diff --git a/workflows/data-fetching/parallel-accession-download/.dockstore.yml b/workflows/data-fetching/parallel-accession-download/.dockstore.yml index 45cdce16d..8b6502719 100644 --- a/workflows/data-fetching/parallel-accession-download/.dockstore.yml +++ b/workflows/data-fetching/parallel-accession-download/.dockstore.yml @@ -1,7 +1,13 @@ version: 1.2 workflows: - name: main - primaryDescriptorPath: /parallel-accession-download.ga subclass: Galaxy + publish: true + primaryDescriptorPath: /parallel-accession-download.ga testParameterFiles: - /parallel-accession-download-tests.yml + authors: + - name: Marius van den Beek + orcid: 0000-0002-9676-7032 + - name: IWC + url: https://github.com/galaxyproject/iwc diff --git a/workflows/data-fetching/parallel-accession-download/CHANGELOG.md b/workflows/data-fetching/parallel-accession-download/CHANGELOG.md index cfbd7e6fc..f77078f30 100644 --- a/workflows/data-fetching/parallel-accession-download/CHANGELOG.md +++ b/workflows/data-fetching/parallel-accession-download/CHANGELOG.md @@ -1,5 +1,10 @@ # Changelog +## [0.1.4] 2023-02-17 + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.11.0+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.0.5+galaxy0` + ## [0.1.3] 2022-02-04 ### 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 0a064617e..9c4bc04a9 100644 --- a/workflows/data-fetching/parallel-accession-download/parallel-accession-download.ga +++ b/workflows/data-fetching/parallel-accession-download/parallel-accession-download.ga @@ -15,7 +15,7 @@ ], "format-version": "0.1", "license": "MIT", - "release": "0.1.3", + "release": "0.1.4", "name": "Parallel Accession Download", "steps": { "0": { @@ -34,20 +34,15 @@ "name": "Input dataset", "outputs": [], "position": { - "bottom": 634.3875122070312, - "height": 61, - "left": 387.4250183105469, - "right": 587.4250183105469, - "top": 573.3875122070312, - "width": 200, - "x": 387.4250183105469, - "y": 573.3875122070312 + "left": 0.0, + "top": 27.0 }, "tool_id": null, - "tool_state": "{\"optional\": false, \"format\": [\"txt\"]}", + "tool_state": "{\"optional\": false, \"format\": [\"txt\"], \"tag\": null}", "tool_version": null, "type": "data_input", "uuid": "e9e5605e-29e1-4f90-9693-0e40a2ddfd8f", + "when": null, "workflow_outputs": [] }, "1": { @@ -71,14 +66,8 @@ } ], "position": { - "bottom": 851.4000244140625, - "height": 132, - "left": 533.9375, - "right": 733.9375, - "top": 719.4000244140625, - "width": 200, - "x": 533.9375, - "y": 719.4000244140625 + "left": 146.51248168945312, + "top": 173.01251220703125 }, "post_job_actions": { "HideDatasetActionlist_output_txt": { @@ -98,6 +87,7 @@ "tool_version": "0.5.0", "type": "tool", "uuid": "f8d776ff-e1ba-4bde-9b4b-392d825fd2b7", + "when": null, "workflow_outputs": [] }, "2": { @@ -121,14 +111,8 @@ } ], "position": { - "bottom": 678.3875122070312, - "height": 132, - "left": 725.4625244140625, - "right": 925.4625244140625, - "top": 546.3875122070312, - "width": 200, - "x": 725.4625244140625, - "y": 546.3875122070312 + "left": 338.0375061035156, + "top": 0.0 }, "post_job_actions": { "HideDatasetActiontext_param": { @@ -138,15 +122,16 @@ } }, "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_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/2.11.0+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.0.5+galaxy0", "errors": null, "id": 3, "input_connections": { @@ -177,14 +162,8 @@ } ], "position": { - "bottom": 889.3624877929688, - "height": 242, - "left": 992.3500366210938, - "right": 1192.3500366210938, - "top": 647.3624877929688, - "width": 200, - "x": 992.3500366210938, - "y": 647.3624877929688 + "left": 604.9250183105469, + "top": 100.9749755859375 }, "post_job_actions": { "HideDatasetActionlist_paired": { @@ -208,17 +187,18 @@ "output_name": "output_collection_other" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.11.0+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.0.5+galaxy0", "tool_shed_repository": { - "changeset_revision": "83c7d564b128", + "changeset_revision": "6ea73833cf67", "name": "sra_tools", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"__job_resource\": {\"__current_case__\": 0, \"__job_resource__select\": \"no\"}, \"adv\": {\"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_version": "2.11.0+galaxy1", + "tool_state": "{\"__job_resource\": {\"__current_case__\": 0, \"__job_resource__select\": \"no\"}, \"adv\": {\"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_version": "3.0.5+galaxy0", "type": "tool", "uuid": "4d328e7b-df7d-4d3e-a60f-1ea12925f317", + "when": null, "workflow_outputs": [] }, "4": { @@ -242,14 +222,8 @@ } ], "position": { - "bottom": 768.3624877929688, - "height": 112, - "left": 1319.425048828125, - "right": 1519.425048828125, - "top": 656.3624877929688, - "width": 200, - "x": 1319.425048828125, - "y": 656.3624877929688 + "left": 932.0000305175781, + "top": 109.9749755859375 }, "post_job_actions": { "TagDatasetActionoutput": { @@ -265,6 +239,7 @@ "tool_version": "1.1.0", "type": "tool", "uuid": "924d2152-5640-40cd-bec3-0ced45469d84", + "when": null, "workflow_outputs": [ { "label": "Paired End Reads", @@ -294,14 +269,8 @@ } ], "position": { - "bottom": 911.4125366210938, - "height": 112, - "left": 1326.4749755859375, - "right": 1526.4749755859375, - "top": 799.4125366210938, - "width": 200, - "x": 1326.4749755859375, - "y": 799.4125366210938 + "left": 939.0499572753906, + "top": 253.0250244140625 }, "post_job_actions": { "TagDatasetActionoutput": { @@ -317,6 +286,7 @@ "tool_version": "1.1.0", "type": "tool", "uuid": "946d9610-c363-4915-b93a-f074169ef812", + "when": null, "workflow_outputs": [ { "label": "Single End Reads", diff --git a/workflows/data-fetching/parallel-accession-download/test-data/SRR044777_head.fastq b/workflows/data-fetching/parallel-accession-download/test-data/SRR044777_head.fastq index 013984ddc..9c35cf9e4 100644 --- a/workflows/data-fetching/parallel-accession-download/test-data/SRR044777_head.fastq +++ b/workflows/data-fetching/parallel-accession-download/test-data/SRR044777_head.fastq @@ -1,10 +1,12 @@ -@SRR044777.1 F47USSH02H1LGA length=160 +@F47USSH02H1LGA/4 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN -+SRR044777.1 F47USSH02H1LGA length=160 ++ !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! -@SRR044777.2 F47USSH02GNP1D length=320 +@F47USSH02GNP1D/4 CACGTAGTTAGCCGGTGCTTATTCTTCCGGTACCGTCAGCACGCAATGGTATTAACATCGCGCTTTTCTTCCCGGACAAAAGTCCTTTACAACCCGAAGGCCTTCTTCAGACACGCGGCATGGCTGGATCAGGGTTGCCCCCATTGTCCAAAATTCCCCACTGCTGCCTCCCGTAGGAGTCTGGGCCGTGTCTCAGTCCCAGTGTGGCGGATCATCCTCTCAGACCCGCTACTGATCGTCGCCTTGGTAGGCCTTTACCCCACCAACCAGCTAATCAGATATCGGCCGCTCAAACAGCGCAAGGCACACAGGGGATAGGN -+SRR044777.2 F47USSH02GNP1D length=320 ++ IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIAAAAIIIHCCCCII@@@@IIIIHHHIIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIII?????IIIIIII@@@@HH6666IFIIIIIIIIHHHIIIIIIIIIIHHHIIIIIIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIIICCCIIIIIIIIIIIIIIIIIIIIIIII??===?@B>>IDCIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIHHHHIIIIII@@@@HIIII! -@SRR044777.3 F47USSH02JNWNH length=78 +@F47USSH02JNWNH/4 GGCCATGCCTGTACCTGGGGTCCCTACTGAGCCAGGATCAAACTCTCTGAGACTGCCAAGGCACACAGGGGGATAGGN ++ +AAIIIIIIIIIIIIIIACCCIHHHIIIIIIIIHHHHIIIHHHIIIIIIIIIIIIICCCCEAIIBB;4-----8<=<