Merge pull request #4 from BertGalle/project1

Added merge count files per pool
nf-cmgg · Apr 23, 2024 · 84f9766 · 84f9766
2 parents 6810f0d + ffc19c7
commit 84f9766
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Showing 2 changed files with 55 additions and 5 deletions.
diff --git a/modules/local/exomedepth/merge_count/main.nf b/modules/local/exomedepth/merge_count/main.nf
@@ -0,0 +1,23 @@
+// MERGE COUNT FILES
+process EXOMEDEPTH_COUNT_MERGE {
+    publishDir "$params.outdir/exomedepth/counts", mode: 'copy'
+
+    input:
+    tuple val(meta), path(files)
+
+    output:
+    tuple val(meta), path("${prefix}.txt")
+
+    script:
+    prefix = task.ext.prefix ?: "${meta.id}_${meta.chr}"
+    """
+    for file in $files; do
+        if [ -f ${prefix}.txt ]; then
+            paste ${prefix}.txt <(awk '{print \$5}' \$file) > temp_auto.txt
+            mv temp_auto.txt ${prefix}.txt
+            else
+            cp \$file ${prefix}.txt
+        fi
+    done
+    """
+}
diff --git a/workflows/exomecnv.nf b/workflows/exomecnv.nf
@@ -11,9 +11,12 @@ include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pi
 include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_exomecnv_pipeline'
 
 // local
-include { CRAM_PREPARE    } from '../subworkflows/local/cram_prepare/main'
-include { EXOMEDEPTH_COUNT as COUNT_X   } from '../subworkflows/local/exomedepth_count/main'
-include { EXOMEDEPTH_COUNT as COUNT_AUTO  } from '../subworkflows/local/exomedepth_count/main'
+include { CRAM_PREPARE                               } from '../subworkflows/local/cram_prepare/main'
+include { EXOMEDEPTH_COUNT as COUNT_X                } from '../subworkflows/local/exomedepth_count/main'
+include { EXOMEDEPTH_COUNT as COUNT_AUTO             } from '../subworkflows/local/exomedepth_count/main'
+include { EXOMEDEPTH_COUNT_MERGE as COUNT_MERGE_AUTO } from '../modules/local/exomedepth/merge_count/main'
+include { EXOMEDEPTH_COUNT_MERGE as COUNT_MERGE_X    } from '../modules/local/exomedepth/merge_count/main'
+
 
 // include { BAM_VARIANT_CALLING_EXOMEDEPTH } from '../subworkflows/local/bam_variant_calling_exomedepth/main'
 /*
@@ -42,8 +45,10 @@ workflow EXOMECNV {
                 BAM: cram.extension == "bam"
             }
             .set{ ch_input_prepare }
-    // ch_input_prepare.BAM.view { "BAM: $it" }
-    // ch_input_prepare.CRAM.view { "CRAM: $it" }
+
+
+    //ch_input_prepare.BAM.view { "BAM: $it" }
+    //ch_input_prepare.CRAM.view { "CRAM: $it" }
 
 
     ch_fasta        = Channel.fromPath(params.fasta).map{ [[id:"reference"], it]}.collect()
@@ -74,10 +79,32 @@ workflow EXOMECNV {
     COUNT_AUTO (
         ch_input_bam, ch_roi_auto
     )
+
+    grouped_counts_auto = COUNT_AUTO.out.count
+        .map { meta, txt ->
+            def new_meta = [id:meta.pool,chr:"autosomal"]
+            [new_meta, txt]
+    }
+    .groupTuple()
+
+    COUNT_MERGE_AUTO (
+        grouped_counts_auto
+    )
+
     COUNT_X (
         ch_input_bam, ch_roi_x
     )
 
+    grouped_counts_X = COUNT_X.out.count
+        .map { meta, txt ->
+            def new_meta = [id:meta.pool,chr:"chrX"]
+            [new_meta, txt]
+    }
+    .groupTuple()
+
+    COUNT_MERGE_X (
+        grouped_counts_X
+    )
     //
     // Collate and save software versions
     //