From e2deaa1fbbe9dc32c208151a5489dc250c4b67dd Mon Sep 17 00:00:00 2001
From: ssnn-airr <20683719+ssnn-airr@users.noreply.github.com>
Date: Wed, 26 Jul 2023 12:59:37 +0200
Subject: [PATCH 1/2] updated config for threshold report with subsample

---
 conf/modules.config | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/conf/modules.config b/conf/modules.config
index 029b68af..0c5a3724 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -434,6 +434,12 @@ process {
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
+        ext.args = ['findthreshold_method':'gmm',
+            'findthreshold_model':'gamma-norm',
+            'findthreshold_edge':0.9,
+            'findthreshold_cutoff':'user',
+            'findthreshold_spc':0.995,
+            'subsample':10000]
     }
 
     withName: DEFINE_CLONES_COMPUTE {

From feedb3f52bad2f51c00ef2ec579eda517c7dbcba Mon Sep 17 00:00:00 2001
From: ssnn-airr <20683719+ssnn-airr@users.noreply.github.com>
Date: Tue, 1 Aug 2023 09:05:29 +0200
Subject: [PATCH 2/2] updated path for enchantr 0.1.4

---
 docs/output.md                           | 6 +++---
 modules/local/enchantr/find_threshold.nf | 4 ++--
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/docs/output.md b/docs/output.md
index e2477c8d..e6632c57 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -388,10 +388,10 @@ This folder is genereated when `detect_contamination` is set to `true`.
 
 - `clonal_analysis/find_threshold/`
   - `*log`: Log of the process that will be parsed to generate a report.
-  - `all_reps_threshold-mean.tsv`: Mean of all hamming distance thresholds of the
-    Junction regions as determined by Shazam.
-  - `all_reps_threshold-summary.tsv`: Thresholds for each group of `--cloneby` samples.
   - `all_reps_dist_report`: Report
+    - `tables/all_reps_threshold-mean.tsv`: Mean of all hamming distance thresholds of the
+    Junction regions as determined by Shazam.
+    - `tables/all_reps_threshold-summary.tsv`: Thresholds for each group of `--cloneby` samples.
 
 </details>
 
diff --git a/modules/local/enchantr/find_threshold.nf b/modules/local/enchantr/find_threshold.nf
index 32ff652e..a87759b1 100644
--- a/modules/local/enchantr/find_threshold.nf
+++ b/modules/local/enchantr/find_threshold.nf
@@ -36,8 +36,8 @@ process FIND_THRESHOLD {
     // tuple val(meta), path("*threshold-pass.tsv"), emit: tab // sequence tsv in AIRR format
     path("*_command_log.txt"), emit: logs //process logs
     path "*_report"
-    path "*_threshold-summary.tsv", emit: threshold_summary
-    path "*_threshold-mean.tsv", emit: mean_threshold
+    path "all_reps_dist_report/tables/*_threshold-summary.tsv", emit: threshold_summary
+    path "all_reps_dist_report/tables/*_threshold-mean.tsv", emit: mean_threshold
     path "versions.yml", emit: versions
 
     script: