From 9dde53baf21870dfed58215a913885f4c4500911 Mon Sep 17 00:00:00 2001
From: ekiernan <ekiernan@broadinstitute.org>
Date: Tue, 23 Jan 2024 15:36:20 -0500
Subject: [PATCH] remove parsebarcodes

---
 tasks/skylab/PairedTagUtils.wdl | 87 ---------------------------------
 1 file changed, 87 deletions(-)

diff --git a/tasks/skylab/PairedTagUtils.wdl b/tasks/skylab/PairedTagUtils.wdl
index c0cbdf60f1..67bae5fbc9 100644
--- a/tasks/skylab/PairedTagUtils.wdl
+++ b/tasks/skylab/PairedTagUtils.wdl
@@ -118,91 +118,4 @@ task AddBBTag {
         File bb_bam = "~{input_id}.bam.BB.bam"
     }
 }
-task ParseBarcodes {
-    input {
-        File atac_h5ad
-        File atac_fragment
-        Int nthreads = 1
-        String cpuPlatform = "Intel Cascade Lake"
-    }
 
-    String atac_base_name = basename(atac_h5ad, ".h5ad")
-    String atac_fragment_base = basename(atac_fragment, ".tsv")
-
-    Int machine_mem_mb = ceil((size(atac_h5ad, "MiB") + size(gex_h5ad, "MiB") + size(atac_fragment, "MiB")) * 3) + 10000
-    Int disk =  ceil((size(atac_h5ad, "GiB") + size(gex_h5ad, "GiB") + size(atac_fragment, "GiB")) * 5) + 10
-
-  parameter_meta {
-      atac_h5ad: "The resulting h5ad from the ATAC workflow."
-      atac_fragment: "The resulting fragment TSV from the ATAC workflow."
-  }
-
-  command <<<
-      set -e pipefail
-
-      python3 <<CODE
-
-      # set parameters
-      atac_h5ad = "~{atac_h5ad}"
-      atac_fragment = "~{atac_fragment}"
-
-    # import anndata to manipulate h5ad files
-      import anndata as ad
-      import pandas as pd
-      print("Reading ATAC h5ad:")
-      print("~{atac_h5ad}")
-      print("Read ATAC fragment file:")
-      print("~{atac_fragment}")
-    
-      atac_data = ad.read_h5ad("~{atac_h5ad}")
-      atac_tsv = pd.read_csv("~{atac_fragment}", sep="\t", names=['chr','start', 'stop', 'barcode','n_reads'])
-      whitelist_atac = pd.read_csv("~{atac_whitelist}", header=None, names=["atac_barcodes"])
-
-      # Separate out CB and preindex in the h5ad
-      print("Creating CB and preindex columns")
-      for x in range(len(atac_data.obs.index)):
-        CB = atac_data.obs.index[x][3:]
-        preindex = atac_data.obs.index[x][:3]
-        atac_data.obs.loc[atac_data.obs.index[x], 'CB'] = CB
-        atac_data.obs.loc[atac_data.obs.index[x], 'preindex'] = preindex
-      
-      # Indentify sample barcodes assigned to more than one cell barcode
-      print("Identifying sample barcodes asigned to multiple cell barcodes in h5ad")
-      list = []
-      for preindex in atac_data.obs.preindex:
-        if preindex not in list:
-          list.append(preindex)
-          CB = atac_data.obs.loc[atac_data.obs['preindex'] == preindex, "CB"]
-          if len(CB)>1:
-            atac_data.obs.loc[atac_data.obs['preindex'] == preindex, "Duplicates"] = '1'
-          else:
-            atac_data.obs.loc[atac_data.obs['preindex'] == preindex, "Duplicates"] = '0'
-
-      # Idenitfy the barcodes in the whitelist that match barcodes in datasets
-      atac_data.write_h5ad("~{atac_base_name}.h5ad")
-      df_fragment.to_csv("~{atac_fragment_base}.tsv", sep='\t', index=False, header = False)
-      CODE
-      
-      # sorting the file
-      echo "Sorting file"
-      sort -k1,1V -k2,2n "~{atac_fragment_base}.tsv" > "~{atac_fragment_base}.sorted.tsv"
-      echo "Starting bgzip"
-      bgzip "~{atac_fragment_base}.sorted.tsv"
-      echo "Starting tabix"
-      tabix -s 1 -b 2 -e 3 "~{atac_fragment_base}.sorted.tsv.gz"
-
-  >>>
-
-  runtime {
-      docker: "us.gcr.io/broad-gotc-prod/snapatac2:1.0.4-2.3.1-1700590229"
-      disks: "local-disk ~{disk} HDD"
-      memory: "${machine_mem_mb} MiB"
-      cpu: nthreads
-  }
-
-  output {
-      File atac_h5ad_file = "~{atac_base_name}.h5ad"
-      File atac_fragment_tsv = "~{atac_fragment_base}.sorted.tsv.gz"
-      File atac_fragment_tsv_tbi = "~{atac_fragment_base}.sorted.tsv.gz.tbi"
-  }
-}