Merge pull request #1125 from planemo-autoupdate/workflows/epigenetics/cutandrun

Updating workflows/epigenetics/cutandrun from 0.15 to 0.16

Author: mvdbeek

workflows/epigenetics/cutandrun/CHANGELOG.md

@@ -1,5 +1,10 @@
 # Changelog
 
+## [0.16] - 2026-03-02
+
+### Automatic update
+- `toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/5.2+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/5.2+galaxy1`
+
 ## [0.15] - 2026-01-19
 
 ### Automatic update

workflows/epigenetics/cutandrun/cutandrun.ga

@@ -177,7 +177,7 @@
         },
         "6": {
             "annotation": "",
-            "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/5.2+galaxy0",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/5.2+galaxy1",
             "errors": null,
             "id": 6,
             "input_connections": {
@@ -235,16 +235,16 @@
                     "output_name": "report"
                 }
             },
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/5.2+galaxy0",
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/5.2+galaxy1",
             "tool_shed_repository": {
-                "changeset_revision": "8e264b67a8c0",
+                "changeset_revision": "5d00fd7847eb",
                 "name": "cutadapt",
                 "owner": "lparsons",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
             "tool_state": "{\"adapter_options\": {\"action\": \"trim\", \"error_rate\": \"0.1\", \"no_indels\": false, \"times\": \"1\", \"overlap\": \"3\", \"match_read_wildcards\": false, \"no_match_adapter_wildcards\": true, \"revcomp\": false}, \"filter_options\": {\"discard_trimmed\": false, \"discard_untrimmed\": false, \"minimum_length\": \"15\", \"minimum_length2\": null, \"maximum_length\": null, \"maximum_length2\": null, \"max_n\": null, \"max_expected_errors\": null, \"max_average_error_rate\": null, \"discard_casava\": false, \"pair_filter\": \"any\"}, \"library\": {\"type\": \"paired_collection\", \"__current_case__\": 2, \"input_1\": {\"__class__\": \"ConnectedValue\"}, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"adapter_source_list\": \"user\", \"__current_case__\": 0, \"adapter_name\": \"Please use: For R1: - For TrueSeq (CUT and RUN): GATCGGAAGAGCACACGTCTGAACTCCAGTCAC or AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC - For Nextera (CUT and TAG): CTGTCTCTTATACACATCTCCGAGCCCACGAGAC \", \"adapter\": {\"__class__\": \"ConnectedValue\"}}, \"single_noindels\": false}], \"front_adapters\": [], \"anywhere_adapters\": []}, \"r2\": {\"adapters2\": [{\"__index__\": 0, \"adapter_source\": {\"adapter_source_list\": \"user\", \"__current_case__\": 0, \"adapter_name\": \"Please use: For R2: - For TruSeq (CUT and RUN): GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT or AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT - For Nextera (CUT and TAG): CTGTCTCTTATACACATCTGACGCTGCCGACGA\", \"adapter\": {\"__class__\": \"ConnectedValue\"}}, \"single_noindels\": false}], \"front_adapters2\": [], \"anywhere_adapters2\": []}, \"pair_adapters\": false}, \"other_trimming_options\": {\"cut\": \"0\", \"cut2\": \"0\", \"quality_cutoff\": \"30\", \"quality_cutoff2\": \"\", \"nextseq_trim\": \"0\", \"trim_n\": false, \"poly_a\": false, \"shorten_options\": {\"shorten_values\": \"False\", \"__current_case__\": 1}, \"shorten_options_r2\": {\"shorten_values_r2\": \"False\", \"__current_case__\": 1}}, \"output_selector\": [\"report\"], \"read_mod_options\": {\"strip_suffix\": \"\", \"length_tag\": \"\", \"rename\": \"\", \"zero_cap\": false}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
             "tool_uuid": null,
-            "tool_version": "5.2+galaxy0",
+            "tool_version": "5.2+galaxy1",
             "type": "tool",
             "uuid": "774b0604-628f-46a1-9088-a59d082e5317",
             "when": null,
@@ -857,7 +857,7 @@
     "tags": [
         "CUTnRUN"
     ],
-    "uuid": "9df1ca74-5b5c-4a83-88e3-a3fdf44d8a68",
+    "uuid": "e171ebbb-42f3-404b-822b-a1c125204774",
     "version": 1,
-    "release": "0.15"
+    "release": "0.16"
 }