From d70a54308963bdbf4873ca988576ba5119062e0d Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Fri, 1 Dec 2023 17:02:46 -0500
Subject: [PATCH] fix: keep all peaks during norm, only keep best for consensus

---
 .../templates/format_merged_bed.R             |  2 +-
 .../templates/normalize_peaks.R               |  1 -
 .../CCBR/custom/normalizepeaks/test.yml       |  4 +--
 .../CCBR/consensus_peaks/test.yml             | 30 ++++++++-----------
 4 files changed, 15 insertions(+), 22 deletions(-)

diff --git a/modules/CCBR/custom/formatmergedbed/templates/format_merged_bed.R b/modules/CCBR/custom/formatmergedbed/templates/format_merged_bed.R
index f202174..adc220e 100644
--- a/modules/CCBR/custom/formatmergedbed/templates/format_merged_bed.R
+++ b/modules/CCBR/custom/formatmergedbed/templates/format_merged_bed.R
@@ -49,7 +49,7 @@ select_best_peak <- function(dat_row) {
     dat_row %>%
       vec_to_df() %>%
       pivot_collapsed_columns() %>%
-      slice_max(pvalue)
+      slice_max(pvalue, n = 1, with_ties = FALSE)
   )
 }
 
diff --git a/modules/CCBR/custom/normalizepeaks/templates/normalize_peaks.R b/modules/CCBR/custom/normalizepeaks/templates/normalize_peaks.R
index aec4054..c98f44e 100644
--- a/modules/CCBR/custom/normalizepeaks/templates/normalize_peaks.R
+++ b/modules/CCBR/custom/normalizepeaks/templates/normalize_peaks.R
@@ -49,7 +49,6 @@ normalize <- function(peak_dat, norm_method = corces) {
         pvalue_norm = norm_method(pvalue),
         qvalue_norm = 10^(-pvalue_norm) %>% p.adjust(method = "BH") %>% -log10(.)
       ) %>%
-      slice_max(pvalue_norm, n = 1, with_ties = FALSE) %>%
       select(-c(pvalue, qvalue)) %>%
       rename(pvalue = pvalue_norm, qvalue = qvalue_norm)
   )
diff --git a/tests/modules/CCBR/custom/normalizepeaks/test.yml b/tests/modules/CCBR/custom/normalizepeaks/test.yml
index 9dfa78c..f57ca7d 100644
--- a/tests/modules/CCBR/custom/normalizepeaks/test.yml
+++ b/tests/modules/CCBR/custom/normalizepeaks/test.yml
@@ -5,9 +5,9 @@
     - custom
   files:
     - path: output/custom_normalizepeaks/SPT5_T0_1_peaks.broadPeak.norm.bed
-      md5sum: 7129eb9aa8927da730105395afab08b7
+      md5sum: b330f110355268468fd775945de0e0d3
     - path: output/custom_normalizepeaks/SPT5_T0_2_peaks.broadPeak.norm.bed
-      md5sum: b0be5d27ea40294c99ba48275dd0e54c
+      md5sum: 16dbbb977799d4b4c8051673671730ad
     - path: output/custom_normalizepeaks/versions.yml
 
 - name: custom normalizepeaks test_custom_normalizepeaks stub
diff --git a/tests/subworkflows/CCBR/consensus_peaks/test.yml b/tests/subworkflows/CCBR/consensus_peaks/test.yml
index 1d2d6e4..0031535 100644
--- a/tests/subworkflows/CCBR/consensus_peaks/test.yml
+++ b/tests/subworkflows/CCBR/consensus_peaks/test.yml
@@ -1,8 +1,6 @@
 - name: consensus_peaks test_consensus_peaks_broad
   command: nextflow run ./tests/subworkflows/CCBR/consensus_peaks -entry test_consensus_peaks_broad -c ./tests/config/nextflow.config
   tags:
-    - bedops
-    - bedops/bedmap
     - bedtools
     - bedtools/merge
     - cat
@@ -27,8 +25,6 @@
 - name: consensus_peaks test_consensus_peaks_mix_norm
   command: nextflow run ./tests/subworkflows/CCBR/consensus_peaks -entry test_consensus_peaks_mix_norm -c ./tests/config/nextflow.config
   tags:
-    - bedops
-    - bedops/bedmap
     - bedtools
     - bedtools/merge
     - cat
@@ -42,35 +38,33 @@
     - subworkflows/consensus_peaks
   files:
     - path: output/bedtools_merge/macs_broad.sorted.merged.bed
-      md5sum: 91dccf5c4f870193980bd298aa03864c
+      md5sum: 3188e022fc25c39a1de73732325fa5c5
     - path: output/bedtools_merge/macs_narrow.sorted.merged.bed
-      md5sum: 51d897e9f46241f7dadfd5bacd023660
+      md5sum: ed5b8726a6e78d1a79cdc1cb02c5858a
     - path: output/cat_cat/macs_broad.bed
-      md5sum: 1789beed3cb0688990ecca83344a8584
+      md5sum: 64bdb72657a26b8bc963f9bd51f39565
     - path: output/cat_cat/macs_narrow.bed
-      md5sum: 063aaba2588582642cab5d511b48482c
+      md5sum: 3974447bc99fc4930b56e171e545bc14
     - path: output/custom_formatmergedbed/macs_broad.sorted.merged.consensus.bed
-      md5sum: 7129eb9aa8927da730105395afab08b7
+      md5sum: 4f4d67389a8e327f21c0fd6d0d482780
     - path: output/custom_formatmergedbed/macs_narrow.sorted.merged.consensus.bed
-      md5sum: 2be28874a8902c61b82db0fecea29dd0
+      md5sum: 51fee8455d9357b659d7c463c26e8158
     - path: output/custom_normalizepeaks/SPT5_T0_1_peaks.broadPeak.norm.bed
-      md5sum: 7129eb9aa8927da730105395afab08b7
+      md5sum: b330f110355268468fd775945de0e0d3
     - path: output/custom_normalizepeaks/SPT5_T0_1_peaks.narrowPeak.norm.bed
-      md5sum: 3a12d0a9387d254273bbeb805ff68bce
+      md5sum: eb5a5ab58387a4fa1c0075056d92a7a9
     - path: output/custom_normalizepeaks/SPT5_T0_2_peaks.broadPeak.norm.bed
-      md5sum: b0be5d27ea40294c99ba48275dd0e54c
+      md5sum: 16dbbb977799d4b4c8051673671730ad
     - path: output/custom_normalizepeaks/SPT5_T0_2_peaks.narrowPeak.norm.bed
-      md5sum: e09e72701b3e85583ba505cdc495e64e
+      md5sum: 3ba07679762e76500620f567e24981e6
     - path: output/sort_bed/macs_broad.sorted.bed
-      md5sum: 1789beed3cb0688990ecca83344a8584
+      md5sum: 04af21722ca9e0ea2742f993a124347e
     - path: output/sort_bed/macs_narrow.sorted.bed
-      md5sum: 063aaba2588582642cab5d511b48482c
+      md5sum: 50f27baf1c44165833ed8e44b627834d
 
 - name: consensus_peaks test_consensus_peaks_broad stub
   command: nextflow run ./tests/subworkflows/CCBR/consensus_peaks -entry test_consensus_peaks_broad -c ./tests/config/nextflow.config -stub
   tags:
-    - bedops
-    - bedops/bedmap
     - bedtools
     - bedtools/merge
     - cat