Updating SimpleGermlineTagger and somatic CNV experimental post-processing workflow #5252
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,60 @@ | ||
| # Unsupported workflow that concatenates the IGV compatible files generated by multiple runs of combine_tracks.wdl | ||
| workflow AggregateCombinedTracksWorkflow { | ||
| String group_id | ||
| Array[File] tumor_with_germline_filtered_segs | ||
| Array[File] normals_igv_compat | ||
| Array[File] tumors_igv_compat | ||
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| call TsvCat as TsvCatTumorGermlinePruned { | ||
| input: | ||
| input_files = tumor_with_germline_filtered_segs, | ||
| id = group_id + "_TumorGermlinePruned" | ||
| } | ||
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| call TsvCat as TsvCatTumor { | ||
| input: | ||
| input_files = tumors_igv_compat, | ||
| id = group_id + "_Tumor" | ||
| } | ||
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| call TsvCat as TsvCatNormal { | ||
| input: | ||
| input_files = normals_igv_compat, | ||
| id = group_id + "_Normal" | ||
| } | ||
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| output { | ||
| File cnv_postprocessing_aggregated_tumors_pre = TsvCatTumor.aggregated_tsv | ||
| File cnv_postprocessing_aggregated_tumors_post = TsvCatTumorGermlinePruned.aggregated_tsv | ||
| File cnv_postprocessing_aggregated_normals = TsvCatNormal.aggregated_tsv | ||
| } | ||
| } | ||
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| task TsvCat { | ||
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| String id | ||
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There was a problem hiding this comment. There is some white space funkiness here and throughout the other WDLs. There was a problem hiding this comment. Fixed it here. Will be on lookout in other files. |
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| Array[File] input_files | ||
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| command <<< | ||
| set -e | ||
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| head -1 ${input_files[0]} > ${id}.aggregated.seg | ||
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| for FILE in ${sep=" " input_files} | ||
| do | ||
| egrep -v "CONTIG|Chromosome" $FILE >> ${id}.aggregated.seg | ||
| done | ||
| >>> | ||
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| output { | ||
| File aggregated_tsv="${id}.aggregated.seg" | ||
| } | ||
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| runtime { | ||
| docker: "ubuntu:16.04" | ||
| memory: "2 GB" | ||
| cpu: "1" | ||
| disks: "local-disk 100 HDD" | ||
| } | ||
| } | ||
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Thanks for catching this. Can you do a find-and-replace on other instances? Should be a few more in the other somatic/germline WDLs as well as the docs. Also may be some instances of
PreprocessIntervals.padding.BTW, where are we with Cromwell exposing task-level parameters automatically for subworkflows? Do we still need to expose all parameters in this way?
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Done and done for padding as well.
Your comment here is related to broadinstitute/cromwell#2912 ... I have not heard about any update on this.