[MODIF] fix pairtools subwkflow

nservant · Dec 22, 2023 · 66d4791 · 66d4791
1 parent fbb7680
commit 66d4791
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Showing 2 changed files with 59 additions and 40 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -142,7 +142,6 @@ process {
             [
                 path: { "${params.outdir}/hicpro/valid_pairs" },
                 mode: 'copy',
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
                 pattern: "*Pairs"
             ]
         ]
@@ -152,7 +151,6 @@ process {
     withName: 'MERGE_STATS' {
         publishDir = [
             path: { "${params.outdir}/hicpro/stats/${meta.id}" },
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
             mode: 'copy',
             pattern: "*stat"
         ]
@@ -190,14 +188,17 @@ process {
        publishDir = [
             path: { "${params.outdir}/bwa" },
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
-            mode: 'copy'
+            mode: 'copy',
+            enabled: params.save_aligned_intermediates
         ]
         ext.args = params.bwa_opts ?: ''
     }
 
     withName: 'PAIRTOOLS_PARSE' {
         publishDir = [
-            enabled: false
+            path: { "${params.outdir}/pairtools/stats/" },
+            mode: 'copy',
+            pattern: "*pairsam.stat"
         ]
         ext.args = { [
             '--add-columns mapq',
@@ -226,49 +227,64 @@ process {
     withName: 'PAIRTOOLS_MERGE' {
         publishDir = [
             enabled: false
-	    ]
+        ]
         ext.prefix = { "${meta.id}_merged" }
     }
 
-    withName: 'PAIRTOOLS_DEDUP' {
+    withName: 'PAIRTOOLS_SPLIT' {
         publishDir = [
-            enabled: false
+            path: { "${params.outdir}/pairtools" },
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+            mode: 'copy',
+            pattern: "*pairs.gz",
+            enabled: params.save_pairs_intermediates
         ]
-        ext.args = { "--mark-dups" }
-        ext.prefix = { "${meta.id}_dedup" }
-        ext.when = !params.keep_dups
+        ext.args = { params.save_interaction_bam ? "--output-sam ${meta.id}_pairtools.bam" : '' }
+    }
+
+    withName: 'SAMTOOLS_SORT' {
+      publishDir = [
+            path: { "${params.outdir}/pairtools" },
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+            mode: 'copy',
+            enabled: params.save_pairs_intermediates
+        ]
+      ext.prefix = { "${meta.id}_pairtools_sorted" }
     }
 
-    withName: 'PAIRTOOLS_SPLIT' {
-        publishDir = [
+    withName: 'SAMTOOLS_INDEX' {
+      publishDir = [
             path: { "${params.outdir}/pairtools" },
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
             mode: 'copy',
             enabled: params.save_pairs_intermediates
         ]
-        ext.args = { params.save_interaction_bam ? "--output-sam ${meta.id}_pairtools.bam" : '' }
+    }
+
+    withName: 'PAIRTOOLS_DEDUP' {
+        publishDir = [
+            path: { "${params.outdir}/pairtools/stats/" },
+            mode: 'copy',
+            pattern: "*.pairs.stat"
+        ]
+        ext.args = { "--mark-dups" }
+	ext.prefix = { "${meta.id}_dedup" }
+        ext.when = !params.keep_dups
     }
 
     withName: 'PAIRTOOLS_SELECT' {
         publishDir = [
-            [
-                path: { "${params.outdir}/pairtools/" },
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
-                mode: 'copy',
-                pattern: "*pairs.gz"
-            ],
-            [
-                path: { "${params.outdir}/pairtools/stats/" },
-                mode: 'copy',
-                pattern: "*stats.txt"
-            ]
+            path: { "${params.outdir}/pairtools/" },
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+            mode: 'copy',
+            pattern: "*pairs.gz"
         ]
         ext.args = { [
             params.min_mapq > 0 ? "(mapq1>${params.min_mapq} and mapq2>${params.min_mapq})" : '',
-            params.min_cis_dist > 0 ? " and (abs(pos1-pos2) > ${params.min_cis_dist})" : '',
-            params.keep_multi ? " and ((pair_type=='UU') or (pair_type=='UR') or (pair_type=='RU') or (pair_type=='MM') or (pair_type=='MU'))" : 
-                                " and ((pair_type=='UU') or (pair_type=='UR') or (pair_type=='RU'))",
-            params.dnase ? '' : " and (abs(int(rfrag1) - int(rfrag2)) > 1)",
+            params.min_cis_dist > 0 ? " and ((chrom1==chrom2 and abs(pos1-pos2) > ${params.min_cis_dist}) or chrom1!=chrom2)" : '',
+            params.keep_multi ? " and ((pair_type.upper()=='UU') or (pair_type.upper()=='UR') or (pair_type.upper()=='RU') or (pair_type.upper()=='MM') or (pair_type.upper()=='MU'))" : 
+                                " and ((pair_type.upper()=='UU') or (pair_type.upper()=='UR') or (pair_type.upper()=='RU'))",
+            params.dnase ? '' : " and ((chrom1==chrom2 and abs(int(rfrag1) - int(rfrag2)) > 1) or chrom1!=chrom2)",
             //params.min_insert_size > 0 ?  " and ( (rfrag_end1 - r1pos) + (rfrag_end2 - r2pos)) > ${params.min_insert_size}" : '',
             //params.max_insert_size > 0 ? " and ( (rfrag_end1 - r1pos) + (rfrag_end2 - r2pos)) < ${params.max_insert_size}" : '',
             //params.min_restriction_fragment_size > 0 ? " -t ${params.min_restriction_fragment_size}" : '',
@@ -278,10 +294,11 @@ process {
 
     withName: 'PAIRTOOLS_STATS' {
         publishDir = [
-            path: { "${params.outdir}/pairtools/stats/" },                                                                                                                                               
+            path: { "${params.outdir}/pairtools/stats/" },
             mode: 'copy',
-            pattern: "*stats.txt"                                                                                                                                                                        
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
+        ext.prefix = { "${meta.id}_select.pairs.stat" }
     }
 
     withName: 'PAIRIX' {

diff --git a/subworkflows/local/pairtools.nf b/subworkflows/local/pairtools.nf
@@ -68,17 +68,12 @@ workflow PAIRTOOLS {
     ch_valid_pairs.multiple
   )
 
-  PAIRTOOLS_MERGE.out.pairs.mix(ch_valid_pairs.single).view()
-
-  PAIRTOOLS_DEDUP(
-    PAIRTOOLS_MERGE.out.pairs.mix(ch_valid_pairs.single)
-  )
-
-  ch_pairsam2split = params.keep_dups ? PAIRTOOLS_MERGE.out.pairs.mix(ch_valid_pairs.single) : PAIRTOOLS_DEDUP.out.pairs
+  // Separate pairs/bam files
   PAIRTOOLS_SPLIT(
-    ch_pairsam2split
+    PAIRTOOLS_MERGE.out.pairs.mix(ch_valid_pairs.single)
   )
 
+  // Manage BAM files
   SAMTOOLS_SORT(
     PAIRTOOLS_SPLIT.out.bam
   )
@@ -87,12 +82,19 @@ workflow PAIRTOOLS {
     SAMTOOLS_SORT.out.bam
   )
 
-  PAIRTOOLS_SELECT(
+  // TODO - add samtools flagstat
+
+  PAIRTOOLS_DEDUP(
     PAIRTOOLS_SPLIT.out.pairs
   )
 
+  ch_pairselect = params.keep_dups ? PAIRTOOLS_SPLIT.out.pairs : PAIRTOOLS_DEDUP.out.pairs
+  PAIRTOOLS_SELECT(
+    ch_pairselect
+  )
+
   PAIRTOOLS_STATS(
-    PAIRTOOLS_SPLIT.out.pairs
+    PAIRTOOLS_SELECT.out.selected
   )
 
   PAIRIX(