Open yoyosef opened 5 years ago
https://github.com/talkowski-lab/gnomad-sv-pipeline/blob/master/gnomad_sv_pipeline_wdls/module_01/01_depth_clustering_by_chrom.wdl
I noticed that the call on make_rdtest_bed didn't include a script as an input, is this by mistake?
call make_rdtest_bed { input: dels=cluster_DELs.clustered_bed, dups=cluster_DUPs.clustered_bed, batch=batch, } call make_depth_vcf { input: bed=make_rdtest_bed.bed, batch=batch, contigs=contigs } call vcf_qc.master_vcf_qc as vcf_qc { input: vcf=make_depth_vcf.vcf, famfile=trios_famfile, ref_build=ref_build, prefix="${batch}_clustered_depth_vcf", sv_per_shard=10000, samples_per_shard=100, Sanders_2015_tarball=Sanders_2015_tarball, Collins_2017_tarball=Collins_2017_tarball, Werling_2018_tarball=Werling_2018_tarball } output { File clustered_vcf = make_depth_vcf.vcf File clustered_vcf_qc = vcf_qc.sv_vcf_qc_output } } task make_rdtest_bed { File dels File dups File script String batch command <<< cat \ <(python3 ${script} ${dels} | sed '1d') \ <(python3 ${script} ${dups} | sed '1d') \ | sort -k1,1V -k2,2n \ | cat <(echo -e "#chrom start end name samples svtype" | sed -e 's/ /\t/g') - \ > ${batch}.depth.bed; >>> output { File bed = "${batch}.depth.bed" }
Additionally,
https://api.firecloud.org/ga4gh/v1/tools/Talkowski-SV:master_SV_VCF_QC/versions/47/plain-WDL/descriptor (which is imported in the wdl file) is a dead link.
https://github.com/talkowski-lab/gnomad-sv-pipeline/blob/master/gnomad_sv_pipeline_wdls/module_01/01_depth_clustering_by_chrom.wdl
I noticed that the call on make_rdtest_bed didn't include a script as an input, is this by mistake?