Updating workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-variant-calling from 0.5.4 to 0.5.5

Author: planemo-autoupdate

workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-variant-calling/CHANGELOG.md

@@ -1,5 +1,12 @@
 # Changelog
 
+## [0.5.5] - 2025-06-09
+
+### Automatic update
+- `toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.24.0+galaxy4` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.24.3+galaxy0`
+- `toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.18` was updated to `toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.19`
+- `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.5+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.5+galaxy2`
+
 ## [0.5.4] - 2025-03-17
 
 ### Automatic update

workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-variant-calling/pe-artic-variation.ga

@@ -1,6 +1,7 @@
 {
     "a_galaxy_workflow": "true",
     "annotation": "The workflow for Illumina-sequenced ARTIC data builds on the RNASeq workflow for paired-end data using the same steps for mapping and variant calling, but adds extra logic for trimming ARTIC primer sequences off reads with the ivar package. In addition, this workflow uses ivar also to identify amplicons affected by ARTIC primer-binding site mutations and tries to exclude reads derived from such tainted amplicons when calculating allele-frequencies of other variants.",
+    "comments": [],
     "creator": [
         {
             "class": "Person",
@@ -11,7 +12,6 @@
     "format-version": "0.1",
     "license": "MIT",
     "name": "COVID-19: variation analysis on ARTIC PE data",
-    "release": "0.5.4",
     "steps": {
         "0": {
             "annotation": "Illumina reads from ARTIC assay with fastqsanger encoding",
@@ -231,7 +231,7 @@
         },
         "8": {
             "annotation": "",
-            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.24.0+galaxy4",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.24.3+galaxy0",
             "errors": null,
             "id": 8,
             "input_connections": {
@@ -273,15 +273,15 @@
                     "output_name": "report_json"
                 }
             },
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.24.0+galaxy4",
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.24.3+galaxy0",
             "tool_shed_repository": {
-                "changeset_revision": "10678d49d39e",
+                "changeset_revision": "480ddbd12a03",
                 "name": "fastp",
                 "owner": "iuc",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
             "tool_state": "{\"filter_options\": {\"quality_filtering_options\": {\"disable_quality_filtering\": false, \"qualified_quality_phred\": null, \"unqualified_percent_limit\": null, \"n_base_limit\": null}, \"length_filtering_options\": {\"disable_length_filtering\": false, \"length_required\": null, \"length_limit\": null}, \"low_complexity_filter\": {\"enable_low_complexity_filter\": false, \"complexity_threshold\": null}}, \"output_options\": {\"report_html\": true, \"report_json\": true}, \"overrepresented_sequence_analysis\": {\"overrepresentation_analysis\": false, \"overrepresentation_sampling\": null}, \"read_mod_options\": {\"polyg_tail_trimming\": {\"trimming_select\": \"\", \"__current_case__\": 1, \"poly_g_min_len\": null}, \"polyx_tail_trimming\": {\"polyx_trimming_select\": \"\", \"__current_case__\": 1}, \"umi_processing\": {\"umi\": false, \"umi_loc\": \"\", \"umi_len\": null, \"umi_prefix\": \"\"}, \"cutting_by_quality_options\": {\"cut_by_quality5\": false, \"cut_by_quality3\": false, \"cut_window_size\": null, \"cut_mean_quality\": null}, \"base_correction_options\": {\"correction\": false}}, \"single_paired\": {\"single_paired_selector\": \"paired_collection\", \"__current_case__\": 1, \"paired_input\": {\"__class__\": \"ConnectedValue\"}, \"merge_reads\": {\"merge\": \"\", \"__current_case__\": 1}, \"adapter_trimming_options\": {\"disable_adapter_trimming\": false, \"adapter_sequence1\": \"\", \"adapter_sequence2\": \"\", \"detect_adapter_for_pe\": false}, \"global_trimming_options\": {\"trim_front1\": null, \"trim_tail1\": null, \"trim_front2\": null, \"trim_tail2\": null}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-            "tool_version": "0.24.0+galaxy4",
+            "tool_version": "0.24.3+galaxy0",
             "type": "tool",
             "uuid": "849d9cac-14b8-4e45-823d-5747709e8b60",
             "when": null,
@@ -403,7 +403,7 @@
         },
         "11": {
             "annotation": "",
-            "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.18",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.19",
             "errors": null,
             "id": 11,
             "input_connections": {
@@ -439,15 +439,15 @@
                 "top": 352.5625
             },
             "post_job_actions": {},
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.18",
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.19",
             "tool_shed_repository": {
-                "changeset_revision": "2477830927ec",
+                "changeset_revision": "1dfc975b48d5",
                 "name": "bwa",
                 "owner": "devteam",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
             "tool_state": "{\"analysis_type\": {\"analysis_type_selector\": \"illumina\", \"__current_case__\": 0}, \"fastq_input\": {\"fastq_input_selector\": \"paired_collection\", \"__current_case__\": 2, \"fastq_input1\": {\"__class__\": \"ConnectedValue\"}, \"iset_stats\": \"\"}, \"output_sort\": \"coordinate\", \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"ref_file\": {\"__class__\": \"ConnectedValue\"}, \"index_a\": \"auto\"}, \"rg\": {\"rg_selector\": \"do_not_set\", \"__current_case__\": 3}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-            "tool_version": "0.7.18",
+            "tool_version": "0.7.19",
             "type": "tool",
             "uuid": "3b5d7080-c168-4bf7-946d-9045c0a4bc4c",
             "when": null,
@@ -1462,7 +1462,7 @@
         },
         "30": {
             "annotation": "",
-            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.5+galaxy0",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.5+galaxy2",
             "errors": null,
             "id": 30,
             "input_connections": {
@@ -1485,15 +1485,15 @@
                 "top": 745.546875
             },
             "post_job_actions": {},
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.5+galaxy0",
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.5+galaxy2",
             "tool_shed_repository": {
-                "changeset_revision": "3dc70b59608c",
+                "changeset_revision": "c41d78ae5fee",
                 "name": "text_processing",
                 "owner": "bgruening",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
             "tool_state": "{\"infile\": {\"__class__\": \"ConnectedValue\"}, \"replacements\": [{\"__index__\": 0, \"find_pattern\": \"^##INFO=<ID=AmpliconBias,.+$\", \"replace_pattern\": \"##INFO=<ID=AmpliconBias,Number=0,Type=Flag,Description=\\\"Indicates that the AF value of the variant could not be corrected for potential amplicon bias.\\\">\", \"sed_options\": null}, {\"__index__\": 1, \"find_pattern\": \"^##INFO=<ID=AF,.+$\", \"replace_pattern\": \"##INFO=<ID=AF,Number=1,Type=Float,Description=\\\"Lofreq Allele Frequency; Fraction of variant-supporting bases with q > --min-bq among all bases at the site\\\">\", \"sed_options\": null}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-            "tool_version": "9.5+galaxy0",
+            "tool_version": "9.5+galaxy2",
             "type": "tool",
             "uuid": "490dbabb-04ee-426d-a8e5-e2ec9e59de3a",
             "when": null,
@@ -1635,5 +1635,7 @@
         "ARTIC",
         "covid19.galaxyproject.org"
     ],
-    "uuid": "864427b0-d25a-499c-b437-f83f2d6b83f2"
+    "uuid": "58bf654a-43e6-4ae2-bae6-99371158ec52",
+    "version": 1,
+    "release": "0.5.5"
 }