Updating workflows/variant-calling/ploidy-aware-genotype-calling from 0.1.1 to 0.1.2

Author: planemo-autoupdate

workflows/variant-calling/ploidy-aware-genotype-calling/CHANGELOG.md

@@ -1,5 +1,14 @@
 # Changelog
 
+## [0.1.2] - 2026-03-23
+
+### Automatic update
+- `toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/1.1.0+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/1.2.0+galaxy0`
+- `toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/5.2+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/5.4+galaxy0`
+- `toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.8` was updated to `toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.9`
+- `toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/5.2+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/5.4+galaxy0`
+- `toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/5.4.0c+galaxy0`
+
 ## [0.1.1] 2026-03-12
 
 - Rename workflow file to remove '+' character from filename.

workflows/variant-calling/ploidy-aware-genotype-calling/genotype-variant-calling-wgs-pe.ga

@@ -50,10 +50,10 @@
         {
             "child_steps": [
                 4,
-                8,
                 7,
                 10,
                 6,
+                8,
                 9
             ],
             "color": "blue",
@@ -86,7 +86,6 @@
     ],
     "format-version": "0.1",
     "license": "MIT",
-    "release": "0.1.1",
     "name": "Paired end variant and ploidy-aware genotype calling",
     "readme": "This workflow performs end-to-end germline variant and genotype calling on paired-end Illumina sequencing data from organisms of any given ploidy. Starting from raw FASTQ reads, the workflow handles quality control, read mapping, duplicate removal, variant and genotype calling with FreeBayes, and functional annotation of the resulting variants.",
     "report": {
@@ -203,7 +202,7 @@
         },
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             "annotation": "Processing of FASTQ files",
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             "errors": null,
             "id": 4,
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@@ -245,16 +244,16 @@
                     "output_name": "report_json"
                 }
             },
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/1.1.0+galaxy0",
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/1.2.0+galaxy0",
             "tool_shed_repository": {
-                "changeset_revision": "ff33957bf802",
+                "changeset_revision": "b2e9a56e5259",
                 "name": "fastp",
                 "owner": "iuc",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
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             "tool_uuid": null,
-            "tool_version": "1.1.0+galaxy0",
+            "tool_version": "1.2.0+galaxy0",
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@@ -268,7 +267,7 @@
         },
         "5": {
             "annotation": "Build SnpEff database from the given reference fasta file",
-            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/5.2+galaxy1",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/5.4+galaxy0",
             "errors": null,
             "id": 5,
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@@ -300,16 +299,16 @@
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+            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/5.4+galaxy0",
             "tool_shed_repository": {
-                "changeset_revision": "3aae4f16ac9e",
+                "changeset_revision": "908f2c5fedec",
                 "name": "snpeff",
                 "owner": "iuc",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
             "tool_state": "{\"codon_table\": \"Standard\", \"genome_version\": \"snpeff_db\", \"input_type\": {\"input_type_selector\": \"gtf\", \"__current_case__\": 2, \"input\": {\"__class__\": \"ConnectedValue\"}, \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"input_fasta\": {\"__class__\": \"ConnectedValue\"}}}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}",
             "tool_uuid": null,
-            "tool_version": "5.2+galaxy1",
+            "tool_version": "5.4+galaxy0",
             "type": "tool",
             "uuid": "b717154e-57de-4980-ba7a-0fdd88765ff9",
             "when": null,
@@ -418,7 +417,7 @@
         },
         "8": {
             "annotation": "Generates statistics of BAM file",
-            "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.8",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.9",
             "errors": null,
             "id": 8,
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@@ -441,16 +440,16 @@
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             "post_job_actions": {},
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.8",
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.9",
             "tool_shed_repository": {
-                "changeset_revision": "57934e90e27c",
+                "changeset_revision": "8fca6e1eac98",
                 "name": "samtools_stats",
                 "owner": "devteam",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
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             "tool_uuid": null,
-            "tool_version": "2.0.8",
+            "tool_version": "2.0.9",
             "type": "tool",
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@@ -686,7 +685,7 @@
         },
         "13": {
             "annotation": "Annotates detected variants",
-            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/5.2+galaxy1",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/5.4+galaxy0",
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@@ -738,16 +737,16 @@
                     "output_name": "snpeff_output"
                 }
             },
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/5.2+galaxy1",
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/5.4+galaxy0",
             "tool_shed_repository": {
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+                "changeset_revision": "908f2c5fedec",
                 "name": "snpeff",
                 "owner": "iuc",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
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@@ -766,7 +765,7 @@
         },
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-            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/5.4.0c+galaxy0",
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@@ -775,12 +774,7 @@
                     "output_name": "snpeff_output"
                 }
             },
-            "inputs": [
-                {
-                    "description": "runtime parameter for tool SnpSift Extract Fields",
-                    "name": "input"
-                }
-            ],
+            "inputs": [],
             "label": "Extract using SnpSift",
             "name": "SnpSift Extract Fields",
             "outputs": [
@@ -794,16 +788,16 @@
                 "top": 644.9675784543903
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             "post_job_actions": {},
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0",
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/5.4.0c+galaxy0",
             "tool_shed_repository": {
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+                "changeset_revision": "0abc5513f795",
                 "name": "snpsift",
                 "owner": "iuc",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
-            "tool_state": "{\"empty_text\": \".\", \"extract\": \"CHROM POS FILTER REF ALT DP AF RO AO SRP SAP EFF[*].IMPACT EFF[*].FUNCLASS EFF[*].EFFECT EFF[*].GENE EFF[*].CODON EFF[*].AA EFF[*].TRID\", \"input\": {\"__class__\": \"RuntimeValue\"}, \"one_effect_per_line\": true, \"separator\": \",\", \"__page__\": 0, \"__rerun_remap_job_id__\": null}",
+            "tool_state": "{\"empty_text\": \".\", \"extract\": \"CHROM POS FILTER REF ALT DP AF RO AO SRP SAP EFF[*].IMPACT EFF[*].FUNCLASS EFF[*].EFFECT EFF[*].GENE EFF[*].CODON EFF[*].AA EFF[*].TRID\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"one_effect_per_line\": true, \"separator\": \",\", \"__page__\": 0, \"__rerun_remap_job_id__\": null}",
             "tool_uuid": null,
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@@ -820,12 +814,7 @@
                     "output_name": "output"
                 }
             },
-            "inputs": [
-                {
-                    "description": "runtime parameter for tool Collapse Collection",
-                    "name": "input_list"
-                }
-            ],
+            "inputs": [],
             "label": "Collapse",
             "name": "Collapse Collection",
             "outputs": [
@@ -854,7 +843,7 @@
                 "owner": "nml",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
-            "tool_state": "{\"filename\": {\"add_name\": true, \"__current_case__\": 0, \"place_name\": \"same_multiple\"}, \"input_list\": {\"__class__\": \"RuntimeValue\"}, \"one_header\": true, \"__page__\": 0, \"__rerun_remap_job_id__\": null}",
+            "tool_state": "{\"filename\": {\"add_name\": true, \"__current_case__\": 0, \"place_name\": \"same_multiple\"}, \"input_list\": {\"__class__\": \"ConnectedValue\"}, \"one_header\": true, \"__page__\": 0, \"__rerun_remap_job_id__\": null}",
             "tool_uuid": null,
             "tool_version": "5.1.0",
             "type": "tool",
@@ -874,6 +863,7 @@
         "Diploid",
         "FreeBayes"
     ],
-    "uuid": "0706c30f-3bfb-42d5-bc55-a50d24824101",
-    "version": 1
+    "uuid": "5f69b314-8149-4401-a35e-56735ca0b5a4",
+    "version": 1,
+    "release": "0.1.2"
 }