--test

Author: VJalili

inputs.json

@@ -104,7 +104,7 @@
   "SVShell.intron_reference": "gs://broad-dsde-methods-vj/sv-shell-inputs/gencode.v39.CDS.intron.tsv.gz",
   "SVShell.par_bed": "gs://broad-dsde-methods-vj/sv-shell-inputs/hg38.par.bed",
   "SVShell.sample_bincov_matrix": "TODO_MAYBE_NOT_NEEEDED",
-  "SVShell.sample_bincov_matrix_idx": "gs://broad-dsde-methods-vj/sv-shell-inputs/NA12878.RD.txt.gz.tbi",
+  "SVShell.sample_bincov_matrix_idx": "TODO: delete this one too",
   "SVShell.PE_metrics": "gs://broad-dsde-methods-vj/sv-shell-inputs/all_samples.pe_metric_file.txt",
   "SVShell.SR_metrics": "gs://broad-dsde-methods-vj/sv-shell-inputs/all_samples.sr_metric_file.txt",
   "SVShell.rmsk": "gs://broad-dsde-methods-vj/sv-shell-inputs/hg38.randomForest_blacklist.withRepMask.bed.gz",

wdl/SVShell.wdl

@@ -6,6 +6,30 @@ workflow SVShell {
   input {
     File gcnv_model_tars_list
     File ref_pesr_split_files_list
+    File ref_pesr_disc_files_list
+    File ref_pesr_sd_files_list
+    File pesr_exclude_intervals
+    File ref_panel_vcf
+    File ref_panel_bincov_matrix
+    File bin_exclude
+    File cytobands
+    File depth_exclude_list
+    Array[File] genome_tracks
+    File mei_bed
+    File manta_region_bed
+    File HERVK_reference
+    File LINE1_reference
+    File intron_reference
+    File? outlier_samples_list
+    File? par_bed
+    File PE_metrics
+    File SR_metrics
+    File rmsk
+    File segdups
+    File genotype_pesr_depth_sepcutoff
+    File genotype_pesr_pesr_sepcutoff
+    File genotype_depth_depth_sepcutoff
+    File genotype_depth_pesr_sepcutoff
   }
 
   Array[File] gcnv_model_tars = read_lines(gcnv_model_tars_list)
@@ -16,31 +40,232 @@ workflow SVShell {
   }
   Array[File] ref_pesr_split_file_indices = ref_pesr_split_file_index
 
+  Array[File] ref_pesr_disc_files = read_lines(ref_pesr_disc_files_list)
+  scatter (ref_pesr_disc_file in ref_pesr_disc_files) {
+    File ref_pesr_disc_file_index = ref_pesr_disc_file + ".tbi"
+  }
+  Array[File] ref_pesr_disc_file_indices = ref_pesr_disc_file_index
+
+  Array[File] ref_pesr_sd_files = read_lines(ref_pesr_sd_files_list)
+  scatter (ref_pesr_sd_file in ref_pesr_sd_files) {
+    File ref_pesr_sd_file_index = ref_pesr_sd_file + ".tbi"
+  }
+  Array[File] ref_pesr_sd_file_indices = ref_pesr_sd_file_index
+
+  scatter (genome_track in genome_tracks) {
+    File genome_track_index = genome_track + ".tbi"
+  }
+  Array[File] genome_tracks_indices = genome_track_index
+
+  File pesr_exclude_intervals_index = pesr_exclude_intervals + ".tbi"
+  File ref_panel_vcf_index = ref_panel_vcf + ".tbi"
+  File ref_panel_bincov_matrix_index = ref_panel_bincov_matrix + ".tbi"
+  File bin_exclude_index = bin_exclude + ".tbi"
+  File cytobands_index = cytobands + ".tbi"
+  File depth_exclude_list_index = depth_exclude_list + ".tbi"
+  File mei_bed_index = mei_bed + ".tbi"
+  File manta_region_bed_index = manta_region_bed + ".tbi"
 
   call RunSVShell {
     input:
       gcnv_model_tars = gcnv_model_tars,
       ref_pesr_split_files = ref_pesr_split_files,
-      ref_pesr_split_files_indices = ref_pesr_split_file_indices
+      ref_pesr_disc_files = ref_pesr_disc_files,
+      ref_pesr_sd_files = ref_pesr_sd_files,
+      ref_pesr_split_files_indices = ref_pesr_split_file_indices,
+      ref_pesr_disc_files_indices = ref_pesr_disc_file_indices,
+      ref_pesr_sd_files_indices = ref_pesr_sd_file_indices,
+      genome_tracks = genome_tracks,
+      genome_tracks_indices = genome_tracks_indices,
+      pesr_exclude_intervals = pesr_exclude_intervals,
+      pesr_exclude_intervals_index = pesr_exclude_intervals_index,
+      ref_panel_vcf = ref_panel_vcf,
+      ref_panel_vcf_index = ref_panel_vcf_index,
+      ref_panel_bincov_matrix = ref_panel_bincov_matrix,
+      ref_panel_bincov_matrix_index = ref_panel_bincov_matrix_index,
+      bin_exclude = bin_exclude,
+      bin_exclude_index = bin_exclude_index,
+      cytobands = cytobands,
+      cytobands_index = cytobands_index,
+      depth_exclude_list = depth_exclude_list,
+      depth_exclude_list_index = depth_exclude_list_index,
+      mei_bed = mei_bed,
+      mei_bed_index = mei_bed_index,
+      manta_region_bed = manta_region_bed,
+      manta_region_bed_index = manta_region_bed_index,
+      HERVK_reference = HERVK_reference,
+      LINE1_reference = LINE1_reference,
+      intron_reference = intron_reference,
+      outlier_samples_list = outlier_samples_list,
+      par_bed = par_bed,
+      PE_metrics = PE_metrics,
+      SR_metrics = SR_metrics,
+      rmsk = rmsk,
+      segdups = segdups,
+      genotype_pesr_depth_sepcutoff = genotype_pesr_depth_sepcutoff,
+      genotype_pesr_pesr_sepcutoff = genotype_pesr_pesr_sepcutoff,
+      genotype_depth_depth_sepcutoff = genotype_depth_depth_sepcutoff,
+      genotype_depth_pesr_sepcutoff = genotype_depth_pesr_sepcutoff,
   }
 
 
   output {
     File inputs_json = RunSVShell.inputs_json
+#    File outputs_json = RunSVShell.outputs_json
+#    File final_vcf = RunSVShell.final_vcf
+#    File final_vcf_idx = RunSVShell.final_vcf_idx
+#    File pre_cleanup_vcf = RunSVShell.pre_cleanup_vcf
+#    File pre_cleanup_vcf_idx = RunSVShell.pre_cleanup_vcf_idx
+#    File stripy_json_output = RunSVShell.stripy_json_output
+#    File stripy_tsv_output = RunSVShell.stripy_tsv_output
+#    File stripy_html_output = RunSVShell.stripy_html_output
+#    File stripy_vcf_output = RunSVShell.stripy_vcf_output
+#    File metrics_file = RunSVShell.metrics_file
+#    File qc_file = RunSVShell.qc_file
+#    File ploidy_matrix = RunSVShell.ploidy_matrix
+#    File ploidy_plots = RunSVShell.ploidy_plots
+#    File non_genotyped_unique_depth_calls = RunSVShell.non_genotyped_unique_depth_calls
   }
 }
 
 task RunSVShell {
   input {
     String batch
+    String sample_id
+    File ref_samples_list
+    File ref_ped_file
+    File genome_file
+    File primary_contigs_list
+    File primary_contigs_fai
+    File reference_fasta
+    File reference_index
+    File reference_dict
+    File ref_panel_vcf
+    File autosome_file
+    File allosome_file
+    File bam_or_cram_file
+    File bam_or_cram_index
+    File preprocessed_intervals
+    File manta_region_bed
+    File manta_region_bed_index
+    File sd_locs_vcf
+    File wham_include_list_bed_file
+    File reference_bwa_alt
+    File reference_bwa_amb
+    File reference_bwa_ann
+    File reference_bwa_bwt
+    File reference_bwa_pac
+    File reference_bwa_sa
+    Boolean run_vcf_qc
+    File wgd_scoring_mask
+    Int min_svsize
+    File contig_ploidy_model_tar
     Array[File] gcnv_model_tars
+    File ref_panel_bincov_matrix
+    Array[File] ref_pesr_disc_files
     Array[File] ref_pesr_split_files
+    Array[File] ref_pesr_sd_files
     Array[File] ref_pesr_split_files_indices
-
+    Array[File] ref_pesr_disc_files_indices
+    Array[File] ref_pesr_sd_files_indices
+    Array[File] genome_tracks_indices
+    File pesr_exclude_intervals_index
+    File ref_panel_vcf_index
+    File ref_panel_bincov_matrix_index
+    File bin_exclude_index
+    File cytobands_index
+    File depth_exclude_list_index
+    File mei_bed_index
+    Int ref_copy_number_autosomal_contigs
+    Int gcnv_qs_cutoff
+    File cnmops_exclude_list
+    Int matrix_qc_distance
+    File? ref_std_manta_vcf_tar
+    File? ref_std_scramble_vcf_tar
+    File? ref_std_wham_vcf_tar
+    File ref_panel_del_bed
+    File ref_panel_dup_bed
+    File depth_exclude_list
+    Float depth_exclude_overlap_fraction
+    Float depth_interval_overlap
+    String? depth_clustering_algorithm
+    File pesr_exclude_intervals
+    Float pesr_interval_overlap
+    String? pesr_clustering_algorithm
+    File cutoffs
+    File genotyping_rd_table
+    File genotyping_pe_table
+    File genotyping_sr_table
+    File bin_exclude
+    Float clean_vcf_min_sr_background_fail_batches
+    File clustering_config_part1
+    File stratification_config_part1
+    File clustering_config_part2
+    File stratification_config_part2
+    Array[String] clustering_track_names
+    Array[File] clustering_track_bed_files
+    File cytobands
+    File mei_bed
+    Int max_shard_size_resolve
+    String chr_x
+    String chr_y
+    File protein_coding_gtf
+    File noncoding_bed
+    Int annotation_sv_per_shard
+    File? external_af_ref_bed
+    String? external_af_ref_bed_prefix
+    Array[String]? external_af_population
+    Int min_pe_cpx
+    Int min_pe_ctx
+    File gq_recalibrator_model_file
+    Array[String] recalibrate_gq_args
+    Array[File] genome_tracks
+    Float no_call_rate_cutoff
+    File sl_cutoff_table
+    String? sl_filter_args
+    File qc_definitions
+    File ref_panel_median_cov
+    File HERVK_reference
+    File LINE1_reference
+    File intron_reference
+    File? outlier_samples_list
+    File? par_bed
+    Boolean run_sampleevidence_metrics
+    File PE_metrics
+    File SR_metrics
+    File rmsk
+    File segdups
+    File genotype_pesr_depth_sepcutoff
+    File genotype_pesr_pesr_sepcutoff
+    File genotype_depth_depth_sepcutoff
+    File genotype_depth_pesr_sepcutoff
+    Int genotyping_n_per_split
+    Int n_RD_genotype_bins
+    Int clean_vcf1b_records_per_shard
+    Int clean_vcf5_records_per_shard
+    Int clean_vcf_max_shards_per_chrom_clean_vcf_step1
+    Int clean_vcf_min_records_per_shard_clean_vcf_step1
+    Int clean_vcf_random_seed
+    Int clean_vcf_samples_per_clean_vcf_step2_shard
+    Int refine_complex_variants_n_per_split
     String sv_shell_docker
     RuntimeAttr? runtime_attr_override
   }
 
+  String final_vcf_filename = sample_id + ".vcf.gz"
+  String final_vcf_idx_filename = final_vcf_filename + ".tbi"
+  String pre_cleanup_vcf_filename = batch + ".annotated.vcf.gz"
+  String pre_cleanup_vcf_idx_filename = pre_cleanup_vcf_filename + ".tbi"
+  String stripy_json_filename = sample_id + ".stripy.json"
+  String stripy_tsv_filename = sample_id + ".stripy.tsv"
+  String stripy_html_filename = sample_id + ".stripy.html"
+  String stripy_vcf_filename = sample_id + ".stripy.vcf"
+  String metrics_filename = "single_sample." + batch + ".metrics.tsv"
+  String qc_filename = "sv_qc." + batch + ".tsv"
+  String ploidy_matrix_filename = batch + "_ploidy_matrix.bed.gz"
+  String ploidy_plots_filename = batch + "_ploidy_plots.tar.gz"
+  String non_genotyped_unique_depth_calls_filename = batch + ".non_genotyped_unique_depth_calls.vcf.gz"
+
   command <<<
     set -Exeuo pipefail
 
@@ -50,10 +275,26 @@ task RunSVShell {
     mkdir -p "${PWD}/wd/tmp"
 
     touch single_sample_pipeline_inputs.json
+
+    df -h
   >>>
 
   output {
     File inputs_json = "single_sample_pipeline_inputs.json"
+#    File outputs_json = "single_sample_pipeline_outputs.json"
+#    File final_vcf = final_vcf_filename
+#    File final_vcf_idx = final_vcf_idx_filename
+#    File pre_cleanup_vcf = pre_cleanup_vcf_filename
+#    File pre_cleanup_vcf_idx = pre_cleanup_vcf_idx_filename
+#    File stripy_json_output = stripy_json_filename
+#    File stripy_tsv_output = stripy_tsv_filename
+#    File stripy_html_output = stripy_html_filename
+#    File stripy_vcf_output = stripy_vcf_filename
+#    File metrics_file = metrics_filename
+#    File qc_file = qc_filename
+#    File ploidy_matrix = ploidy_matrix_filename
+#    File ploidy_plots = ploidy_plots_filename
+#    File non_genotyped_unique_depth_calls = non_genotyped_unique_depth_calls_filename
   }
 
   RuntimeAttr default_attr = object {