Improve worklow names as shown in Galaxy

workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4.ga

@@ -21,7 +21,7 @@
     "format-version": "0.1",
     "license": "CC-BY-4.0",
     "release": "0.2.2",
-    "name": "Assembly-Hifi-HiC-phasing-VGP4",
+    "name": "Contiging Solo with HiC data VGP4",
     "report": {
         "markdown": "\n# Workflow Execution Report\n\nTime workflow was invoked:\n\n```galaxy\ninvocation_time()\n```\nGalaxy version :\n\n```galaxy\ngenerate_galaxy_version()\n```\n\n## Raw unitig graph\n\n```galaxy\nhistory_dataset_as_image(output=\"raw unitig graph image\")\n```\n\n## Merqury results\n\n### Merqury QV\n\n```galaxy\nhistory_dataset_as_table(output=\"merqury_qv\")\n```\n\n### Merqury completeness\n\n```galaxy\nhistory_dataset_as_table(output=\"merqury_stats\")\n```\n\n### Merqury plots\n\n\nspectra-cn:\n\n\n```galaxy\nhistory_dataset_as_image(output=\"output_merqury.spectra-cn.fl\")\n```\n\nspectra-asm:\n\n```galaxy\nhistory_dataset_as_image(output=\"output_merqury.spectra-asm.fl\")\n```\n\nhap1 spectra-cn:\n\n```galaxy\nhistory_dataset_as_image(output=\"output_merqury.assembly_01.spectra-cn.fl\")\n```\n\nhap2 spectra-cn:\n\n```galaxy\nhistory_dataset_as_image(output=\"output_merqury.assembly_02.spectra-cn.fl\")\n```\n\n## BUSCO results (Vertebrata database)\n\nHap1\n\n```galaxy\nhistory_dataset_as_image(output=\"Busco Summary Image Hap1\")\n```\n\nHap2\n\n```galaxy\nhistory_dataset_as_image(output=\"Busco Summary Image Hap2\")\n```\n\n## Assembly statistics\n\n\n```galaxy\nhistory_dataset_as_table(output=\"clean_stats\")\n```\n\n\n## Nx and Size plots\n\n\n```galaxy\nhistory_dataset_as_image(output=\"Nx Plot\")\n```\n\n\n```galaxy\nhistory_dataset_as_image(output=\"Size Plot\")\n```\n\n\n\n## Current Workflow\n```galaxy\nworkflow_display()\n```\n"
     },

workflows/VGP-assembly-v2/Assembly-Hifi-Trio-phasing-VGP5/Assembly-Hifi-Trio-phasing-VGP5.ga

@@ -16,7 +16,7 @@
     "format-version": "0.1",
     "license": "CC-BY-4.0",
     "release": "0.2",
-    "name": "Assembly-Hifi-Trio-phasing-VGP5",
+    "name": "Assembly with Hifi reads and Trio Data VGP5",
     "report": {
         "markdown": "\n# Workflow Execution Report\n\nTime workflow was invoked:\n\n```galaxy\ninvocation_time()\n```\nGalaxy version :\n\n```galaxy\ngenerate_galaxy_version()\n```\n\n## Raw unitig graph\n\n```galaxy\nhistory_dataset_as_image(output=\"raw unitig graph image\")\n```\n\n## Merqury results\n\n### Merqury QV\n\n```galaxy\nhistory_dataset_as_table(output=merqury_stats)\n```\n\n### Merqury completeness\n\n```galaxy\nhistory_dataset_as_table(output=\"merqury_stats\")\n```\n\n### Merqury plots\n\n\nspectra-cn:\n\n\n```galaxy\nhistory_dataset_as_image(output=\"output_merqury.spectra-cn.fl\")\n```\n\nspectra-asm:\n\n```galaxy\nhistory_dataset_as_image(output=\"output_merqury.spectra-asm.fl\")\n```\n\n\nhap1 spectra-cn:\n\n\r\n```galaxy\nhistory_dataset_as_image(output=\"output_merqury.assembly_01.spectra-cn.fl\")\n```\r\n\n\nhap2 spectra-cn:\n\n```galaxy\nhistory_dataset_as_image(output=\"output_merqury.assembly_02.spectra-cn.fl\")\n```\n\n## BUSCO results (Vertebrata database)\n\nHap1\n\n```galaxy\nhistory_dataset_as_image(output=\"Busco Summary Image Hap1\")\n```\n\nHap2\n\n```galaxy\nhistory_dataset_as_image(output=\"Busco Summary Image Hap2\")\n```\n\n## Assembly statistics\n\n\n```galaxy\nhistory_dataset_as_table(output=\"clean_stats\")\n```\n\n\n## Nx and Size plots\n\n\n```galaxy\nhistory_dataset_as_image(output=\"Nx Plot\")\n```\n\n\n```galaxy\nhistory_dataset_as_image(output=\"Size Plot\")\n```\n\n\n\n## Current Workflow\n```galaxy\nworkflow_display()\n```\n"
     },

workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3.ga

@@ -16,7 +16,7 @@
     "format-version": "0.1",
     "license": "CC-BY-4.0",
     "release": "0.2.1",
-    "name": "Assembly-Hifi-only-VGP3",
+    "name": "Contiging Solo VGP3",
     "report": {
         "markdown": "\n# Workflow Execution Report\n\nTime workflow was invoked:\n\n```galaxy\ninvocation_time()\n```\nGalaxy version :\n\n```galaxy\ngenerate_galaxy_version()\n```\n\n## Raw unitig graph\n\n```galaxy\nhistory_dataset_as_image(output=\"raw unitig graph image\")\n```\n\n## Merqury results\n\n### Merqury QV\n\n```galaxy\nhistory_dataset_as_table(output=\"merqury_qv\")\n```\n\n### Merqury completeness\n\n```galaxy\nhistory_dataset_as_table(output=\"merqury_stats\")\n```\n\n### Merqury plots\n\n\nspectra-cn:\n\n\n```galaxy\nhistory_dataset_as_image(output=\"output_merqury.spectra-cn.fl\")\n```\n\nspectra-asm:\n\n```galaxy\nhistory_dataset_as_image(output=\"output_merqury.spectra-asm.fl\")\n```\n\nhap1 spectra-cn:\n\n```galaxy\nhistory_dataset_as_image(output=\"output_merqury.assembly_01.spectra-cn.fl\")\n```\n\n\n## BUSCO results (Vertebrata database)\n\n\n\n## Assembly statistics\n\n\n```galaxy\nhistory_dataset_as_table(output=\"clean_stats\")\n```\n\n\n## Nx and Size plots\n\n\n```galaxy\nhistory_dataset_as_image(output=\"Nx Plot\")\n```\n\n\n```galaxy\nhistory_dataset_as_image(output=\"Size Plot\")\n```\n\n\n\n## Current Workflow\n```galaxy\nworkflow_display()\n```\n"
     },

workflows/VGP-assembly-v2/Assembly-decontamination-VGP9/Assembly-decontamination-VGP9.ga

@@ -12,9 +12,9 @@
     "format-version": "0.1",
     "license": "BSD-3-Clause",
     "release": "0.3",
-    "name": "Assembly-decontamination-VGP9",
+    "name": "Assembly decontamination VGP9",
     "report": {
-        "markdown": "\n# Workflow Execution Report\n\n### Worflow ran on: \n\n```galaxy\ninvocation_time()\n```\n\n# List of contaminants\n\n\r\n```galaxy\nhistory_dataset_as_table(output=\"contaminants_table\")\n```\r\n\n\n# List of Mitochondrial scaffolds\n\r\n```galaxy\nhistory_dataset_as_table(output=\"mito_scaff_names\")\n```\r\n\n\n\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n"
+        "markdown": "\n# Workflow Execution Report\n\n### Workflow ran on: \n\n```galaxy\ninvocation_time()\n```\n\n# List of contaminants\n\n\r\n```galaxy\nhistory_dataset_as_table(output=\"contaminants_table\")\n```\r\n\n\n# List of Mitochondrial scaffolds\n\r\n```galaxy\nhistory_dataset_as_table(output=\"mito_scaff_names\")\n```\r\n\n\n\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n"
     },
     "steps": {
         "0": {

workflows/VGP-assembly-v2/Mitogenome-assembly-VGP0/Mitogenome-Assembly-VGP0.ga

@@ -15,7 +15,7 @@
     ],
     "format-version": "0.1",
     "license": "CC-BY-4.0",
-    "name": "Mitogenome-Assembly-VGP0",
+    "name": "Mitogenome Assembly VGP0",
     "release": "0.1",
     "steps": {
         "0": {

workflows/VGP-assembly-v2/Purge-duplicate-contigs-VGP6/Purge-duplicate-contigs-VGP6.ga

@@ -16,7 +16,7 @@
     "format-version": "0.1",
     "license": "CC-BY-4.0",
     "release": "0.4",
-    "name": "Purge-duplicate-contigs-VGP6",
+    "name": "Purge duplicate contigs VGP6",
     "report": {
         "markdown": "\n# Workflow Execution Report\n\nTime workflow was invoked\n\n```galaxy\ninvocation_time()\n```\n\n```galaxy\ngenerate_galaxy_version()\n```\n\n## Merqury results\n\nMerqury QV:\n\n```galaxy\nhistory_dataset_as_table(output=\"merqury_QV\")\n```\n\nMerqury completeness:\n\n```galaxy\nhistory_dataset_as_table(output=\"merqury_stats\")\n```\n\nMerqury plots:\n\nspectra-cn:\n\n\n```galaxy\nhistory_dataset_as_image(output=\"output_merqury.spectra-cn.fl\")\n```\n\n\nspectra-asm:\n\n\n```galaxy\nhistory_dataset_as_image(output=\"output_merqury.spectra-asm.fl\")\n```\n\n\nhap1/Primary spectra-cn:\n\n\n```galaxy\nhistory_dataset_as_image(output=\"output_merqury.assembly_01.spectra-cn.fl\")\n```\n\n\nhap2/alternate spectra-cn:\n\n```galaxy\nhistory_dataset_as_image(output=\"output_merqury.assembly_02.spectra-cn.fl\")\n```\n\n\n\n\n## BUSCO results (Vertebrata database)\n\nPurged hap1/primary Assembly\n\n\n```galaxy\nhistory_dataset_as_image(output=\"Busco on Purged Primary assembly: summary image\")\n```\n\n\n## Assembly statistics\n\n\n```galaxy\nhistory_dataset_as_table(output=\"clean_stats\")\n```\n\n\n## Nx and Size plots\n\n\n```galaxy\nhistory_dataset_as_image(output=\"Nx Plot\")\n```\n\n\n```galaxy\nhistory_dataset_as_image(output=\"Size Plot\")\n```\n\n\n\n## Current Workflow\n```galaxy\nworkflow_display()\n```\n"
     },

workflows/VGP-assembly-v2/Purge-duplicates-one-haplotype-VGP6b/Purging-duplicates-one-haplotype-VGP6b.ga

@@ -16,7 +16,7 @@
     "format-version": "0.1",
     "license": "CC-BY-4.0",
     "release": "0.7.1",
-    "name": "Purging-duplicates-one-haplotype-VGP6b ",
+    "name": "Purge Duplicate Contigs VGP6b",
     "report": {
         "markdown": "\n# Workflow Execution Report\n\nTime workflow was invoked\n\n```galaxy\ninvocation_time()\n```\n\n```galaxy\ngenerate_galaxy_version()\n```\n\n## Merqury results\n\nMerqury QV:\n\n```galaxy\nhistory_dataset_as_table(output=\"merqury_QV\")\n```\n\nMerqury completeness:\n\n```galaxy\nhistory_dataset_as_table(output=\"merqury_stats\")\n```\n\nMerqury plots:\n\nspectra-cn:\n\n\n```galaxy\nhistory_dataset_as_image(output=\"output_merqury.spectra-cn.fl\")\n```\n\n\nspectra-asm:\n\n\n```galaxy\nhistory_dataset_as_image(output=\"output_merqury.spectra-asm.fl\")\n```\n\n\nhap1 spectra-cn:\n\n\n```galaxy\nhistory_dataset_as_image(output=\"output_merqury.assembly_01.spectra-cn.fl\")\n```\n\n\nhap2 spectra-cn:\n\n```galaxy\nhistory_dataset_as_image(output=\"output_merqury.assembly_02.spectra-cn.fl\")\n```\n\n\n\n\n## BUSCO results (Vertebrata database)\n\nPurged Assembly\n\n\n```galaxy\nhistory_dataset_as_image(output=\"Busco on Purged Primary assembly: summary image\")\n```\n\n\n## Assembly statistics\n\n\n```galaxy\nhistory_dataset_as_table(output=\"clean_stats\")\n```\n\n\n## Nx and Size plots\n\n\n```galaxy\nhistory_dataset_as_image(output=\"Nx Plot\")\n```\n\n\n```galaxy\nhistory_dataset_as_image(output=\"Size Plot\")\n```\n\n\n\n## Current Workflow\n```galaxy\nworkflow_display()\n```\n"
     },

workflows/VGP-assembly-v2/Scaffolding-Bionano-VGP7/Scaffolding-BioNano-VGP7.ga

@@ -16,7 +16,7 @@
     "format-version": "0.1",
     "license": "CC-BY-4.0",
     "release": "0.1.4",
-    "name": "Scaffolding-BioNano-VGP7",
+    "name": "Scaffolding with BioNano data VGP7",
     "report": {
         "markdown": "\n# Workflow Execution Report\n\n## Invocation time\n```galaxy\ninvocation_time()\n```\n\n## Assembly statistics\n\n```galaxy\nhistory_dataset_as_table(output=\"clean_stats\")\n```\n\n## Size plot\n\n\n```galaxy\nhistory_dataset_as_image(output=\"Size Plot\")\n```\n\n\n## Nx plot\n```galaxy\nhistory_dataset_as_image(output=\"Nx Plot\")\n```\n\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n"
     },

workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/Scaffolding-HiC-VGP8.ga

@@ -16,7 +16,7 @@
     "format-version": "0.1",
     "license": "CC-BY-4.0",
     "release": "0.2.7",
-    "name": "Scaffolding-HiC-VGP8",
+    "name": "Scaffolding with HiC data VGP8",
     "report": {
         "markdown": "# Workflow Execution Report\n\nTime workflow was invoked\n\n```galaxy\ninvocation_time()\n```\n\n```galaxy\ngenerate_galaxy_version()\n```\n\n\n## BUSCO results (Vertebrata database)\n\n\n```galaxy\nhistory_dataset_as_image(output=\"Busco Summary image\")\n```\n\n\n## Assembly statistics\n\n\n```galaxy\nhistory_dataset_as_table(output=\"clean_stats\")\n```\n\n\n## Nx and Size plots\n\n\n```galaxy\nhistory_dataset_as_image(output=\"Nx Plot\")\n```\n\n\n```galaxy\nhistory_dataset_as_image(output=\"Size Plot\")\n```\n\n## PretextMap\n\n### Before Scaffolding\n\n\r\n```galaxy\nhistory_dataset_as_image(output=\"Pretext Map Before HiC scaffolding\")\n```\r\n\n\n### After Scaffolding\r\n```galaxy\nhistory_dataset_as_image(output=\"Pretext Map After HiC scaffolding\")\n```\r\n\n\n\n\n## Current Workflow\n```galaxy\nworkflow_display()\n```\n"
     },

workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/kmer-profiling-hifi-VGP1.ga

@@ -16,7 +16,7 @@
     "format-version": "0.1",
     "license": "CC-BY-4.0",
     "release": "0.1.7",
-    "name": "kmer-profiling-hifi-VGP1",
+    "name": "K-mer profiling for PacBio HiFi data VGP1",
     "report": {
         "markdown": "\n# Workflow Execution Report\n\n\n```galaxy\ninvocation_time()\n```\n\n\n```galaxy\nhistory_dataset_as_image(output=\"GenomeScope linear plot\")\n```\n\n```galaxy\nhistory_dataset_as_image(output=\"GenomeScope log plot\")\n```\n\n```galaxy\nhistory_dataset_as_image(output=\"GenomeScope transformed linear plot\")\n```\n\n```galaxy\nhistory_dataset_as_image(output=\"GenomeScope transformed log plot\")\n```\n\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n"
     },

workflows/VGP-assembly-v2/kmer-profiling-hifi-trio-VGP2/kmer-profiling-hifi-trio-VGP2.ga

@@ -15,7 +15,7 @@
     "format-version": "0.1",
     "license": "CC-BY-4.0",
     "release": "0.1.4",
-    "name": "kmer-profiling-hifi-trio-VGP2",
+    "name": "K-mer profiling with HiFi trio data VGP2",
     "steps": {
         "0": {
             "annotation": "",

workflows/amplicon/dada2/dada2_paired.ga

@@ -1,6 +1,6 @@
 {
     "a_galaxy_workflow": "true",
-    "annotation": "dada2 amplicon analysis for paired end data\n\nThe workflow has three main outputs: \n- the sequence table (output of makeSequenceTable)\n- the taxonomy (output of assignTaxonomy)\n- the counts which allow to track the number of sequences in the samples through the steps (output of sequence counts)",
+    "annotation": "DADA2 amplicon analysis for paired end data\n\nThe workflow has three main outputs: \n- the sequence table (output of makeSequenceTable)\n- the taxonomy (output of assignTaxonomy)\n- the counts which allow to track the number of sequences in the samples through the steps (output of sequence counts)",
     "creator": [
         {
             "class": "Person",
@@ -14,7 +14,7 @@
     ],
     "format-version": "0.1",
     "license": "MIT",
-    "name": "dada2 amplicon analysis pipeline - for paired end data",
+    "name": "DADA2 amplicon analysis for paired end data",
     "release": "0.2",
     "steps": {
         "0": {

workflows/amplicon/qiime2/qiime2-I-import/QIIME2-Ia-multiplexed-data-single-end.ga

@@ -1,6 +1,6 @@
 {
     "a_galaxy_workflow": "true",
-    "annotation": "Importing single-end multiplexed data (not demultiplexed yet)",
+    "annotation": "Importing single read multiplexed data (not demultiplexed yet)",
     "creator": [
         {
             "class": "Person",
@@ -16,17 +16,17 @@
     "format-version": "0.1",
     "license": "MIT",
     "release": "0.2",
-    "name": "QIIME2 Ia: multiplexed data (single-end)",
+    "name": "QIIME2 Ia: multiplexed data (single read)",
     "steps": {
         "0": {
-            "annotation": "Single-end sequences",
+            "annotation": "single read sequences",
             "content_id": null,
             "errors": null,
             "id": 0,
             "input_connections": {},
             "inputs": [
                 {
-                    "description": "Single-end sequences",
+                    "description": "single read sequences",
                     "name": "Sequences"
                 }
             ],
@@ -189,7 +189,7 @@
                 },
                 "RenameDatasetActionimported_data": {
                     "action_arguments": {
-                        "newname": "input-data-single-end"
+                        "newname": "input-data-single-read"
                     },
                     "action_type": "RenameDatasetAction",
                     "output_name": "imported_data"
@@ -285,7 +285,7 @@
                 }
             },
             "inputs": [],
-            "label": "Demultiplex single-end data",
+            "label": "Demultiplex single read data",
             "name": "qiime2 demux emp-single",
             "outputs": [
                 {
@@ -316,7 +316,7 @@
                 },
                 "RenameDatasetActionper_sample_sequences": {
                     "action_arguments": {
-                        "newname": "demux-single-end"
+                        "newname": "demux-single-read"
                     },
                     "action_type": "RenameDatasetAction",
                     "output_name": "per_sample_sequences"
@@ -336,7 +336,7 @@
             "when": null,
             "workflow_outputs": [
                 {
-                    "label": "Demultiplexed single-end data",
+                    "label": "Demultiplexed single read data",
                     "output_name": "per_sample_sequences",
                     "uuid": "9cdc6089-1547-403c-a790-d2070d111e08"
                 }
@@ -369,7 +369,7 @@
             "post_job_actions": {
                 "RenameDatasetActionvisualization": {
                     "action_arguments": {
-                        "newname": "demux-single-end-visualization"
+                        "newname": "demux-single-read-visualization"
                     },
                     "action_type": "RenameDatasetAction",
                     "output_name": "visualization"

workflows/amplicon/qiime2/qiime2-I-import/QIIME2-Ib-multiplexed-data-paired-end.ga

@@ -1,6 +1,6 @@
 {
     "a_galaxy_workflow": "true",
-    "annotation": "Importing paired-end multiplexed data (not demultiplexed yet)",
+    "annotation": "Importing paired end multiplexed data (not demultiplexed yet)",
     "creator": [
         {
             "class": "Person",
@@ -16,7 +16,7 @@
     "format-version": "0.1",
     "license": "MIT",
     "release": "0.2",
-    "name": "QIIME2 Ib: multiplexed data (paired-end)",
+    "name": "QIIME2 Ib: multiplexed data (paired end)",
     "steps": {
         "0": {
             "annotation": "All the forward-directed FASTQ sequences",
@@ -293,7 +293,7 @@
             "workflow_outputs": []
         },
         "8": {
-            "annotation": "qiime2 demux emp-paired\nDemultiplex paired-end sequence data generated with the EMP protocol.",
+            "annotation": "qiime2 demux emp-paired\nDemultiplex paired end sequence data generated with the EMP protocol.",
             "content_id": "toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__demux__emp_paired/qiime2__demux__emp_paired/2023.5.0+q2galaxy.2023.5.0.2",
             "errors": null,
             "id": 8,
@@ -316,7 +316,7 @@
                 }
             },
             "inputs": [],
-            "label": "Demultiplex paired-end sequences",
+            "label": "Demultiplex paired end sequences",
             "name": "qiime2 demux emp-paired",
             "outputs": [
                 {
@@ -367,7 +367,7 @@
             "when": null,
             "workflow_outputs": [
                 {
-                    "label": "Demultiplexed paired-end output",
+                    "label": "Demultiplexed paired end output",
                     "output_name": "per_sample_sequences",
                     "uuid": "d582d835-3dfd-43d5-b31f-79ddcc04ff70"
                 }

workflows/amplicon/qiime2/qiime2-I-import/QIIME2-Ic-demultiplexed-data-single-end.ga

@@ -1,6 +1,6 @@
 {
     "a_galaxy_workflow": "true",
-    "annotation": "Importing demultiplexed data (single-end)",
+    "annotation": "Importing demultiplexed data (single read)",
     "creator": [
         {
             "class": "Person",
@@ -16,17 +16,17 @@
     "format-version": "0.1",
     "license": "MIT",
     "release": "0.2",
-    "name": "QIIME2 Ic: Demultiplexed data (single-end)",
+    "name": "QIIME2 Ic: Demultiplexed data (single read)",
     "steps": {
         "0": {
-            "annotation": "A collection of single-end demultiplexed sequences",
+            "annotation": "A collection of single read demultiplexed sequences",
             "content_id": null,
             "errors": null,
             "id": 0,
             "input_connections": {},
             "inputs": [
                 {
-                    "description": "A collection of single-end demultiplexed sequences",
+                    "description": "A collection of single read demultiplexed sequences",
                     "name": "Sequence collection"
                 }
             ],

workflows/amplicon/qiime2/qiime2-I-import/QIIME2-Id-demultiplexed-data-paired-end.ga

@@ -1,6 +1,6 @@
 {
     "a_galaxy_workflow": "true",
-    "annotation": "Importing demultiplexed data (paired-end)",
+    "annotation": "Importing demultiplexed data (paired end)",
     "creator": [
         {
             "class": "Person",
@@ -16,17 +16,17 @@
     "format-version": "0.1",
     "release": "0.2",
     "license": "MIT",
-    "name": "QIIME2 Id: Demultiplexed data (paired-end)",
+    "name": "QIIME2 Id: Demultiplexed data (paired end)",
     "steps": {
         "0": {
-            "annotation": "Import of the paired-end demultiplexed sequences",
+            "annotation": "Import of the paired end demultiplexed sequences",
             "content_id": null,
             "errors": null,
             "id": 0,
             "input_connections": {},
             "inputs": [
                 {
-                    "description": "Import of the paired-end demultiplexed sequences",
+                    "description": "Import of the paired end demultiplexed sequences",
                     "name": "Sequence collection"
                 }
             ],