Updating workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-…

…wgs-variant-calling from 0.2.6 to 0.2.7
galaxyproject · May 27, 2024 · 6754a75 · 6754a75
1 parent 543d769
commit 6754a75
Showing 1 changed file with 10 additions and 47 deletions.
diff --git a/...sars-cov-2-variant-calling/sars-cov-2-pe-illumina-wgs-variant-calling/pe-wgs-variation.ga b/...sars-cov-2-variant-calling/sars-cov-2-pe-illumina-wgs-variant-calling/pe-wgs-variation.ga
@@ -11,7 +11,7 @@
     "format-version": "0.1",
     "license": "MIT",
     "name": "COVID-19: variation analysis on WGS PE data",
-    "release": "0.2.6",
+    "release": "0.2.7",
     "steps": {
         "0": {
             "annotation": "Illumina reads with fastqsanger encoding",
@@ -138,7 +138,7 @@
         },
         "3": {
             "annotation": "",
-            "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.18",
             "errors": null,
             "id": 3,
             "input_connections": {
@@ -174,15 +174,15 @@
                 "top": 327.0
             },
             "post_job_actions": {},
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2",
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.18",
             "tool_shed_repository": {
-                "changeset_revision": "e188dc7a68e6",
+                "changeset_revision": "2477830927ec",
                 "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": "0.7.17.2",
+            "tool_version": "0.7.18",
             "type": "tool",
             "uuid": "ff1eb4ed-6403-4017-8538-c16200b33cdb",
             "when": null,
@@ -205,12 +205,7 @@
                     "output_name": "bam_output"
                 }
             },
-            "inputs": [
-                {
-                    "description": "runtime parameter for tool Samtools view",
-                    "name": "input"
-                }
-            ],
+            "inputs": [],
             "label": null,
             "name": "Samtools view",
             "outputs": [
@@ -263,12 +258,7 @@
                     "output_name": "outputsam"
                 }
             },
-            "inputs": [
-                {
-                    "description": "runtime parameter for tool MarkDuplicates",
-                    "name": "inputFile"
-                }
-            ],
+            "inputs": [],
             "label": null,
             "name": "MarkDuplicates",
             "outputs": [
@@ -322,12 +312,7 @@
                     "output_name": "outputsam"
                 }
             },
-            "inputs": [
-                {
-                    "description": "runtime parameter for tool Samtools stats",
-                    "name": "input"
-                }
-            ],
+            "inputs": [],
             "label": null,
             "name": "Samtools stats",
             "outputs": [
@@ -377,10 +362,6 @@
                 }
             },
             "inputs": [
-                {
-                    "description": "runtime parameter for tool Realign reads",
-                    "name": "reads"
-                },
                 {
                     "description": "runtime parameter for tool Realign reads",
                     "name": "reference_source"
@@ -504,12 +485,7 @@
                     "output_name": "output"
                 }
             },
-            "inputs": [
-                {
-                    "description": "runtime parameter for tool Insert indel qualities",
-                    "name": "reads"
-                }
-            ],
+            "inputs": [],
             "label": null,
             "name": "Insert indel qualities",
             "outputs": [
@@ -567,10 +543,6 @@
                 }
             },
             "inputs": [
-                {
-                    "description": "runtime parameter for tool Call variants",
-                    "name": "reads"
-                },
                 {
                     "description": "runtime parameter for tool Call variants",
                     "name": "reference_source"
@@ -620,12 +592,7 @@
                     "output_name": "variants"
                 }
             },
-            "inputs": [
-                {
-                    "description": "runtime parameter for tool Lofreq filter",
-                    "name": "invcf"
-                }
-            ],
+            "inputs": [],
             "label": null,
             "name": "Lofreq filter",
             "outputs": [
@@ -671,10 +638,6 @@
                 }
             },
             "inputs": [
-                {
-                    "description": "runtime parameter for tool SnpEff eff:",
-                    "name": "input"
-                },
                 {
                     "description": "runtime parameter for tool SnpEff eff:",
                     "name": "intervals"