: fgbio_fastq_to_bam_sort type: boolean? doc: >- Fgbio FastqToBam: If true, queryname sort the BAM file, otherwise preserve input order. 'sbg:x': 0 - 'sbg:y': 2883.515625 + 'sbg:y': 2773.5625 - id: sequencing-center type: string doc: The sequencing center from which the data originated 'sbg:x': 0 - 'sbg:y': 427.1875 + 'sbg:y': 426.71875 - id: sample type: string doc: The name of the sequenced sample. 'sbg:x': 0 - 'sbg:y': 533.984375 + 'sbg:y': 533.3984375 - id: run-date type: string? doc: >- Date the run was produced, to insert into the read group header (Iso8601Date) 'sbg:x': 0 - 'sbg:y': 640.78125 + 'sbg:y': 640.0234375 - id: read-structures type: 'string[]?' doc: 'Fgbio FastqToBam: Read structures, one for each of the FASTQs.' 'sbg:x': 0 - 'sbg:y': 854.375 + 'sbg:y': 853.2734375 - id: read-group-id type: string doc: Read group ID to use in the file header. 'sbg:x': 0 - 'sbg:y': 961.171875 + 'sbg:y': 959.953125 - id: fgbio_fastq_to_bam_predicted-insert-size type: int? doc: >- Fgbio FastqToBam: Predicted median insert size, to insert into the read group header 'sbg:x': 0 - 'sbg:y': 2990.3125 + 'sbg:y': 2880.296875 - id: platform-unit type: string doc: Platform unit (e.g. "..") 'sbg:x': 0 - 'sbg:y': 1388.359375 + 'sbg:y': 1386.6171875 - id: platform-model type: string doc: >- Platform model to insert into the group header (ex. miseq, hiseq2500, hiseqX) 'sbg:x': 0 - 'sbg:y': 1495.15625 + 'sbg:y': 1493.2421875 - id: platform type: string doc: Sequencing Platform. 'sbg:x': 0 - 'sbg:y': 1601.953125 + 'sbg:y': 1599.8671875 - id: fgbio_fastq_to_bam_output_file_name type: string? doc: 'Fgbio FastqToBam: The output SAM or BAM file to be written.' 'sbg:x': 0 - 'sbg:y': 3097.109375 + 'sbg:y': 2987.03125 - id: library type: string doc: The name/ID of the sequenced library. 'sbg:x': 0 - 'sbg:y': 2242.734375 + 'sbg:y': 2133.15625 - id: description type: string? doc: Description of the read group. 'sbg:x': 0 - 'sbg:y': 4485.46875 + 'sbg:y': 4693.6328125 - id: comment type: string? doc: Comments to include in the output file’s header. 'sbg:x': 0 - 'sbg:y': 4592.265625 + 'sbg:y': 4800.2578125 - id: validation_stringency type: string doc: >- @@ -112,12 +112,12 @@ inputs: type: string? doc: Name of the Unpaired Fastq File 'sbg:x': 0 - 'sbg:y': 106.796875 + 'sbg:y': 106.6796875 - id: gatk_sam_to_fastq_include_non_primary_alignments type: boolean? doc: "\tIf true, include non-primary alignments in the output. Support of \n\tnon-primary alignments in SamToFastq is not comprehensive, so there \n\tmay be exceptions if this is set to true and there are paired reads \n\twith non-primary alignments." 'sbg:x': 0 - 'sbg:y': 2349.53125 + 'sbg:y': 2239.890625 - id: gatk_sam_to_fastq_include_non_pf_reads type: boolean? doc: >- @@ -125,17 +125,17 @@ inputs: means 'passes filtering'. Reads whose 'not passing quality controls' flag is set are non-PF reads. See GATK Dictionary for more info. 'sbg:x': 0 - 'sbg:y': 2456.328125 + 'sbg:y': 2346.625 - id: R1_output_fastq type: string doc: Name of the R1 output Fastq File 'sbg:x': 0 - 'sbg:y': 1281.5625 + 'sbg:y': 1279.9921875 - id: R2_output_fastq type: string doc: Name of the R2 Fastq File 'sbg:x': 0 - 'sbg:y': 1174.765625 + 'sbg:y': 1173.3671875 - id: reference_sequence type: File doc: >- @@ -151,7 +151,7 @@ inputs: - .bwt - .pac 'sbg:x': 0 - 'sbg:y': 747.578125 + 'sbg:y': 746.6484375 - id: fastp_unpaired2_output_file_name type: string? doc: >- @@ -159,19 +159,19 @@ inputs: to unpaired2. If --unpaired2 is same as --unpaired1 (default mode), both unpaired reads will be written to this same file. 'sbg:x': 0 - 'sbg:y': 3417.5 + 'sbg:y': 3307.1796875 - id: fastp_unpaired1_output_file_name type: string? doc: >- Fastp: for PE input, if read1 passed QC but read2 not, it will be written to unpaired1. Default is to discard it. 'sbg:x': 0 - 'sbg:y': 3524.296875 + 'sbg:y': 3413.8046875 - id: fastp_read2_output_file_name type: string? doc: 'Fastp: Read2 output File Name' 'sbg:x': 0 - 'sbg:y': 3631.09375 + 'sbg:y': 3520.4296875 - id: fastp_read2_adapter_sequence type: string? doc: >- @@ -179,12 +179,12 @@ inputs: found not overlapped. If not specified, it will be the same as (string) 'sbg:x': 0 - 'sbg:y': 3737.890625 + 'sbg:y': 3627.0546875 - id: fastp_read1_output_file_name type: string doc: 'Fastp: Read1 output File Name' 'sbg:x': 0 - 'sbg:y': 3844.6875 + 'sbg:y': 3733.6796875 - id: fastp_read1_adapter_sequence type: string? doc: >- @@ -192,81 +192,81 @@ inputs: will be auto-detected. For PE data, this is used if R1/R2 are found not overlapped. 'sbg:x': 0 - 'sbg:y': 3951.484375 + 'sbg:y': 3840.3046875 - id: fastp_minimum_read_length type: int? doc: >- Fastp: reads shorter than length_required will be discarded, default is 15. 'sbg:x': 0 - 'sbg:y': 4058.28125 + 'sbg:y': 3946.984375 - id: fastp_json_output_file_name type: string doc: 'Fastp: the json format report file name' 'sbg:x': 0 - 'sbg:y': 4165.078125 + 'sbg:y': 4373.703125 - id: fastp_html_output_file_name type: string doc: 'Fastp: the html format report file name' 'sbg:x': 0 - 'sbg:y': 4271.875 + 'sbg:y': 4480.3828125 - id: fastp_failed_reads_output_file_name type: string? doc: 'Fastp: specify the file to store reads that cannot pass the filters.' 'sbg:x': 0 - 'sbg:y': 4378.671875 + 'sbg:y': 4587.0078125 - id: bwa_mem_Y type: boolean? doc: 'BWA MEM: use soft clipping for supplementary alignments' 'sbg:x': 0 - 'sbg:y': 4805.859375 + 'sbg:y': 5013.5078125 - id: bwa_mem_T type: int? doc: 'BWA MEM: minimum score to output [30]' 'sbg:x': 0 - 'sbg:y': 4912.65625 + 'sbg:y': 5120.1328125 - id: sort_order type: string doc: 'GATK: The order in which the reads should be output.' 'sbg:x': 0 - 'sbg:y': 320.390625 + 'sbg:y': 320.0390625 - id: bwa_mem_P type: boolean? doc: 'BWA MEM: skip pairing; mate rescue performed unless -S also in use' 'sbg:x': 0 - 'sbg:y': 5019.453125 + 'sbg:y': 5226.7578125 - id: picard_addRG_output_file_name type: string? doc: Output BAM file name 'sbg:x': 0 - 'sbg:y': 1922.34375 + 'sbg:y': 1919.7421875 - id: bwa_mem_output type: string? doc: Output SAM file name 'sbg:x': 0 - 'sbg:y': 5126.25 + 'sbg:y': 5333.3828125 - id: bwa_mem_M type: boolean? doc: 'BWA MEM: mark shorter split hits as secondary' 'sbg:x': 0 - 'sbg:y': 5233.046875 + 'sbg:y': 5440.0078125 - id: bwa_mem_K type: int? doc: >- process INT input bases in each batch regardless of nThreads (for reproducibility) 'sbg:x': 0 - 'sbg:y': 5339.84375 + 'sbg:y': 5546.6328125 - id: create_bam_index type: boolean doc: 'GATK: Generate BAM index file when possible' - 'sbg:x': 1470.083740234375 - 'sbg:y': 2830.1171875 + 'sbg:x': 1470.052490234375 + 'sbg:y': 2933.390625 - id: gatk_merge_bam_alignment_output_file_name type: string? doc: Output BAM file name 'sbg:x': 0 - 'sbg:y': 2669.921875 + 'sbg:y': 2560.09375 - id: optical_duplicate_pixel_distance type: int? doc: >- @@ -275,15 +275,15 @@ inputs: for unpatterned versions of the Illumina platform. For the patterned flowcell models, 2500 is more appropriate. For other platforms and models, users should experiment to find what works best. - 'sbg:x': 2037.8697509765625 - 'sbg:y': 2156.1328125 + 'sbg:x': 2037.8385009765625 + 'sbg:y': 2245.828125 - id: duplicate_scoring_strategy type: string? doc: >- Picard MarkDuplicates: The scoring strategy for choosing the non-duplicate among candidates. - 'sbg:x': 2037.8697509765625 - 'sbg:y': 3183.7109375 + 'sbg:x': 2037.8385009765625 + 'sbg:y': 3300.8046875 - id: read_name_regex type: string? doc: >- @@ -303,121 +303,110 @@ inputs: to be tile, x and y values. For 7 element names (CASAVA 1.8), the 5th, 6th, and 7th elements are assumed to be tile, x and y values. 'sbg:x': 0 - 'sbg:y': 1067.96875 + 'sbg:y': 1066.6875 - id: gatk_mark_duplicates_output_file_name type: string? doc: 'Picard MarkDuplicates: The output file to write marked records to' - 'sbg:x': 2037.8697509765625 - 'sbg:y': 2560.5234375 + 'sbg:x': 2037.8385009765625 + 'sbg:y': 2649.9765625 - id: gatk_mark_duplicates_duplication_metrics_file_name type: string doc: 'Picard MarkDuplicates: File to write duplication metrics to' - 'sbg:x': 2037.8697509765625 - 'sbg:y': 2667.3203125 + 'sbg:x': 2037.8385009765625 + 'sbg:y': 2756.7109375 - id: gatk_mark_duplicates_assume_sort_order type: string? doc: >- Picard MarkDuplicates: If not null, assume that the input file has this order even if the header says otherwise. - 'sbg:x': 2037.8697509765625 - 'sbg:y': 2774.1171875 + 'sbg:x': 2037.8385009765625 + 'sbg:y': 2863.4453125 - id: abra2_window_size type: string? doc: >- ABRA2: Processing window size and overlap (size,overlap) (default: 400,200) - 'sbg:x': 2566.080078125 - 'sbg:y': 2710.125 + 'sbg:x': 2590.802734375 + 'sbg:y': 2653.5625 - id: abra2_soft_clip_contig type: string? doc: >- ABRA2: Soft clip contig args [maxcontigs,min_base_qual,frac high_qual_bases,min_soft_clip_len] (default:16,13,80,15) - 'sbg:x': 2566.080078125 - 'sbg:y': 2816.921875 + 'sbg:x': 2590.802734375 + 'sbg:y': 2866.9765625 - id: abra2_scoring_gap_alignments type: string? - 'sbg:x': 2566.080078125 - 'sbg:y': 2923.71875 + 'sbg:x': 2590.802734375 + 'sbg:y': 2973.7109375 - id: abra2_output_bams type: - string - type: array items: string doc: Required list of output sam or bam file - 'sbg:x': 2566.080078125 - 'sbg:y': 3030.515625 + 'sbg:x': 2590.802734375 + 'sbg:y': 3080.390625 - id: abra2_maximum_average_depth type: int? doc: >- ABRA2: Regions with average depth exceeding this value will be downsampled (default: 1000) - 'sbg:x': 2566.080078125 - 'sbg:y': 3457.703125 + 'sbg:x': 2590.802734375 + 'sbg:y': 3507.0546875 - id: abra2_bam_index type: boolean? doc: 'ABRA2: Generate BAM Index' - 'sbg:x': 2566.080078125 - 'sbg:y': 3778.09375 + 'sbg:x': 2590.802734375 + 'sbg:y': 3827.09375 - id: abra2_contig_anchor type: string? - 'sbg:x': 2566.080078125 - 'sbg:y': 3564.5 + 'sbg:x': 2590.802734375 + 'sbg:y': 3613.7890625 - id: abra2_consensus_sequence type: boolean? doc: >- ABRA2: Contig anchor [M_bases_at_contig_edge,max_mismatches_near_edge] (default:10,2) - 'sbg:x': 2566.080078125 - 'sbg:y': 3671.296875 - - id: bedtools_merge_distance_between_features - type: int? - 'sbg:x': 2566.080078125 - 'sbg:y': 2095.734375 + 'sbg:x': 2590.802734375 + 'sbg:y': 3720.46875 - id: abra2_maximum_mixmatch_rate type: float? doc: |- max allowed mismatch rate when mapping reads back to contigs (default: 0.05) - 'sbg:x': 2566.080078125 - 'sbg:y': 3350.90625 - - id: bedtools_genomecov_option_bedgraph - type: boolean? - doc: >- - bedtools genomecov: option flag parameter to choose output file format. - -bg refers to bedgraph format - 'sbg:x': 2566.080078125 - 'sbg:y': 2202.53125 + 'sbg:x': 2590.802734375 + 'sbg:y': 3400.375 - id: picard_fixmateinformation_output_file_name type: string? doc: 'Picard FixMateInformation: The output BAM file to write to' 'sbg:x': 0 - 'sbg:y': 1708.75 + 'sbg:y': 1706.4921875 - id: abra2_no_sort type: boolean? doc: 'ABRA2: Do not attempt to sort final output' - 'sbg:x': 2566.080078125 - 'sbg:y': 3137.3125 + 'sbg:x': 2590.802734375 + 'sbg:y': 3187.015625 - id: abra2_no_edge_complex_indel type: boolean? doc: 'ABRA2: Prevent output of complex indels at read start or read end' - 'sbg:x': 2566.080078125 - 'sbg:y': 3244.109375 + 'sbg:x': 2590.802734375 + 'sbg:y': 3293.6953125 - id: merge_sam_files_sort_order type: string doc: 'GATK MergeSamFiles: Sort order of output file' 'sbg:x': 0 - 'sbg:y': 2029.140625 + 'sbg:y': 2026.421875 - id: gatk_merge_sam_files_output_file_name type: string? doc: 'GATK MergeSamFiles: SAM or BAM file to write merged result to' 'sbg:x': 0 - 'sbg:y': 2563.125 + 'sbg:y': 2453.359375 - id: bwa_number_of_threads type: int? doc: 'BWA MEM: Number of threads' 'sbg:x': 0 - 'sbg:y': 4699.0625 + 'sbg:y': 4906.8828125 - id: fgbio_fastq_to_bam_input type: type: array @@ -428,85 +417,89 @@ inputs: Fgbio FastqToBam: Fastq files corresponding to each sequencing read ( e.g. R1, I1, etc.). 'sbg:x': 0 - 'sbg:y': 3203.90625 + 'sbg:y': 3093.765625 - id: picard_addRG_sort_order type: string 'sbg:x': 0 - 'sbg:y': 1815.546875 + 'sbg:y': 1813.1171875 - id: disable_trim_poly_g type: boolean? - 'sbg:x': 1470.083740234375 - 'sbg:y': 2616.5234375 + 'sbg:x': 1470.052490234375 + 'sbg:y': 2719.9765625 - id: disable_quality_filtering type: boolean? - 'sbg:x': 1470.083740234375 - 'sbg:y': 2723.3203125 + 'sbg:x': 1470.052490234375 + 'sbg:y': 2826.7109375 - id: temporary_directory type: string? 'sbg:x': 0 - 'sbg:y': 213.59375 + 'sbg:y': 213.359375 - id: fgbio_async_io type: string? 'sbg:x': 0 - 'sbg:y': 3310.703125 + 'sbg:y': 3200.5 - id: fastp_maximum_read_length type: int? 'sbg:x': 0 - 'sbg:y': 2135.9375 + 'sbg:y': 4053.71875 - id: fastp_max_len_read1 type: int? - 'sbg:x': 1773.6907958984375 - 'sbg:y': 3302.252197265625 + 'sbg:x': 0 + 'sbg:y': 4267.0234375 - id: fastp_max_len_read2 type: int? - 'sbg:x': 1686.5479736328125 - 'sbg:y': 3223.680908203125 + 'sbg:x': 0 + 'sbg:y': 4160.3984375 + - id: abra2_targets + type: File + 'sbg:x': 2590.802734375 + 'sbg:y': 2760.2421875 outputs: - id: gatk_sam_to_fastq_unpaired_fastq outputSource: - gatk_sam_to_fastq_4_1_8_0/gatk_sam_to_fastq_unpaired_fastq type: File? - 'sbg:x': 2037.8697509765625 - 'sbg:y': 2262.9296875 + 'sbg:x': 2037.8385009765625 + 'sbg:y': 2352.5078125 - id: fastp_unpaired2_output outputSource: - fastp_0_20_1/fastp_unpaired2_output type: File? - 'sbg:x': 2566.080078125 - 'sbg:y': 1668.546875 + 'sbg:x': 2590.802734375 + 'sbg:y': 1826.21875 - id: fastp_unpaired1_output outputSource: - fastp_0_20_1/fastp_unpaired1_output type: File? - 'sbg:x': 2566.080078125 - 'sbg:y': 1775.34375 + 'sbg:x': 2590.802734375 + 'sbg:y': 1932.84375 - id: fastp_json_output outputSource: - fastp_0_20_1/fastp_json_output type: File - 'sbg:x': 2566.080078125 - 'sbg:y': 1882.140625 + 'sbg:x': 2590.802734375 + 'sbg:y': 2039.5234375 - id: fastp_html_output outputSource: - fastp_0_20_1/fastp_html_output type: File - 'sbg:x': 2566.080078125 - 'sbg:y': 1988.9375 + 'sbg:x': 2590.802734375 + 'sbg:y': 2146.203125 - id: picard_mark_duplicates_metrics outputSource: - picard_mark_duplicates_4_1_8_1/picard_mark_duplicates_metrics type: File - 'sbg:x': 3337.63134765625 - 'sbg:y': 2483.5234375 + 'sbg:x': 3362.353515625 + 'sbg:y': 2593.9765625 - id: indel_realignment_bam outputSource: - - indel_realignment/indel_realignment_bam + - indel_realignment_staticbed/indel_realignment_bam type: File doc: This bam file will be used for collapsing secondaryFiles: - ^.bai - 'sbg:x': 3946.0361328125 - 'sbg:y': 2669.921875 + 'sbg:x': 3953.07421875 + 'sbg:y': 2773.2890625 steps: - id: fgbio_fastq_to_bam_1_2_0 in: @@ -555,8 +548,8 @@ steps: scatter: - input scatterMethod: dotproduct - 'sbg:x': 477.984375 - 'sbg:y': 2550.921875 + 'sbg:x': 477.953125 + 'sbg:y': 2654.2890625 - id: gatk_sam_to_fastq_4_1_8_0 in: - id: fastq @@ -583,8 +576,8 @@ steps: - id: gatk_sam_to_fastq_second_end_fastq run: command_line_tools/gatk_sam_to_fastq_4.1.8.0/gatk_sam_to_fastq_4.1.8.0.cwl label: GATK-SamToFastq - 'sbg:x': 1470.083740234375 - 'sbg:y': 2453.7265625 + 'sbg:x': 1470.052490234375 + 'sbg:y': 2557.296875 - id: fastp_0_20_1 in: - id: read1_input @@ -630,8 +623,8 @@ steps: - id: fastp_unpaired2_output run: command_line_tools/fastp_0.20.1/fastp_0.20.1.cwl label: fastp_0.20.1 - 'sbg:x': 2037.8697509765625 - 'sbg:y': 2978.9140625 + 'sbg:x': 2037.8385009765625 + 'sbg:y': 3082.125 - id: alignment in: - id: create_bam_index @@ -684,8 +677,8 @@ steps: - id: picard_add_or_replace_read_groups_bam run: subworkflows/alignment/alignment.cwl label: alignment - 'sbg:x': 2566.080078125 - 'sbg:y': 2456.328125 + 'sbg:x': 2590.802734375 + 'sbg:y': 2399.8828125 - id: gatk_merge_bam_alignment_4_1_8_0 in: - id: unmapped_bam @@ -709,8 +702,8 @@ steps: run: >- command_line_tools/gatk_merge_bam_alignment_4.1.8.0/gatk_merge_bam_alignment_4.1.8.0.cwl label: GATK-MergeBamAlignment - 'sbg:x': 2037.8697509765625 - 'sbg:y': 2411.7265625 + 'sbg:x': 2037.8385009765625 + 'sbg:y': 2501.2421875 - id: picard_mark_duplicates_4_1_8_1 in: - id: input @@ -739,9 +732,9 @@ steps: run: >- command_line_tools/picard_mark_duplicates_4.1.8.1/picard_mark_duplicates_4.1.8.1.cwl label: picard_mark_duplicates_4.1.8.1 - 'sbg:x': 2566.080078125 - 'sbg:y': 1498.75 - - id: indel_realignment + 'sbg:x': 2590.802734375 + 'sbg:y': 1656.59375 + - id: indel_realignment_staticbed in: - id: window_size source: abra2_window_size @@ -765,12 +758,8 @@ steps: source: abra2_consensus_sequence - id: bam_index source: abra2_bam_index - - id: option_bedgraph - source: bedtools_genomecov_option_bedgraph - id: no_edge_complex_indel source: abra2_no_edge_complex_indel - - id: distance_between_features - source: bedtools_merge_distance_between_features - id: output_bams source: - abra2_output_bams @@ -784,12 +773,14 @@ steps: source: create_bam_index - id: temporary_directory source: temporary_directory + - id: targets + source: abra2_targets out: - id: indel_realignment_bam - run: subworkflows/indel_realignment/indel_realignment.cwl + run: subworkflows/indel_realignment/indel_realignment_staticbed.cwl label: indel_realignment - 'sbg:x': 3337.63134765625 - 'sbg:y': 2723.3203125 + 'sbg:x': 3362.353515625 + 'sbg:y': 2826.65625 - id: gatk_merge_sam_files_4_1_8_0 in: - id: input @@ -810,8 +801,8 @@ steps: run: >- command_line_tools/gatk_merge_sam_files_4.1.8.0/gatk_merge_sam_files_4.1.8.0.cwl label: GATK-MergeSamFiles - 'sbg:x': 1053.5369873046875 - 'sbg:y': 2634.921875 + 'sbg:x': 1053.5057373046875 + 'sbg:y': 2738.2890625 requirements: - class: SubworkflowFeatureRequirement - class: ScatterFeatureRequirement From 6822bc63be3b8c726eeb3b4a9c1994caaffadb4b Mon Sep 17 00:00:00 2001 From: Ronak Shah Date: Tue, 21 Jan 2025 10:58:44 -0500 Subject: [PATCH 3/6] Update subworkflows --- subworkflows | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows b/subworkflows index 5d99719..2d3fef0 160000 --- a/subworkflows +++ b/subworkflows @@ -1 +1 @@ -Subproject commit 5d99719d1daad2e62b78eb1d4aa0708f80958ffc +Subproject commit 2d3fef0e39c1e36b93de47fe92f17ea10568b2a5 From 068064f2a094558de5a796e33e57179a761a499b Mon Sep 17 00:00:00 2001 From: Ronak Shah Date: Tue, 21 Jan 2025 11:02:32 -0500 Subject: [PATCH 4/6] Update to specific version of submodules subworkflows v1.2.7 commandlinetools v1.3.5 --- command_line_tools | 2 +- subworkflows | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/command_line_tools b/command_line_tools index 082f3a3..b8c66ac 160000 --- a/command_line_tools +++ b/command_line_tools @@ -1 +1 @@ -Subproject commit 082f3a3177a845acfd717ad1783ae5b6a668095e +Subproject commit b8c66acf773e623f94947a16f969dc6d53d434f9 diff --git a/subworkflows b/subworkflows index 2d3fef0..8ad4846 160000 --- a/subworkflows +++ b/subworkflows @@ -1 +1 @@ -Subproject commit 2d3fef0e39c1e36b93de47fe92f17ea10568b2a5 +Subproject commit 8ad4846cec9e47414f535e5c3758195c55125357 From 2e63782a844248e484e6b371b6fd23a59f01887b Mon Sep 17 00:00:00 2001 From: Ronak Shah Date: Wed, 22 Jan 2025 11:40:38 -0500 Subject: [PATCH 5/6] Update subworkflows --- subworkflows | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows b/subworkflows index 8ad4846..fed5e6c 160000 --- a/subworkflows +++ b/subworkflows @@ -1 +1 @@ -Subproject commit 8ad4846cec9e47414f535e5c3758195c55125357 +Subproject commit fed5e6c3cc088d4f8d62f6bbf3283d4aa00aa8f4 From dc91e86c351c2fc5f525597173dccb073872daa9 Mon Sep 17 00:00:00 2001 From: Ronak Shah Date: Wed, 22 Jan 2025 11:40:51 -0500 Subject: [PATCH 6/6] Update subworkflows --- subworkflows | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows b/subworkflows index fed5e6c..5f6a4f7 160000 --- a/subworkflows +++ b/subworkflows @@ -1 +1 @@ -Subproject commit fed5e6c3cc088d4f8d62f6bbf3283d4aa00aa8f4 +Subproject commit 5f6a4f764d7a7d45f899ca9eba8c788d3f4b3316