From 1a387b40ae610aa79fa807486d07aca9473c18c4 Mon Sep 17 00:00:00 2001
From: Aleksandra Galitsyna <agalitzina@gmail.com>
Date: Sun, 20 Mar 2022 22:26:31 +0300
Subject: [PATCH] Multiple complementarity rules added and tested.

---
 modules/rklib/rk_check_complementary/main.nf | 17 +++++++-----
 params-redc.yml                              | 28 +++++++++++++++-----
 subworkflows/local/oligos_map.nf             | 10 ++++++-
 3 files changed, 41 insertions(+), 14 deletions(-)

diff --git a/modules/rklib/rk_check_complementary/main.nf b/modules/rklib/rk_check_complementary/main.nf
index 308db07..dddec7b 100644
--- a/modules/rklib/rk_check_complementary/main.nf
+++ b/modules/rklib/rk_check_complementary/main.nf
@@ -7,7 +7,7 @@ options        = initOptions(params.options)
 def VERSION = '0.0'
 
 process RKLIB_CHECK_COMPLEMENTARY {
-    tag "$meta.id"
+    tag "$meta.id $meta_compl.id"
     label 'process_low'
     publishDir "${params.outdir}",
         mode: params.publish_dir_mode,
@@ -22,13 +22,14 @@ process RKLIB_CHECK_COMPLEMENTARY {
     val(meta_compl)
 
     output:
-    tuple val(meta), path("*.complHits.tsv"), emit: hits
+    tuple val(meta), path("*.tsv"), emit: hits
     path  "*.version.txt"         , emit: version
 
 
     script:
     def software = getSoftwareName(task.process)
     def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def complName = meta_compl.getOrDefault("id", "compl")
 
     def rna_compl_length = meta_compl.length as Integer
     def extraN = "N"*(500+3*rna_compl_length)
@@ -87,13 +88,17 @@ process RKLIB_CHECK_COMPLEMENTARY {
     # Merge two tabular outputs:
     # 1. Design header
     head -n 1 ${prefix}.hits_compl.R1.tsv \\
-     | sed 's/\\t/_compl_R1\\t/g' | sed 's/\$/_compl_R1/' | sed 's/#//g' | tr '\\n' '\\t' > ${prefix}.complHits.tsv
+     | sed 's/\\t/_${complName}_R1\\t/g' | sed 's/\$/_${complName}_R1/' | sed 's/#//g' | tr '\\n' '\\t' > ${prefix}.${complName}.tsv
     head -n 1 ${prefix}.hits_compl.R2.tsv \\
-     | sed 's/\\t/_compl_R2\\t/g' | sed 's/\$/_compl_R2/' | sed 's/#//g' | tr '\\n' '\\t' >> ${prefix}.complHits.tsv
-    sed -i "s/\\t\$/\\n/" ${prefix}.complHits.tsv
+     | sed 's/\\t/_${complName}_R2\\t/g' | sed 's/\$/_${complName}_R2/' | sed 's/#//g' | tr '\\n' '\\t' >> ${prefix}.${complName}.tsv
+    sed -i "s/\\t\$/\\n/" ${prefix}.${complName}.tsv
     # 2. Write to the body
     paste <(tail -n +2 ${prefix}.hits_compl.R1.tsv) \\
-        <(tail -n +2 ${prefix}.hits_compl.R2.tsv) >> ${prefix}.complHits.tsv
+        <(tail -n +2 ${prefix}.hits_compl.R2.tsv) >> ${prefix}.${complName}.tsv
+
+    # Remove temporary files:
+    rm ${prefix}.hits_compl.R1.tsv
+    rm ${prefix}.hits_compl.R2.tsv
 
     echo $VERSION > ${software}.version.txt
     """
diff --git a/params-redc.yml b/params-redc.yml
index 02cc43c..ddcdf34 100644
--- a/params-redc.yml
+++ b/params-redc.yml
@@ -1,4 +1,4 @@
-input: 'samplesheet_redc.csv' # required
+input: 'samplesheet_test.csv' # required
 cache: 'lenient'
 outdir: "output_redc/"
 enable_conda: true
@@ -106,6 +106,10 @@ oligos:
         expected_length: 16
         right_to_left: true # Search right-to-left (3'-5') instead of regular left-to-right (5'-3')
 
+# The output of "short_oligos" section will be added to the output stats as:
+# oligo_<title>_at_35
+# for example:
+# oligo_ga_at_35
 short_oligos:
     ga:
         sequence: 'GA'
@@ -120,13 +124,23 @@ short_oligos:
 #        position: 0
 #        side: 2
 
+# The output of the "complementary" section will be added to the output stats as:
+# start_hit_<title>_R1, end_hit_<title>_R1, start_hit_<title>_R2, end_hit_<title>_R2
+# for example:
+# start_hit_compl_R1, end_hit_compl_R1, start_hit_compl_R2, end_hit_compl_R2
 complementary:
-    length: 14
-    left_side: 1
-    left_reference_oligo: bridge_forward
-    right_side: 2
-    right_reference_oligo: ggg
-
+    compl:
+        length: 14
+        left_side: 1
+        left_reference_oligo: bridge_forward
+        right_side: 2
+        right_reference_oligo: ggg
+#    compl_additional:
+#        length: 8
+#        left_side: 1
+#        left_reference_oligo: bridge_forward
+#        right_side: 2
+#        right_reference_oligo: ggg
 
 fragments:
 #    dna_noext:
diff --git a/subworkflows/local/oligos_map.nf b/subworkflows/local/oligos_map.nf
index da2261b..e999fa0 100644
--- a/subworkflows/local/oligos_map.nf
+++ b/subworkflows/local/oligos_map.nf
@@ -100,7 +100,15 @@ workflow OLIGOS_MAP {
             HitsComplementary = Channel.empty()
         } else {
             /* Step 1: Collect information about left and right side of complementary regions */
-            ComplementaryInput = Channel.from(params.complementary)
+            ComplementaryInput  = Channel
+                           .from( params.complementary.keySet().withIndex() )
+                           .map { it, idx -> [it, idx, params.complementary[it]] } // meta for each complementary fragment
+                           .map { compl_name, idx, meta ->
+                                    meta.id = compl_name
+                                    meta.idx = idx
+                                    meta.single_end = true
+                                [meta]
+                           }.view()
 
             InputComplementary = TableChunks
                 .combine(IndexedFastqs)