Skip to content

Commit d1f02fd

Browse files
VJaliliVJalili
committed
test
1 parent 334ed99 commit d1f02fd

File tree

1 file changed

+11
-168
lines changed

1 file changed

+11
-168
lines changed

‎wdl/SVShell.wdl‎

Lines changed: 11 additions & 168 deletions
Original file line numberDiff line numberDiff line change
@@ -260,17 +260,17 @@ task RunSVShell {
260260

261261
# String final_vcf_filename = sample_id + ".vcf.gz"
262262
# String final_vcf_idx_filename = final_vcf_filename + ".tbi"
263-
String pre_cleanup_vcf_filename = batch + ".annotated.vcf.gz"
264-
String pre_cleanup_vcf_idx_filename = pre_cleanup_vcf_filename + ".tbi"
265-
String stripy_json_filename = sample_id + ".stripy.json"
266-
String stripy_tsv_filename = sample_id + ".stripy.tsv"
267-
String stripy_html_filename = sample_id + ".stripy.html"
268-
String stripy_vcf_filename = sample_id + ".stripy.vcf"
269-
String metrics_filename = "single_sample." + batch + ".metrics.tsv"
270-
String qc_filename = "sv_qc." + batch + ".tsv"
271-
String ploidy_matrix_filename = batch + "_ploidy_matrix.bed.gz"
272-
String ploidy_plots_filename = batch + "_ploidy_plots.tar.gz"
273-
String non_genotyped_unique_depth_calls_filename = batch + ".non_genotyped_unique_depth_calls.vcf.gz"
263+
# String pre_cleanup_vcf_filename = batch + ".annotated.vcf.gz"
264+
# String pre_cleanup_vcf_idx_filename = pre_cleanup_vcf_filename + ".tbi"
265+
# String stripy_json_filename = sample_id + ".stripy.json"
266+
# String stripy_tsv_filename = sample_id + ".stripy.tsv"
267+
# String stripy_html_filename = sample_id + ".stripy.html"
268+
# String stripy_vcf_filename = sample_id + ".stripy.vcf"
269+
# String metrics_filename = "single_sample." + batch + ".metrics.tsv"
270+
# String qc_filename = "sv_qc." + batch + ".tsv"
271+
# String ploidy_matrix_filename = batch + "_ploidy_matrix.bed.gz"
272+
# String ploidy_plots_filename = batch + "_ploidy_plots.tar.gz"
273+
# String non_genotyped_unique_depth_calls_filename = batch + ".non_genotyped_unique_depth_calls.vcf.gz"
274274
275275
command <<<
276276
set -Exeuo pipefail
@@ -281,163 +281,6 @@ task RunSVShell {
281281
mkdir -p "${PWD}/wd/tmp"
282282
283283
df -h
284-
285-
# jq -n \
286-
# --arg batch "~{batch}" \
287-
# --arg sample_id "~{sample_id}" \
288-
# --arg ref_samples_list "~{ref_samples_list}" \
289-
# --arg ref_ped_file "~{ref_ped_file}" \
290-
# --arg genome_file "~{genome_file}" \
291-
# --arg primary_contigs_list "~{primary_contigs_list}" \
292-
# --arg primary_contigs_fai "~{primary_contigs_fai}" \
293-
# --arg reference_fasta "~{reference_fasta}" \
294-
# --arg reference_index "~{reference_index}" \
295-
# --arg reference_dict "~{reference_dict}" \
296-
# --arg ref_panel_vcf "~{ref_panel_vcf}" \
297-
# --arg autosome_file "~{autosome_file}" \
298-
# --arg allosome_file "~{allosome_file}" \
299-
# --arg bam_or_cram_file "~{bam_or_cram_file}" \
300-
# --arg bam_or_cram_index "~{bam_or_cram_index}" \
301-
# --arg preprocessed_intervals "~{preprocessed_intervals}" \
302-
# --arg manta_region_bed "~{manta_region_bed}" \
303-
# --arg sd_locs_vcf "~{sd_locs_vcf}" \
304-
# --arg wham_include_list_bed_file "~{wham_include_list_bed_file}" \
305-
# --arg reference_bwa_alt "~{reference_bwa_alt}" \
306-
# --arg reference_bwa_amb "~{reference_bwa_amb}" \
307-
# --arg reference_bwa_ann "~{reference_bwa_ann}" \
308-
# --arg reference_bwa_bwt "~{reference_bwa_bwt}" \
309-
# --arg reference_bwa_pac "~{reference_bwa_pac}" \
310-
# --arg reference_bwa_sa "~{reference_bwa_sa}" \
311-
# --argjson run_vcf_qc ~{run_vcf_qc} \
312-
# --arg wgd_scoring_mask "~{wgd_scoring_mask}" \
313-
# --argjson min_svsize ~{min_svsize} \
314-
# --arg contig_ploidy_model_tar "~{contig_ploidy_model_tar}" \
315-
# --arg gcnv_model_tars_list "~{write_lines(gcnv_model_tars)}" \
316-
# --arg ref_panel_bincov_matrix "~{ref_panel_bincov_matrix}" \
317-
# --arg ref_pesr_disc_files_list "~{write_lines(ref_pesr_disc_files)}" \
318-
# --arg ref_pesr_split_files_list "~{write_lines(ref_pesr_split_files)}" \
319-
# --arg ref_pesr_sd_files_list "~{write_lines(ref_pesr_sd_files)}" \
320-
# --argjson ref_copy_number_autosomal_contigs ~{ref_copy_number_autosomal_contigs} \
321-
# --argjson gcnv_qs_cutoff ~{gcnv_qs_cutoff} \
322-
# --arg cnmops_exclude_list "~{cnmops_exclude_list}" \
323-
# --argjson matrix_qc_distance ~{matrix_qc_distance} \
324-
# --arg ref_std_manta_vcf_tar "~{ref_std_manta_vcf_tar}" \
325-
# --arg ref_std_scramble_vcf_tar "~{ref_std_scramble_vcf_tar}" \
326-
# --arg ref_std_wham_vcf_tar "~{ref_std_wham_vcf_tar}" \
327-
# --arg ref_panel_del_bed "~{ref_panel_del_bed}" \
328-
# --arg ref_panel_dup_bed "~{ref_panel_dup_bed}" \
329-
# --arg depth_exclude_list "~{depth_exclude_list}" \
330-
# --argjson depth_exclude_overlap_fraction ~{depth_exclude_overlap_fraction} \
331-
# --argjson depth_interval_overlap ~{depth_interval_overlap} \
332-
# --arg depth_clustering_algorithm "~{select_first([depth_clustering_algorithm, ""])}" \
333-
# --arg pesr_exclude_intervals "~{pesr_exclude_intervals}" \
334-
# --argjson pesr_interval_overlap ~{pesr_interval_overlap} \
335-
# --arg pesr_clustering_algorithm "~{select_first([pesr_clustering_algorithm, ""])}" \
336-
# --arg cutoffs "~{cutoffs}" \
337-
# --arg genotyping_rd_table "~{genotyping_rd_table}" \
338-
# --arg genotyping_pe_table "~{genotyping_pe_table}" \
339-
# --arg genotyping_sr_table "~{genotyping_sr_table}" \
340-
# --arg bin_exclude "~{bin_exclude}" \
341-
# --argjson clean_vcf_min_sr_background_fail_batches ~{clean_vcf_min_sr_background_fail_batches} \
342-
# --arg clustering_config_part1 "~{clustering_config_part1}" \
343-
# --arg stratification_config_part1 "~{stratification_config_part1}" \
344-
# --arg clustering_config_part2 "~{clustering_config_part2}" \
345-
# --arg stratification_config_part2 "~{stratification_config_part2}" \
346-
# --argjson clustering_track_names "$(jq -R . < ~{write_lines(clustering_track_names)} | jq -s .)" \
347-
# --argjson clustering_track_bed_files "$(jq -R . < ~{write_lines(clustering_track_bed_files)} | jq -s .)" \
348-
# --arg cytobands "~{cytobands}" \
349-
# --arg mei_bed "~{mei_bed}" \
350-
# --argjson max_shard_size_resolve ~{max_shard_size_resolve} \
351-
# --arg chr_x "~{chr_x}" \
352-
# --arg chr_y "~{chr_y}" \
353-
# --arg protein_coding_gtf "~{protein_coding_gtf}" \
354-
# --arg noncoding_bed "~{noncoding_bed}" \
355-
# --argjson annotation_sv_per_shard ~{annotation_sv_per_shard} \
356-
# --arg external_af_ref_bed "~{select_first([external_af_ref_bed, ""])}" \
357-
# --arg external_af_ref_bed_prefix "~{select_first([external_af_ref_bed_prefix, ""])}" \
358-
# --argjson external_af_population "$(jq -R . < ~{write_lines(select_first([external_af_population, []]))} | jq -s .)" \
359-
# --argjson min_pe_cpx ~{min_pe_cpx} \
360-
# --argjson min_pe_ctx ~{min_pe_ctx} \
361-
# --arg gq_recalibrator_model_file "~{gq_recalibrator_model_file}" \
362-
# --argjson recalibrate_gq_args "$(jq -R . < ~{write_lines(recalibrate_gq_args)} | jq -s .)" \
363-
# --argjson genome_tracks "$(jq -R . < ~{write_lines(genome_tracks)} | jq -s .)" \
364-
# --argjson no_call_rate_cutoff ~{no_call_rate_cutoff} \
365-
# --arg sl_cutoff_table "~{sl_cutoff_table}" \
366-
# --arg sl_filter_args "~{select_first([sl_filter_args, ""])}" \
367-
# --arg qc_definitions "~{qc_definitions}" \
368-
# --arg ref_panel_median_cov "~{ref_panel_median_cov}" \
369-
# --arg manta_region_bed_index "~{manta_region_bed_index}" \
370-
# --arg HERVK_reference "~{HERVK_reference}" \
371-
# --arg LINE1_reference "~{LINE1_reference}" \
372-
# --arg intron_reference "~{intron_reference}" \
373-
# --arg outlier_samples_list "~{outlier_samples_list}" \
374-
# --arg par_bed "~{par_bed}" \
375-
# --argjson run_sampleevidence_metrics ~{run_sampleevidence_metrics} \
376-
# --arg sample_bincov_matrix "~{sample_bincov_matrix}" \
377-
# --arg sample_bincov_matrix_idx "~{sample_bincov_matrix_idx}" \
378-
# --arg PE_metrics "~{PE_metrics}" \
379-
# --arg SR_metrics "~{SR_metrics}" \
380-
# --arg rmsk "~{rmsk}" \
381-
# --arg segdups "~{segdups}" \
382-
# --arg genotype_pesr_depth_sepcutoff "~{genotype_pesr_depth_sepcutoff}" \
383-
# --arg genotype_pesr_pesr_sepcutoff "~{genotype_pesr_pesr_sepcutoff}" \
384-
# --arg genotype_depth_depth_sepcutoff "~{genotype_depth_depth_sepcutoff}" \
385-
# --arg genotype_depth_pesr_sepcutoff "~{genotype_depth_pesr_sepcutoff}" \
386-
# --argjson genotyping_n_per_split ~{genotyping_n_per_split} \
387-
# --argjson n_RD_genotype_bins ~{n_RD_genotype_bins} \
388-
# --argjson clean_vcf1b_records_per_shard ~{clean_vcf1b_records_per_shard} \
389-
# --argjson clean_vcf5_records_per_shard ~{clean_vcf5_records_per_shard} \
390-
# --argjson clean_vcf_max_shards_per_chrom_clean_vcf_step1 ~{clean_vcf_max_shards_per_chrom_clean_vcf_step1} \
391-
# --argjson clean_vcf_min_records_per_shard_clean_vcf_step1 ~{clean_vcf_min_records_per_shard_clean_vcf_step1} \
392-
# --argjson clean_vcf_random_seed ~{clean_vcf_random_seed} \
393-
# --argjson clean_vcf_samples_per_clean_vcf_step2_shard ~{clean_vcf_samples_per_clean_vcf_step2_shard} \
394-
# --argjson "RefineComplexVariants.n_per_split" ~{refine_complex_variants_n_per_split} \
395-
# '$ARGS.named | with_entries(select(.value != "" and .value != null))' > "${SV_SHELL_BASE_DIR}/single_sample_pipeline_inputs.json"
396-
#
397-
# bash /opt/sv_shell/single_sample_pipeline.sh \
398-
# "${SV_SHELL_BASE_DIR}/single_sample_pipeline_inputs.json" \
399-
# "${SV_SHELL_BASE_DIR}/single_sample_pipeline_outputs.json"
400-
401-
# echo "----------------------"
402-
# echo "${PWD}"
403-
# cp "${SV_SHELL_BASE_DIR}/single_sample_pipeline_inputs.json" "${BASE_DIR}/"
404-
# cp "${SV_SHELL_BASE_DIR}/single_sample_pipeline_outputs.json" "${BASE_DIR}/"
405-
# ls
406-
#
407-
# final_vcf_path=$(jq -r '.final_vcf' "${BASE_DIR}/single_sample_pipeline_outputs.json")
408-
# mv "${final_vcf_path}" "${BASE_DIR}/~{final_vcf_filename}"
409-
# mv "${final_vcf_path}.tbi" "${BASE_DIR}/~{final_vcf_idx_filename}"
410-
#
411-
# pre_cleanup_vcf_path=$(jq -r '.pre_cleanup_vcf' "${BASE_DIR}/single_sample_pipeline_outputs.json")
412-
# mv "${pre_cleanup_vcf_path}" "${BASE_DIR}/~{pre_cleanup_vcf_filename}"
413-
# mv "${pre_cleanup_vcf_path}.tbi" "${BASE_DIR}/~{pre_cleanup_vcf_idx_filename}"
414-
#
415-
# stripy_json_path=$(jq -r '.stripy_json_output' "${BASE_DIR}/single_sample_pipeline_outputs.json")
416-
# mv "${stripy_json_path}" "${BASE_DIR}/~{stripy_json_filename}"
417-
#
418-
# stripy_tsv_path=$(jq -r '.stripy_tsv_output' "${BASE_DIR}/single_sample_pipeline_outputs.json")
419-
# mv "${stripy_tsv_path}" "${BASE_DIR}/~{stripy_tsv_filename}"
420-
#
421-
# stripy_html_path=$(jq -r '.stripy_html_output' "${BASE_DIR}/single_sample_pipeline_outputs.json")
422-
# mv "${stripy_html_path}" "${BASE_DIR}/~{stripy_html_filename}"
423-
#
424-
# stripy_vcf_path=$(jq -r '.stripy_vcf_output' "${BASE_DIR}/single_sample_pipeline_outputs.json")
425-
# mv "${stripy_vcf_path}" "${BASE_DIR}/~{stripy_vcf_filename}"
426-
#
427-
# metrics_path=$(jq -r '.metrics_file' "${BASE_DIR}/single_sample_pipeline_outputs.json")
428-
# mv "${metrics_path}" "${BASE_DIR}/~{metrics_filename}"
429-
#
430-
# qc_path=$(jq -r '.qc_file' "${BASE_DIR}/single_sample_pipeline_outputs.json")
431-
# mv "${qc_path}" "${BASE_DIR}/~{qc_filename}"
432-
#
433-
# ploidy_matrix_path=$(jq -r '.ploidy_matrix' "${BASE_DIR}/single_sample_pipeline_outputs.json")
434-
# mv "${ploidy_matrix_path}" "${BASE_DIR}/~{ploidy_matrix_filename}"
435-
#
436-
# ploidy_plots_path=$(jq -r '.ploidy_plots' "${BASE_DIR}/single_sample_pipeline_outputs.json")
437-
# mv "${ploidy_plots_path}" "${BASE_DIR}/~{ploidy_plots_filename}"
438-
#
439-
# non_genotyped_path=$(jq -r '.non_genotyped_unique_depth_calls' "${BASE_DIR}/single_sample_pipeline_outputs.json")
440-
# mv "${non_genotyped_path}" "${BASE_DIR}/~{non_genotyped_unique_depth_calls_filename}"
441284
>>>
442285

443286
output {

0 commit comments

Comments
 (0)