From d0aead9a8e89a7e16e7a72433233a0d4a0ef9f1d Mon Sep 17 00:00:00 2001
From: Edmund Miller <git@edmundmiller.dev>
Date: Sat, 30 Mar 2024 12:21:13 -0500
Subject: [PATCH] fix(dreg): Move all awk scripts to bin/

Also fixes a counting error
---
 .../local/dreg_prep/scripts => bin}/pe_1.awk  |   1 +
 .../local/dreg_prep/scripts => bin}/pe_2.awk  |   1 +
 .../local/dreg_prep/scripts => bin}/pe_3.awk  |   1 +
 .../scripts/pe_6.awk => bin/pe_4.awk          |   9 +-
 .../local/dreg_prep/scripts => bin}/pe_5.awk  |   8 +-
 .../scripts/pe_7.awk => bin/pe_6.awk          |   2 +
 .../scripts/pe_8.awk => bin/pe_7.awk          |   1 +
 .../scripts/pe_9.awk => bin/pe_8.awk          |   1 +
 .../local/dreg_prep/scripts => bin}/se_1.awk  |   1 +
 .../local/dreg_prep/scripts => bin}/se_2.awk  |   2 +
 .../local/dreg_prep/scripts => bin}/se_3.awk  |   2 +
 .../local/dreg_prep/scripts => bin}/se_4.awk  |   1 +
 modules/local/dreg_prep/templates/proseq2.0   |  26 ++--
 modules/local/dreg_prep/tests/main.nf.test    |   6 +-
 .../local/dreg_prep/tests/main.nf.test.snap   | 132 +++++++++++++++---
 15 files changed, 152 insertions(+), 42 deletions(-)
 rename {modules/local/dreg_prep/scripts => bin}/pe_1.awk (89%)
 mode change 100644 => 100755
 rename {modules/local/dreg_prep/scripts => bin}/pe_2.awk (90%)
 mode change 100644 => 100755
 rename {modules/local/dreg_prep/scripts => bin}/pe_3.awk (90%)
 mode change 100644 => 100755
 rename modules/local/dreg_prep/scripts/pe_6.awk => bin/pe_4.awk (90%)
 mode change 100644 => 100755
 rename {modules/local/dreg_prep/scripts => bin}/pe_5.awk (89%)
 mode change 100644 => 100755
 rename modules/local/dreg_prep/scripts/pe_7.awk => bin/pe_6.awk (89%)
 mode change 100644 => 100755
 rename modules/local/dreg_prep/scripts/pe_8.awk => bin/pe_7.awk (90%)
 mode change 100644 => 100755
 rename modules/local/dreg_prep/scripts/pe_9.awk => bin/pe_8.awk (89%)
 mode change 100644 => 100755
 rename {modules/local/dreg_prep/scripts => bin}/se_1.awk (91%)
 mode change 100644 => 100755
 rename {modules/local/dreg_prep/scripts => bin}/se_2.awk (90%)
 mode change 100644 => 100755
 rename {modules/local/dreg_prep/scripts => bin}/se_3.awk (78%)
 mode change 100644 => 100755
 rename {modules/local/dreg_prep/scripts => bin}/se_4.awk (84%)
 mode change 100644 => 100755

diff --git a/modules/local/dreg_prep/scripts/pe_1.awk b/bin/pe_1.awk
old mode 100644
new mode 100755
similarity index 89%
rename from modules/local/dreg_prep/scripts/pe_1.awk
rename to bin/pe_1.awk
index 97dc1612..2e99042f
--- a/modules/local/dreg_prep/scripts/pe_1.awk
+++ b/bin/pe_1.awk
@@ -1,3 +1,4 @@
+#!/bin/awk -f
 BEGIN {
 	OFS = "\t"
 }
diff --git a/modules/local/dreg_prep/scripts/pe_2.awk b/bin/pe_2.awk
old mode 100644
new mode 100755
similarity index 90%
rename from modules/local/dreg_prep/scripts/pe_2.awk
rename to bin/pe_2.awk
index fd965dbe..a7877105
--- a/modules/local/dreg_prep/scripts/pe_2.awk
+++ b/bin/pe_2.awk
@@ -1,3 +1,4 @@
+#!/bin/awk -f
 BEGIN {
 	OFS = "\t"
 }
diff --git a/modules/local/dreg_prep/scripts/pe_3.awk b/bin/pe_3.awk
old mode 100644
new mode 100755
similarity index 90%
rename from modules/local/dreg_prep/scripts/pe_3.awk
rename to bin/pe_3.awk
index f7a3fa4e..8ebf797d
--- a/modules/local/dreg_prep/scripts/pe_3.awk
+++ b/bin/pe_3.awk
@@ -1,3 +1,4 @@
+#!/bin/awk -f
 BEGIN {
 	OFS = "\t"
 }
diff --git a/modules/local/dreg_prep/scripts/pe_6.awk b/bin/pe_4.awk
old mode 100644
new mode 100755
similarity index 90%
rename from modules/local/dreg_prep/scripts/pe_6.awk
rename to bin/pe_4.awk
index bd492463..d48697e4
--- a/modules/local/dreg_prep/scripts/pe_6.awk
+++ b/bin/pe_4.awk
@@ -1,11 +1,12 @@
+#!/bin/awk -f
 BEGIN {
 	OFS = "\t"
 }
 
-($10 == "+") {
-	print $1, $5, $5 + 1, $7, $8, $10
-}
-
 ($10 == "-") {
 	print $1, $6 - 1, $6, $7, $8, $10
 }
+
+($10 == "+") {
+	print $1, $5, $5 + 1, $7, $8, $10
+}
diff --git a/modules/local/dreg_prep/scripts/pe_5.awk b/bin/pe_5.awk
old mode 100644
new mode 100755
similarity index 89%
rename from modules/local/dreg_prep/scripts/pe_5.awk
rename to bin/pe_5.awk
index f0d01a43..0e665204
--- a/modules/local/dreg_prep/scripts/pe_5.awk
+++ b/bin/pe_5.awk
@@ -1,11 +1,13 @@
+#!/bin/awk -f
 BEGIN {
 	OFS = "\t"
 }
 
+($10 == "+") {
+	print $1, $5, $5 + 1, $7, $8, $10
+}
+
 ($10 == "-") {
 	print $1, $6 - 1, $6, $7, $8, $10
 }
 
-($10 == "+") {
-	print $1, $5, $5 + 1, $7, $8, $10
-}
diff --git a/modules/local/dreg_prep/scripts/pe_7.awk b/bin/pe_6.awk
old mode 100644
new mode 100755
similarity index 89%
rename from modules/local/dreg_prep/scripts/pe_7.awk
rename to bin/pe_6.awk
index f7a3fa4e..f8c5f03d
--- a/modules/local/dreg_prep/scripts/pe_7.awk
+++ b/bin/pe_6.awk
@@ -1,3 +1,4 @@
+#!/bin/awk -f
 BEGIN {
 	OFS = "\t"
 }
@@ -9,3 +10,4 @@ BEGIN {
 ($9 == "-") {
 	print $1, $3 - 1, $3, $7, $8, $10
 }
+
diff --git a/modules/local/dreg_prep/scripts/pe_8.awk b/bin/pe_7.awk
old mode 100644
new mode 100755
similarity index 90%
rename from modules/local/dreg_prep/scripts/pe_8.awk
rename to bin/pe_7.awk
index cd31e86b..1c563bf5
--- a/modules/local/dreg_prep/scripts/pe_8.awk
+++ b/bin/pe_7.awk
@@ -1,3 +1,4 @@
+#!/bin/awk -f
 BEGIN {
 	OFS = "\t"
 }
diff --git a/modules/local/dreg_prep/scripts/pe_9.awk b/bin/pe_8.awk
old mode 100644
new mode 100755
similarity index 89%
rename from modules/local/dreg_prep/scripts/pe_9.awk
rename to bin/pe_8.awk
index 97dc1612..2e99042f
--- a/modules/local/dreg_prep/scripts/pe_9.awk
+++ b/bin/pe_8.awk
@@ -1,3 +1,4 @@
+#!/bin/awk -f
 BEGIN {
 	OFS = "\t"
 }
diff --git a/modules/local/dreg_prep/scripts/se_1.awk b/bin/se_1.awk
old mode 100644
new mode 100755
similarity index 91%
rename from modules/local/dreg_prep/scripts/se_1.awk
rename to bin/se_1.awk
index 9840d562..e66d6493
--- a/modules/local/dreg_prep/scripts/se_1.awk
+++ b/bin/se_1.awk
@@ -1,3 +1,4 @@
+#!/bin/awk -f
 BEGIN {
 	OFS = "\t"
 }
diff --git a/modules/local/dreg_prep/scripts/se_2.awk b/bin/se_2.awk
old mode 100644
new mode 100755
similarity index 90%
rename from modules/local/dreg_prep/scripts/se_2.awk
rename to bin/se_2.awk
index dffc0f17..2146f5e0
--- a/modules/local/dreg_prep/scripts/se_2.awk
+++ b/bin/se_2.awk
@@ -1,3 +1,4 @@
+#!/bin/awk -f
 BEGIN {
 	OFS = "\t"
 }
@@ -13,3 +14,4 @@ BEGIN {
 ($6 == "-") {
 	print $1, $3 - 1, $3, $4, $5, "+"
 }
+
diff --git a/modules/local/dreg_prep/scripts/se_3.awk b/bin/se_3.awk
old mode 100644
new mode 100755
similarity index 78%
rename from modules/local/dreg_prep/scripts/se_3.awk
rename to bin/se_3.awk
index 042c6b54..8d8ae15b
--- a/modules/local/dreg_prep/scripts/se_3.awk
+++ b/bin/se_3.awk
@@ -1,3 +1,4 @@
+#!/bin/awk -f
 BEGIN {
 	OFS = "\t"
 }
@@ -5,3 +6,4 @@ BEGIN {
 {
 	print $1, $2, $3, -1 * $4
 }
+
diff --git a/modules/local/dreg_prep/scripts/se_4.awk b/bin/se_4.awk
old mode 100644
new mode 100755
similarity index 84%
rename from modules/local/dreg_prep/scripts/se_4.awk
rename to bin/se_4.awk
index 69e6ac26..84682d9f
--- a/modules/local/dreg_prep/scripts/se_4.awk
+++ b/bin/se_4.awk
@@ -1,3 +1,4 @@
+#!/bin/awk -f
 BEGIN {
 	OFS = "\t"
 }
diff --git a/modules/local/dreg_prep/templates/proseq2.0 b/modules/local/dreg_prep/templates/proseq2.0
index a35213f4..3ca2f0bf 100755
--- a/modules/local/dreg_prep/templates/proseq2.0
+++ b/modules/local/dreg_prep/templates/proseq2.0
@@ -19,10 +19,10 @@ echo "Writing bigWigs:"
 if [[ "$meta.single_end" == "true" ]]; then
     echo "SE"
     if [[ "$assay_type" == "GROseq" ]]; then
-        bedtools bamtobed -i $bam_file | awk -f ${moduleDir}/scripts/se_1.awk | gzip >${prefix}.bed.gz
+        bedtools bamtobed -i $bam_file | se_1.awk | gzip >${prefix}.bed.gz
         #elif [[ "\${RNA3}" == "R1_5prime" && "\${OPP}" == "TRUE" ]] ; then  #like PRO-seq
     elif [[ "$assay_type" == "PROseq" ]]; then
-        bedtools bamtobed -i $bam_file | awk -f ${moduleDir}/scripts/se_2.awk | gzip >${prefix}.bed.gz
+        bedtools bamtobed -i $bam_file | se_2.awk | gzip >${prefix}.bed.gz
     fi
 else
     echo "PE"
@@ -31,17 +31,17 @@ else
         if true; then
             # HACK Map5 not supported for now
             if true; then ## report The 5' end of the RNA. Danko lab leChRO-Seq protocol is on the 5' of _R1 readl, same strand of R1 (\$9)
-                bedtools bamtobed -bedpe -mate1 -i $bam_file | awk -f ${moduleDir}/scripts/pe_1.awk | gzip >${prefix}.bed.gz
+                bedtools bamtobed -bedpe -mate1 -i $bam_file | pe_1.awk | gzip >${prefix}.bed.gz
             else ## report The 3' end of the RNA.  Danko lab leChRO-Seq protocol is on the 5 prime of _R2 read, opposite strand of R2 (R2 strand \$10, R1 strand \$9)
-                bedtools bamtobed -bedpe -mate1 -i $bam_file | awk -f ${moduleDir}/scripts/pe_2.awk | gzip >${prefix}.bed.gz
+                bedtools bamtobed -bedpe -mate1 -i $bam_file | pe_2.awk | gzip >${prefix}.bed.gz
             fi
         # HACK Opposite-strand not supported for now
         elif false; then
             # HACK Map5 not supported for now
             if true; then ## report The 5' end of the RNA.
-                bedtools bamtobed -bedpe -mate1 -i $bam_file | awk -f ${moduleDir}/scripts/pe_4.awk | gzip >${prefix}.bed.gz
+                bedtools bamtobed -bedpe -mate1 -i $bam_file | pe_3.awk | gzip >${prefix}.bed.gz
             else ## report The 3' end of the RNA.
-                bedtools bamtobed -bedpe -mate1 -i $bam_file | awk -f ${moduleDir}/scripts/pe_5.awk | gzip >${prefix}.bed.gz
+                bedtools bamtobed -bedpe -mate1 -i $bam_file | pe_4.awk | gzip >${prefix}.bed.gz
             fi
         fi
     elif [ "$assay_type" == "R2_5" ]; then
@@ -49,17 +49,17 @@ else
         if true; then
             # HACK Map5 not supported for now
             if true; then #report the 5 prime end of RNA, in Engreitz data is 5 prime end of R2, same strand
-                bedtools bamtobed -bedpe -mate1 -i $bam_file | awk -f ${moduleDir}/scripts/pe_6.awk | gzip >${prefix}.bed.gz
+                bedtools bamtobed -bedpe -mate1 -i $bam_file | pe_5.awk | gzip >${prefix}.bed.gz
             else ## report the 3-prime end of the RNA, in Engreitz data is the 5' end of R1 read, but opposite strand
-                bedtools bamtobed -bedpe -mate1 -i $bam_file | awk -f ${moduleDir}/scripts/pe_7.awk | gzip >${prefix}.bed.gz
+                bedtools bamtobed -bedpe -mate1 -i $bam_file | pe_6.awk | gzip >${prefix}.bed.gz
             fi
         # HACK Opposite-strand not supported for now
         elif false; then
             # HACK Map5 not supported for now
             if true; then #report the 5 prime end of RNA, in Engreitz data is 5 prime end of R2, same strand
-                bedtools bamtobed -bedpe -mate1 -i $bam_file | awk -f ${moduleDir}/scripts/pe_8.awk | gzip >${prefix}.bed.gz
+                bedtools bamtobed -bedpe -mate1 -i $bam_file | pe_7.awk | gzip >${prefix}.bed.gz
             else ## report the 3-prime end of the RNA, in Engreitz data is the 5' end of R1 read, but opposite strand
-                bedtools bamtobed -bedpe -mate1 -i $bam_file | awk -f ${moduleDir}/scripts/pe_8.awk | gzip >${prefix}.bed.gz
+                bedtools bamtobed -bedpe -mate1 -i $bam_file | pe_8.awk | gzip >${prefix}.bed.gz
             fi
         fi
     fi
@@ -79,11 +79,11 @@ bedtools genomecov -bg -i ${prefix}.nr.rs.bed.gz -g ${sizes} -strand + >${prefix
 bedtools genomecov -bg -i ${prefix}.nr.rs.bed.gz -g ${sizes} -strand - >${prefix}_minus.noinv.bedGraph
 
 ## Invert minus strand.
-cat ${prefix}_minus.noinv.bedGraph | awk -f ${moduleDir}/scripts/se_3.awk >${prefix}_minus.bedGraph ## Invert read counts on the minus strand.
+cat ${prefix}_minus.noinv.bedGraph | se_3.awk >${prefix}_minus.bedGraph ## Invert read counts on the minus strand.
 
 ## normalized by RPM
-cat ${prefix}_plus.bedGraph | awk -f ${moduleDir}/scripts/se_4.awk -v readCount="\$readCount" >${prefix}_plus.rpm.bedGraph
-cat ${prefix}_minus.bedGraph | awk -f ${moduleDir}/scripts/se_4.awk -v readCount="\$readCount" >${prefix}_minus.rpm.bedGraph
+cat ${prefix}_plus.bedGraph | se_4.awk -v readCount="\$readCount" >${prefix}_plus.rpm.bedGraph
+cat ${prefix}_minus.bedGraph | se_4.awk -v readCount="\$readCount" >${prefix}_minus.rpm.bedGraph
 ## Then to bigWig (nomalized and non-nomrmalized ones)
 bedGraphToBigWig ${prefix}_plus.rpm.bedGraph ${sizes} ${prefix}_plus.rpm.bw
 bedGraphToBigWig ${prefix}_minus.rpm.bedGraph ${sizes} ${prefix}_minus.rpm.bw
diff --git a/modules/local/dreg_prep/tests/main.nf.test b/modules/local/dreg_prep/tests/main.nf.test
index fe0e2f26..eaa93b4e 100644
--- a/modules/local/dreg_prep/tests/main.nf.test
+++ b/modules/local/dreg_prep/tests/main.nf.test
@@ -26,8 +26,7 @@ nextflow_process {
 
         then {
             assertAll(
-                // TODO
-                { assert process.failed },
+                { assert process.success },
                 { assert snapshot(process.out).match("paired-end") }
             )
         }
@@ -53,8 +52,7 @@ nextflow_process {
 
         then {
             assertAll(
-                // FIXME
-                { assert process.failed },
+                { assert process.success },
                 { assert snapshot(process.out).match("single-end") }
             )
         }
diff --git a/modules/local/dreg_prep/tests/main.nf.test.snap b/modules/local/dreg_prep/tests/main.nf.test.snap
index fae30cce..28a96876 100644
--- a/modules/local/dreg_prep/tests/main.nf.test.snap
+++ b/modules/local/dreg_prep/tests/main.nf.test.snap
@@ -3,28 +3,76 @@
         "content": [
             {
                 "0": [
-                    
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.dreg_plus.rpm.bw:md5,c723fc5bdb582655ea1aa1f324cb71b4"
+                    ]
                 ],
                 "1": [
-                    
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.dreg_minus.rpm.bw:md5,2c78d94d8abc4a2bad792fd597d434be"
+                    ]
                 ],
                 "2": [
-                    
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.dreg_plus.bw:md5,fd77f4d72b9f77ed71166d21de1b48bd"
+                    ]
                 ],
                 "3": [
-                    
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.dreg_minus.bw:md5,92c7a60a606a1668a388c3f45d8f07f0"
+                    ]
                 ],
                 "minus_bigwig": [
-                    
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.dreg_minus.bw:md5,92c7a60a606a1668a388c3f45d8f07f0"
+                    ]
                 ],
                 "minus_rpm_bigwig": [
-                    
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.dreg_minus.rpm.bw:md5,2c78d94d8abc4a2bad792fd597d434be"
+                    ]
                 ],
                 "plus_bigwig": [
-                    
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.dreg_plus.bw:md5,fd77f4d72b9f77ed71166d21de1b48bd"
+                    ]
                 ],
                 "plus_rpm_bigwig": [
-                    
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.dreg_plus.rpm.bw:md5,c723fc5bdb582655ea1aa1f324cb71b4"
+                    ]
                 ]
             }
         ],
@@ -32,34 +80,82 @@
             "nf-test": "0.8.4",
             "nextflow": "23.10.1"
         },
-        "timestamp": "2024-03-30T14:10:02.23320779"
+        "timestamp": "2024-03-30T14:19:05.327654675"
     },
     "paired-end": {
         "content": [
             {
                 "0": [
-                    
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.dreg_plus.rpm.bw:md5,289652b9b07dec1d0c402e0de9001d9b"
+                    ]
                 ],
                 "1": [
-                    
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.dreg_minus.rpm.bw:md5,5c7c70cecb2ff37236dffa8cd6e64e8f"
+                    ]
                 ],
                 "2": [
-                    
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.dreg_plus.bw:md5,7098afd4d0a3927a97bca0f390318ef0"
+                    ]
                 ],
                 "3": [
-                    
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.dreg_minus.bw:md5,6fc8a8d47c17b9c3e9fa00302cf4b388"
+                    ]
                 ],
                 "minus_bigwig": [
-                    
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.dreg_minus.bw:md5,6fc8a8d47c17b9c3e9fa00302cf4b388"
+                    ]
                 ],
                 "minus_rpm_bigwig": [
-                    
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.dreg_minus.rpm.bw:md5,5c7c70cecb2ff37236dffa8cd6e64e8f"
+                    ]
                 ],
                 "plus_bigwig": [
-                    
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.dreg_plus.bw:md5,7098afd4d0a3927a97bca0f390318ef0"
+                    ]
                 ],
                 "plus_rpm_bigwig": [
-                    
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.dreg_plus.rpm.bw:md5,289652b9b07dec1d0c402e0de9001d9b"
+                    ]
                 ]
             }
         ],
@@ -67,6 +163,6 @@
             "nf-test": "0.8.4",
             "nextflow": "23.10.1"
         },
-        "timestamp": "2024-03-30T14:09:52.151543045"
+        "timestamp": "2024-03-30T14:18:55.16822952"
     }
 }
\ No newline at end of file