diff --git a/workflows/data-fetching/parallel-accession-download/CHANGELOG.md b/workflows/data-fetching/parallel-accession-download/CHANGELOG.md index 5ebdf7b95..d36a372b1 100644 --- a/workflows/data-fetching/parallel-accession-download/CHANGELOG.md +++ b/workflows/data-fetching/parallel-accession-download/CHANGELOG.md @@ -1,5 +1,11 @@ # Changelog +## [0.1.12] 2024-04-16 + +### Changed + +- Remove unnecessary param_value_from_file step and directly pass file with identifiers to fasterqdump + ## [0.1.11] 2024-04-08 ### Automatic update diff --git a/workflows/data-fetching/parallel-accession-download/parallel-accession-download.ga b/workflows/data-fetching/parallel-accession-download/parallel-accession-download.ga index a7caa9709..6266a2fcf 100644 --- a/workflows/data-fetching/parallel-accession-download/parallel-accession-download.ga +++ b/workflows/data-fetching/parallel-accession-download/parallel-accession-download.ga @@ -1,6 +1,7 @@ { "a_galaxy_workflow": "true", "annotation": "Downloads fastq files for sequencing run accessions provided in a text file using fasterq-dump. Creates one job per listed run accession.", + "comments": [], "creator": [ { "class": "Person", @@ -15,7 +16,7 @@ ], "format-version": "0.1", "license": "MIT", - "release": "0.1.11", + "release": "0.1.12", "name": "Parallel Accession Download", "steps": { "0": { @@ -34,8 +35,8 @@ "name": "Input dataset", "outputs": [], "position": { - "left": 0.0, - "top": 27.0 + "left": 0, + "top": 0 }, "tool_id": null, "tool_state": "{\"optional\": false, \"format\": [\"txt\"], \"tag\": null}", @@ -71,8 +72,8 @@ } ], "position": { - "left": 146.51248168945312, - "top": 173.01251220703125 + "left": 279.51666259765625, + "top": 86.01666259765625 }, "post_job_actions": { "HideDatasetActionlist_output_txt": { @@ -97,54 +98,15 @@ }, "2": { "annotation": "", - "content_id": "param_value_from_file", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.1.0+galaxy0", "errors": null, "id": 2, "input_connections": { - "input1": { + "input|file_list": { "id": 1, "output_name": "list_output_txt" } }, - "inputs": [], - "label": "to parameter", - "name": "Parse parameter value", - "outputs": [ - { - "name": "text_param", - "type": "expression.json" - } - ], - "position": { - "left": 338.0375061035156, - "top": 0.0 - }, - "post_job_actions": { - "HideDatasetActiontext_param": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "text_param" - } - }, - "tool_id": "param_value_from_file", - "tool_state": "{\"input1\": {\"__class__\": \"ConnectedValue\"}, \"param_type\": \"text\", \"remove_newlines\": true, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "0.1.0", - "type": "tool", - "uuid": "570d0317-259f-42b1-91f4-74f050e754b5", - "when": null, - "workflow_outputs": [] - }, - "3": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.1.0+galaxy0", - "errors": null, - "id": 3, - "input_connections": { - "input|accession": { - "id": 2, - "output_name": "text_param" - } - }, "inputs": [ { "description": "runtime parameter for tool Faster Download and Extract Reads in FASTQ", @@ -172,8 +134,8 @@ } ], "position": { - "left": 604.9250183105469, - "top": 100.9749755859375 + "left": 570.9250183105469, + "top": 62.9749755859375 }, "post_job_actions": { "HideDatasetActionlist_paired": { @@ -204,21 +166,21 @@ "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"__job_resource\": {\"__current_case__\": 0, \"__job_resource__select\": \"no\"}, \"adv\": {\"seq_defline\": \"@$sn/$ri\", \"minlen\": null, \"split\": \"--split-3\", \"skip_technical\": true}, \"input\": {\"input_select\": \"accession_number\", \"__current_case__\": 0, \"accession\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"adv\": {\"seq_defline\": \"@$sn/$ri\", \"minlen\": null, \"split\": \"--split-3\", \"skip_technical\": true}, \"input\": {\"input_select\": \"file_list\", \"__current_case__\": 2, \"file_list\": {\"__class__\": \"RuntimeValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "3.1.0+galaxy0", "type": "tool", "uuid": "4d328e7b-df7d-4d3e-a60f-1ea12925f317", "when": null, "workflow_outputs": [] }, - "4": { + "3": { "annotation": "", "content_id": "__APPLY_RULES__", "errors": null, - "id": 4, + "id": 3, "input_connections": { "input": { - "id": 3, + "id": 2, "output_name": "list_paired" } }, @@ -232,8 +194,8 @@ } ], "position": { - "left": 932.0000305175781, - "top": 109.9749755859375 + "left": 898.0000305175781, + "top": 71.9749755859375 }, "post_job_actions": { "TagDatasetActionoutput": { @@ -258,14 +220,14 @@ } ] }, - "5": { + "4": { "annotation": "", "content_id": "__APPLY_RULES__", "errors": null, - "id": 5, + "id": 4, "input_connections": { "input": { - "id": 3, + "id": 2, "output_name": "output_collection" } }, @@ -279,8 +241,8 @@ } ], "position": { - "left": 939.0499572753906, - "top": 253.0250244140625 + "left": 905.0499572753906, + "top": 215.0250244140625 }, "post_job_actions": { "TagDatasetActionoutput": { @@ -309,4 +271,4 @@ "tags": [], "uuid": "15c3229d-8786-457f-a020-7aa64c0cf6e8", "version": 10 -} \ No newline at end of file +}