From c2c1fb49326af40e4b243f1af11d6dabbe562adb Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Thu, 28 Nov 2024 10:54:14 +0100
Subject: [PATCH] fix bowtie2 options in ATAC

---
 workflows/epigenetics/atacseq/CHANGELOG.md |  8 +++++++
 workflows/epigenetics/atacseq/atacseq.ga   | 25 +++++++++-------------
 2 files changed, 18 insertions(+), 15 deletions(-)

diff --git a/workflows/epigenetics/atacseq/CHANGELOG.md b/workflows/epigenetics/atacseq/CHANGELOG.md
index 4b0e6dc95..2b737e9cc 100644
--- a/workflows/epigenetics/atacseq/CHANGELOG.md
+++ b/workflows/epigenetics/atacseq/CHANGELOG.md
@@ -1,5 +1,13 @@
 # Changelog
 
+## [1.0] 2024-11-28
+
+### Manual update
+
+Use the options like written in the README: in all previous versions, bowtie2 was running with `--very-sensitive` option but without allowing dovetail and without fragment length up to 1kb. Bowtie2 has been adjusted and is now running with these options: allow dovetail and fragment length up to 1kb.
+
+I am really sorry for this.
+
 ## [0.17] 2024-09-23
 
 ### Automatic update
diff --git a/workflows/epigenetics/atacseq/atacseq.ga b/workflows/epigenetics/atacseq/atacseq.ga
index a885049d5..664948390 100644
--- a/workflows/epigenetics/atacseq/atacseq.ga
+++ b/workflows/epigenetics/atacseq/atacseq.ga
@@ -11,7 +11,7 @@
     ],
     "format-version": "0.1",
     "license": "MIT",
-    "release": "0.17",
+    "release": "1.0",
     "name": "ATACseq",
     "steps": {
         "0": {
@@ -257,7 +257,7 @@
                 "owner": "devteam",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
-            "tool_state": "{\"__job_resource\": {\"__current_case__\": 0, \"__job_resource__select\": \"no\"}, \"analysis_type\": {\"analysis_type_selector\": \"simple\", \"__current_case__\": 0, \"presets\": \"--very-sensitive\"}, \"library\": {\"type\": \"paired_collection\", \"__current_case__\": 2, \"input_1\": {\"__class__\": \"ConnectedValue\"}, \"unaligned_file\": false, \"aligned_file\": false, \"paired_options\": {\"paired_options_selector\": \"no\", \"__current_case__\": 1}}, \"reference_genome\": {\"source\": \"indexed\", \"__current_case__\": 0, \"index\": {\"__class__\": \"ConnectedValue\"}}, \"rg\": {\"rg_selector\": \"do_not_set\", \"__current_case__\": 3}, \"sam_options\": {\"sam_options_selector\": \"no\", \"__current_case__\": 1}, \"save_mapping_stats\": true, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_state": "{\"analysis_type\": {\"analysis_type_selector\": \"simple\", \"__current_case__\": 0, \"presets\": \"--very-sensitive\"}, \"library\": {\"type\": \"paired_collection\", \"__current_case__\": 2, \"input_1\": {\"__class__\": \"RuntimeValue\"}, \"unaligned_file\": false, \"aligned_file\": false, \"paired_options\": {\"paired_options_selector\": \"yes\", \"__current_case__\": 0, \"I\": \"0\", \"X\": \"1000\", \"fr_rf_ff\": \"--fr\", \"no_mixed\": false, \"no_discordant\": false, \"dovetail\": true, \"no_contain\": false, \"no_overlap\": false}}, \"reference_genome\": {\"source\": \"indexed\", \"__current_case__\": 0, \"index\": {\"__class__\": \"ConnectedValue\"}}, \"rg\": {\"rg_selector\": \"do_not_set\", \"__current_case__\": 3}, \"sam_options\": {\"sam_options_selector\": \"no\", \"__current_case__\": 1}, \"save_mapping_stats\": true, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
             "tool_version": "2.5.3+galaxy1",
             "type": "tool",
             "uuid": "c32a3847-f673-487f-af98-8d50999f2d21",
@@ -433,15 +433,15 @@
             "uuid": "d0a9998c-18a9-4579-8d33-f0897e1ceaeb",
             "when": null,
             "workflow_outputs": [
-                {
-                    "label": "BAM filtered rmDup",
-                    "output_name": "outFile",
-                    "uuid": "5f4d5cc5-c2f2-40f3-b941-df5dd7347d25"
-                },
                 {
                     "label": "MarkDuplicates metrics",
                     "output_name": "metrics_file",
                     "uuid": "144745aa-8898-45e6-a328-53e2518202b9"
+                },
+                {
+                    "label": "BAM filtered rmDup",
+                    "output_name": "outFile",
+                    "uuid": "5f4d5cc5-c2f2-40f3-b941-df5dd7347d25"
                 }
             ]
         },
@@ -799,12 +799,7 @@
                     "output_name": "output2"
                 }
             },
-            "inputs": [
-                {
-                    "description": "runtime parameter for tool Search in textfiles",
-                    "name": "infile"
-                }
-            ],
+            "inputs": [],
             "label": "remove comments lines",
             "name": "Search in textfiles",
             "outputs": [
@@ -825,7 +820,7 @@
                 "owner": "bgruening",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
-            "tool_state": "{\"case_sensitive\": \"-i\", \"color\": \"NOCOLOR\", \"infile\": {\"__class__\": \"RuntimeValue\"}, \"invert\": \"-v\", \"lines_after\": \"0\", \"lines_before\": \"0\", \"regex_type\": \"-P\", \"url_paste\": \"^#\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_state": "{\"case_sensitive\": \"-i\", \"color\": \"NOCOLOR\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"invert\": \"-v\", \"lines_after\": \"0\", \"lines_before\": \"0\", \"regex_type\": \"-P\", \"url_paste\": \"^#\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
             "tool_version": "9.3+galaxy1",
             "type": "tool",
             "uuid": "c06960f8-9d4e-483e-8f07-12976f8b802a",
@@ -1709,6 +1704,6 @@
     "tags": [
         "ATACseq"
     ],
-    "uuid": "9debc3c9-ccbd-4ce6-a7de-80580e663cac",
+    "uuid": "747f2432-7493-44b8-a5ee-82d104407cad",
     "version": 1
 }
\ No newline at end of file