Revert "Add filter_NonPassCalls_BCFtools"

This reverts commit 46e6c18.
uclahs-cds · Dec 18, 2021 · 7c8111d · 7c8111d
1 parent 46e6c18
commit 7c8111d
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Showing 4 changed files with 10 additions and 57 deletions.
diff --git a/pipeline/call-sSV.nf b/pipeline/call-sSV.nf
@@ -39,9 +39,9 @@ Starting workflow...
 .stripIndent()
 
 include { run_validate_PipeVal } from './modules/validation'
-include { query_SampleName_BCFtools; filter_NonPassCalls_BCFtools } from './modules/bcftools'
+include { query_SampleName_BCFtools } from './modules/bcftools'
 include { call_sSV_Delly; filter_sSV_Delly } from './modules/delly'
-include { generate_sha512; generate_sha512 as generate_sha512_NonPassFiltering } from './modules/sha512'
+include { generate_sha512 } from './modules/sha512'
 
 /**
 * Check the params
@@ -89,7 +89,7 @@ input_validation = Channel
 
 if (params.verbose){
     input_validation.view()
-    }
+}
 
 /**
 * Create input_paired_bams_ch to get the paired turmor sample and control sample
@@ -109,7 +109,7 @@ input_paired_bams_ch = Channel
 
 if (params.verbose){
     input_paired_bams_ch.view()
-    }
+}
 
 /**
 * Create tumor_bams_ch to only get the turmor samples.
@@ -129,7 +129,7 @@ tumor_bams_ch = Channel
 
 if (params.verbose){
     tumor_bams_ch.view()
-    }
+}
 
 workflow{
     /**
@@ -196,18 +196,5 @@ workflow{
     /**
     * Generate one sha512 checksum for the output files.
     */
-    generate_sha512(call_sSV_Delly.out.nt_call_bcf.mix(
-            call_sSV_Delly.out.nt_call_bcf_csi, 
-            filter_sSV_Delly.out.somatic_bcf, 
-            filter_sSV_Delly.out.somatic_bcf_csi))
-
-    /**
-    * Call "bcftools view -i 'FILTER=="PASS"' -O b -o "non_pass_filtered_${input_bcf}" $input_bcf"
-    * to filter out NonPass calls
-    * and further generate sha512 for the output
-    */
-    if (params.non_pass_filtering) {
-        filter_NonPassCalls_BCFtools(filter_sSV_Delly.out.somatic_bcf)
-        generate_sha512_NonPassFiltering(filter_NonPassCalls_BCFtools.out.nonPassCallsFiltered.mix(filter_NonPassCalls_BCFtools.out.nonPassCallsFiltered_csi))
-        }
+    generate_sha512(call_sSV_Delly.out.nt_call_bcf.mix(call_sSV_Delly.out.nt_call_bcf_csi, filter_sSV_Delly.out.filtered_somatic_bcf, filter_sSV_Delly.out.filtered_somatic_bcf_csi))
     }
diff --git a/pipeline/config/nextflow.config b/pipeline/config/nextflow.config
@@ -30,8 +30,6 @@ params {
     map_qual = 20
     min_clique_size = 5
     mad_cutoff = 15
-
-    non_pass_filtering = true
     }
 
 includeConfig "${projectDir}/config/methods.config"

diff --git a/pipeline/modules/bcftools.nf b/pipeline/modules/bcftools.nf
@@ -39,35 +39,4 @@ process query_SampleName_BCFtools {
 
         paste ${tmp_samples} samples_type > "${tmp_samples}.tsv"
         """
-    }
-
-process filter_NonPassCalls_BCFtools {
-    container params.docker_image_bcftools
-
-    publishDir "${params.output_dir}/output",
-        pattern: "${filename_base}_nonPassCallsFiltered.bcf*",
-        mode: "copy"
-
-    publishDir "${params.log_output_dir}/process-log",
-        pattern: ".command.*",
-        mode: "copy",
-        saveAs: { "${task.process.replace(':', '/')}/log${file(it).getName()}" }
-
-    input:
-        path input_bcf
-
-    output:
-        path ".command.*"
-        path "${filename_base}_nonPassCallsFiltered.bcf", emit: nonPassCallsFiltered
-        path "${filename_base}_nonPassCallsFiltered.bcf.csi", emit: nonPassCallsFiltered_csi
-
-    script:
-        filename_base = file(input_bcf).baseName
-        """
-        set -euo pipefail
-
-        bcftools view -i 'FILTER=="PASS"' -O b -o "${filename_base}_nonPassCallsFiltered.bcf" $input_bcf
-        
-        bcftools index "${filename_base}_nonPassCallsFiltered.bcf"
-        """
     }
diff --git a/pipeline/modules/delly.nf b/pipeline/modules/delly.nf
@@ -54,7 +54,7 @@ process filter_sSV_Delly{
     container params.docker_image_delly
 
     publishDir "$params.output_dir/output",
-        pattern: "${filename_base}_somatic.bcf*",
+        pattern: "filtered_somatic_${tumor_sample_name}.bcf*",
         mode: "copy"
 
     publishDir "$params.log_output_dir/process-log",
@@ -69,14 +69,13 @@ process filter_sSV_Delly{
         val tumor_sample_name
 
     output:
-        path "${filename_base}_somatic.bcf", emit: somatic_bcf
-        path "${filename_base}_somatic.bcf.csi", emit: somatic_bcf_csi
+        path "filtered_somatic_${tumor_sample_name}.bcf", emit: filtered_somatic_bcf
+        path "filtered_somatic_${tumor_sample_name}.bcf.csi", emit: filtered_somatic_bcf_csi
         path ".command.*"
 
     script:
-        filename_base = file(input_bcf).baseName
         """
         set -euo pipefail
-        delly filter -f somatic -s ${samples} -o ${filename_base}_somatic.bcf "$input_bcf"
+        delly filter -f somatic -s ${samples} -o filtered_somatic_${tumor_sample_name}.bcf "$input_bcf"
         """
     }