diff --git a/.github/workflows/workflow_test.yml b/.github/workflows/workflow_test.yml index ee7feb0e8..893bae9f1 100644 --- a/.github/workflows/workflow_test.yml +++ b/.github/workflows/workflow_test.yml @@ -98,22 +98,22 @@ jobs: id: check with: mode: check - - name: Get PR object + - uses: jwalton/gh-find-current-pr@v1 if: failure() - uses: 8BitJonny/gh-get-current-pr@2.2.0 - id: failed_pr_number + id: findPr with: - sha: ${{ github.event.pull_request.head.sha }} - - name: Debug GetPR output + # Can be "open", "closed", or "all". Defaults to "open". + state: all + - run: echo "Your PR is ${PR}" if: failure() - run: | - echo ${{ steps.failed_pr_number.outputs.number }} + env: + PR: ${{ github.event.number || steps.findPr.outputs.pr }} - name: Post comment with test report if: failure() uses: peter-evans/create-or-update-comment@v3 with: token: ${{ secrets.PAT }} - issue-number: ${{ steps.failed_pr_number.outputs.number }} + issue-number: ${{ github.event.number || steps.findPr.outputs.number }} body-path: upload/tool_test_output.md # deploy workflows to organization diff --git a/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4.ga b/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4.ga index c49b850fe..01e210f94 100644 --- a/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4.ga +++ b/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4.ga @@ -19,18 +19,18 @@ ], "format-version": "0.1", "license": "CC-BY-4.0", - "release": "0.1.4", + "release": "0.1.6", "name": "Assembly-Hifi-HiC-phasing-VGP4", "steps": { "0": { - "annotation": "", + "annotation": "A simple list containing PacBio data in either fasta or fastq formats.", "content_id": null, "errors": null, "id": 0, "input_connections": {}, "inputs": [ { - "description": "", + "description": "A simple list containing PacBio data in either fasta or fastq formats.", "name": "Pacbio Reads Collection" } ], @@ -39,7 +39,7 @@ "outputs": [], "position": { "left": 0, - "top": 492.03749084472656 + "top": 54.86661965562355 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list\"}", @@ -50,14 +50,14 @@ "workflow_outputs": [] }, "1": { - "annotation": "", + "annotation": "Forward reads as a single dataset in fastq format", "content_id": null, "errors": null, "id": 1, "input_connections": {}, "inputs": [ { - "description": "", + "description": "Forward reads as a single dataset in fastq format", "name": "HiC forward reads" } ], @@ -65,8 +65,8 @@ "name": "Input dataset", "outputs": [], "position": { - "left": 85.37493896484375, - "top": 654.0750122070312 + "left": 5.227635768494666, + "top": 146.68167273687337 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": null}", @@ -77,14 +77,14 @@ "workflow_outputs": [] }, "2": { - "annotation": "", + "annotation": "Reverse reads as a single dataset in fastq format", "content_id": null, "errors": null, "id": 2, "input_connections": {}, "inputs": [ { - "description": "", + "description": "Reverse reads as a single dataset in fastq format", "name": "HiC reverse reads" } ], @@ -92,8 +92,8 @@ "name": "Input dataset", "outputs": [], "position": { - "left": 148.04995727539062, - "top": 795.737548828125 + "left": 14.512079824566827, + "top": 240.65230620636626 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": \"\"}", @@ -104,110 +104,110 @@ "workflow_outputs": [] }, "3": { - "annotation": "", + "annotation": "GenomeScope summary generated by K-mer profiling workflow", "content_id": null, "errors": null, "id": 3, "input_connections": {}, "inputs": [ { - "description": "", - "name": "Genomescope Model Parameters" + "description": "GenomeScope summary generated by K-mer profiling workflow", + "name": "Genomescope Summary" } ], - "label": "Genomescope Model Parameters", + "label": "Genomescope Summary", "name": "Input dataset", "outputs": [], "position": { - "left": 234.49996948242188, - "top": 954.4125366210938 + "left": 18.350006103515625, + "top": 338.7749938964844 }, "tool_id": null, - "tool_state": "{\"optional\": false, \"tag\": \"genomescope_params\"}", + "tool_state": "{\"optional\": false, \"tag\": \"genomescope_summ\"}", "tool_version": null, "type": "data_input", - "uuid": "0735f7ce-74e8-4ae0-8142-e6d2fd89c89e", + "uuid": "1844cbb3-ba5f-4997-a3cd-ce70f4570a99", "when": null, "workflow_outputs": [] }, "4": { - "annotation": "", + "annotation": "GenomeScope model parameters generated by K-mer profiling workflow", "content_id": null, "errors": null, "id": 4, "input_connections": {}, "inputs": [ { - "description": "", - "name": "Genomescope Summary" + "description": "GenomeScope model parameters generated by K-mer profiling workflow", + "name": "Genomescope Model Parameters" } ], - "label": "Genomescope Summary", + "label": "Genomescope Model Parameters", "name": "Input dataset", "outputs": [], "position": { - "left": 312.4125061035156, - "top": 1098.375 + "left": 30.902209445950454, + "top": 431.8791830657761 }, "tool_id": null, - "tool_state": "{\"optional\": false, \"tag\": \"genomescope_summ\"}", + "tool_state": "{\"optional\": false, \"tag\": \"genomescope_params\"}", "tool_version": null, "type": "data_input", - "uuid": "1844cbb3-ba5f-4997-a3cd-ce70f4570a99", + "uuid": "0735f7ce-74e8-4ae0-8142-e6d2fd89c89e", "when": null, "workflow_outputs": [] }, "5": { - "annotation": "", + "annotation": "Meryl database generated by K-mer profiling workflow", "content_id": null, "errors": null, "id": 5, "input_connections": {}, "inputs": [ { - "description": "", - "name": "Lineage" + "description": "Meryl database generated by K-mer profiling workflow", + "name": "Meryl Database" } ], - "label": "Lineage", - "name": "Input parameter", + "label": "Meryl Database", + "name": "Input dataset", "outputs": [], "position": { - "left": 333.19976806640625, - "top": 1229.4000549316406 + "left": 37.64677777016476, + "top": 523.9735404662978 }, "tool_id": null, - "tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}", + "tool_state": "{\"optional\": false, \"tag\": \"meryl_db\"}", "tool_version": null, - "type": "parameter_input", - "uuid": "a9df063c-37ef-440d-93e6-212ac3a598e8", + "type": "data_input", + "uuid": "fcb0f86e-455a-4a6e-9c86-d8994caf0493", "when": null, "workflow_outputs": [] }, "6": { - "annotation": "", + "annotation": "Taxonomic lineage for the organism being assembled for Busco analysis", "content_id": null, "errors": null, "id": 6, "input_connections": {}, "inputs": [ { - "description": "", - "name": "Meryl Database" + "description": "Taxonomic lineage for the organism being assembled for Busco analysis", + "name": "Lineage" } ], - "label": "Meryl Database", - "name": "Input dataset", + "label": "Lineage", + "name": "Input parameter", "outputs": [], "position": { - "left": 406.9874748480204, - "top": 1393.2250061035156 + "left": 49.49551283744214, + "top": 597.7803958491536 }, "tool_id": null, - "tool_state": "{\"optional\": false, \"tag\": \"meryl_db\"}", + "tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}", "tool_version": null, - "type": "data_input", - "uuid": "fcb0f86e-455a-4a6e-9c86-d8994caf0493", + "type": "parameter_input", + "uuid": "a9df063c-37ef-440d-93e6-212ac3a598e8", "when": null, "workflow_outputs": [] }, @@ -220,75 +220,75 @@ "inputs": [ { "description": "", - "name": "SAK input file" + "name": "Name for Haplotype 1" } ], - "label": "SAK input file", - "name": "Input dataset", + "label": "Name for Haplotype 1", + "name": "Input parameter", "outputs": [], "position": { - "left": 427.0000141585672, - "top": 1550.8499755859375 + "left": 66.71469378816481, + "top": 670.9107953985914 }, "tool_id": null, - "tool_state": "{\"optional\": true, \"tag\": \"\"}", + "tool_state": "{\"default\": \"Hap1\", \"parameter_type\": \"text\", \"optional\": true}", "tool_version": null, - "type": "data_input", - "uuid": "557a2e2b-008c-4566-836a-6509950aa85b", + "type": "parameter_input", + "uuid": "41d1bb31-75f9-4034-abad-96aed4916b45", "when": null, "workflow_outputs": [] }, "8": { - "annotation": "Defaults to 37 if not specified. For genomes much larger than human, applying -f38 or even -f39 is preferred to save memory on k-mer counting.", + "annotation": "", "content_id": null, "errors": null, "id": 8, "input_connections": {}, "inputs": [ { - "description": "Defaults to 37 if not specified. For genomes much larger than human, applying -f38 or even -f39 is preferred to save memory on k-mer counting.", - "name": "Bits for bloom filter" + "description": "", + "name": "Name for Haplotype 2" } ], - "label": "Bits for bloom filter", + "label": "Name for Haplotype 2", "name": "Input parameter", "outputs": [], "position": { - "left": 974.8312377929688, - "top": 1702.4624963613278 + "left": 78.38870701261258, + "top": 769.8272396352553 }, "tool_id": null, - "tool_state": "{\"default\": 37, \"parameter_type\": \"integer\", \"optional\": true}", + "tool_state": "{\"default\": \"Hap2\", \"parameter_type\": \"text\", \"optional\": true}", "tool_version": null, "type": "parameter_input", - "uuid": "b949921b-95a3-4d43-81b2-4006a4909e4b", + "uuid": "6d5afa06-c3e8-4eb7-8819-8cfe8300c462", "when": null, "workflow_outputs": [] }, "9": { - "annotation": "", + "annotation": "Defaults to 37 if not specified. For genomes much larger than human, applying -f38 or even -f39 is preferred to save memory on k-mer counting.", "content_id": null, "errors": null, "id": 9, "input_connections": {}, "inputs": [ { - "description": "", - "name": "Name for Haplotype 1" + "description": "Defaults to 37 if not specified. For genomes much larger than human, applying -f38 or even -f39 is preferred to save memory on k-mer counting.", + "name": "Bits for bloom filter" } ], - "label": "Name for Haplotype 1", + "label": "Bits for bloom filter", "name": "Input parameter", "outputs": [], "position": { - "left": 3698.661507346414, - "top": 1521.9591042862808 + "left": 96.0148601509567, + "top": 866.2253241049863 }, "tool_id": null, - "tool_state": "{\"default\": \"Hap1\", \"parameter_type\": \"text\", \"optional\": true}", + "tool_state": "{\"default\": 37, \"parameter_type\": \"integer\", \"optional\": true}", "tool_version": null, "type": "parameter_input", - "uuid": "41d1bb31-75f9-4034-abad-96aed4916b45", + "uuid": "b949921b-95a3-4d43-81b2-4006a4909e4b", "when": null, "workflow_outputs": [] }, @@ -301,21 +301,21 @@ "inputs": [ { "description": "", - "name": "Name for Haplotype 2" + "name": "SAK input file" } ], - "label": "Name for Haplotype 2", - "name": "Input parameter", + "label": "SAK input file", + "name": "Input dataset", "outputs": [], "position": { - 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"tool_version": "1.1.1", + "tool_state": "{\"avoid_scientific_notation\": false, \"error_handling\": {\"auto_col_types\": true, \"fail_on_non_existent_columns\": true, \"non_computable\": {\"action\": \"--fail-on-non-computable\", \"__current_case__\": 0}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"ops\": {\"header_lines_select\": \"no\", \"__current_case__\": 0, \"expressions\": [{\"__index__\": 0, \"cond\": \"c3*2\", \"add_column\": {\"mode\": \"\", \"__current_case__\": 0, \"pos\": \"\"}}]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "2.0", "type": "tool", - "uuid": "72b7138a-e0d4-4922-9895-c6cbacddbb90", + "uuid": "bfa738cb-d9c1-4b3c-a89b-71135d65a3b6", "when": null, "workflow_outputs": [] }, @@ -503,8 +503,8 @@ } ], "position": { - "left": 1086.1959552186909, - "top": 786.1344268478335 + "left": 1419.8172527091565, + "top": 388 }, "post_job_actions": {}, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1", @@ -523,12 +523,57 @@ }, "15": { "annotation": "", - 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"uuid": "b37cd2e6-bc13-4cbd-8521-016411c4666a", - "version": 1 + "uuid": "31801875-3aee-498b-b396-c6a164dd7509", + "version": 6 } \ No newline at end of file diff --git a/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/CHANGELOG.md b/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/CHANGELOG.md index 590599024..facf66478 100644 --- a/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/CHANGELOG.md +++ b/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/CHANGELOG.md @@ -1,5 +1,14 @@ # Changelog +## [0.1.5] 2023-11-15 + +### Added + +- more descriptive labels for inputs + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0` + ## [0.1.4] 2023-11-08 ### Automatic update diff --git a/workflows/VGP-assembly-v2/Assembly-decontamination-VGP9/Assembly-decontamination-VGP9.ga b/workflows/VGP-assembly-v2/Assembly-decontamination-VGP9/Assembly-decontamination-VGP9.ga index 6595e41a7..aab87f9f0 100644 --- a/workflows/VGP-assembly-v2/Assembly-decontamination-VGP9/Assembly-decontamination-VGP9.ga +++ b/workflows/VGP-assembly-v2/Assembly-decontamination-VGP9/Assembly-decontamination-VGP9.ga @@ -10,7 +10,7 @@ ], "format-version": "0.1", "license": "BSD-3-Clause", - "release": "0.1.1", + "release": "0.1.2", "name": "Assembly-decontamination-VGP9", "steps": { "0": { @@ -116,7 +116,7 @@ }, "3": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_dustmasker_wrapper/2.14.1+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_dustmasker_wrapper/2.14.1+galaxy1", "errors": null, "id": 3, "input_connections": { @@ -139,15 +139,15 @@ "top": 176.06640625 }, "post_job_actions": {}, - "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_dustmasker_wrapper/2.14.1+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_dustmasker_wrapper/2.14.1+galaxy1", "tool_shed_repository": { - "changeset_revision": "a52d2d93e595", + "changeset_revision": "d999e774072a", "name": "ncbi_blast_plus", "owner": "devteam", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"db_opts\": {\"db_opts_selector\": \"file\", \"__current_case__\": 2, \"database\": \"\", \"histdb\": \"\", \"subject\": {\"__class__\": \"ConnectedValue\"}}, \"level\": \"40\", \"linker\": \"1\", \"outformat\": \"fasta\", \"window\": \"64\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2.14.1+galaxy0", + "tool_version": "2.14.1+galaxy1", "type": "tool", "uuid": "903a13af-2be0-48a9-8355-1e2486d857cf", "when": null, @@ -265,7 +265,7 @@ }, "6": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/2.14.1+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/2.14.1+galaxy1", "errors": null, "id": 6, "input_connections": { @@ -288,15 +288,15 @@ "top": 392.03515625 }, "post_job_actions": {}, - "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/2.14.1+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/2.14.1+galaxy1", "tool_shed_repository": { - "changeset_revision": "a52d2d93e595", + "changeset_revision": "d999e774072a", "name": "ncbi_blast_plus", "owner": "devteam", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"adv_opts\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"blast_type\": \"blastn\", \"db_opts\": {\"db_opts_selector\": \"db\", \"__current_case__\": 0, \"database\": [\"refseq_mitochondrion\"], \"histdb\": \"\", \"subject\": \"\"}, \"evalue_cutoff\": \"0.001\", \"output\": {\"out_format\": \"cols\", \"__current_case__\": 2, \"std_cols\": [\"qseqid\", \"sseqid\", \"length\", \"qstart\", \"qend\", \"evalue\"], \"ext_cols\": [\"qlen\"], \"ids_cols\": null, \"misc_cols\": [\"qcovs\", \"qcovhsp\"], \"tax_cols\": null}, \"query\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2.14.1+galaxy0", + "tool_version": "2.14.1+galaxy1", "type": "tool", "uuid": "1737bad0-48d9-489e-9a45-d6f3d3fcb900", "when": null, diff --git a/workflows/VGP-assembly-v2/Assembly-decontamination-VGP9/CHANGELOG.md b/workflows/VGP-assembly-v2/Assembly-decontamination-VGP9/CHANGELOG.md index 459ea3ef8..11808fb56 100644 --- a/workflows/VGP-assembly-v2/Assembly-decontamination-VGP9/CHANGELOG.md +++ b/workflows/VGP-assembly-v2/Assembly-decontamination-VGP9/CHANGELOG.md @@ -1,5 +1,11 @@ # Changelog +## [0.1.2] 2023-11-20 + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_dustmasker_wrapper/2.14.1+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_dustmasker_wrapper/2.14.1+galaxy1` +- `toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/2.14.1+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/2.14.1+galaxy1` + ## [0.1.1] 2023-11-09 ### Automatic update diff --git a/workflows/VGP-assembly-v2/Purge-duplicate-contigs-VGP6/CHANGELOG.md b/workflows/VGP-assembly-v2/Purge-duplicate-contigs-VGP6/CHANGELOG.md index 0f056ed84..712df0c41 100644 --- a/workflows/VGP-assembly-v2/Purge-duplicate-contigs-VGP6/CHANGELOG.md +++ b/workflows/VGP-assembly-v2/Purge-duplicate-contigs-VGP6/CHANGELOG.md @@ -1,5 +1,11 @@ # Changelog +## [0.3.2] - 2023-11-15 + +### Added + +- more descriptive lables for inputs + ## [0.3.1] 2023-11-09 ### Automatic update diff --git a/workflows/VGP-assembly-v2/Purge-duplicate-contigs-VGP6/Purge-duplicate-contigs-VGP6.ga b/workflows/VGP-assembly-v2/Purge-duplicate-contigs-VGP6/Purge-duplicate-contigs-VGP6.ga index 753b3e618..0ee8430ca 100644 --- a/workflows/VGP-assembly-v2/Purge-duplicate-contigs-VGP6/Purge-duplicate-contigs-VGP6.ga +++ b/workflows/VGP-assembly-v2/Purge-duplicate-contigs-VGP6/Purge-duplicate-contigs-VGP6.ga @@ -14,18 +14,18 @@ ], "format-version": "0.1", "license": "CC-BY-4.0", - "release": "0.3.1", + "release": "0.3.2", "name": "Purge-duplicate-contigs-VGP6", "steps": { "0": { - "annotation": "", + "annotation": "A simple list containing PacBio data in either fasta or fastq formats with trimmed adapters. These are usually generated by contiging workflows and have tag \"trimmed_hifi\" associated with them.\n", "content_id": null, "errors": null, "id": 0, "input_connections": {}, "inputs": [ { - "description": "", + "description": "A simple list containing PacBio data in either fasta or fastq formats with trimmed adapters. These are usually generated by contiging workflows and have tag \"trimmed_hifi\" associated with them.\n", "name": "Pacbio Reads Collection - Trimmed" } ], @@ -37,7 +37,7 @@ "top": 0 }, "tool_id": null, - "tool_state": "{\"optional\": false, \"tag\": \"\", \"collection_type\": \"list\"}", + "tool_state": "{\"optional\": false, \"tag\": \"trimmed_hifi\", \"collection_type\": \"list\"}", "tool_version": null, "type": "data_collection_input", "uuid": "0df002ab-91cf-4767-a348-9ce31f439a01", @@ -45,14 +45,14 @@ "workflow_outputs": [] }, "1": { - "annotation": "", + "annotation": "Primary assembly generated by contiging workflow in fasta format.", "content_id": null, "errors": null, "id": 1, "input_connections": {}, "inputs": [ { - "description": "", + "description": "Primary assembly generated by contiging workflow in fasta format.", "name": "Hifiasm Primary assembly" } ], @@ -60,8 +60,8 @@ "name": "Input dataset", "outputs": [], "position": { - "left": 21.921875, - "top": 101.10000610351562 + "left": 21.7890625, + "top": 101.30078125 }, "tool_id": null, "tool_state": "{\"optional\": false, \"format\": [\"fasta\"], \"tag\": \"hifiasm_hic_hap1\"}", @@ -72,14 +72,14 @@ "workflow_outputs": [] }, "2": { - "annotation": "", + "annotation": "Alternate assembly generated by contiging workflow in fasta format.", "content_id": null, "errors": null, "id": 2, "input_connections": {}, "inputs": [ { - "description": "", + "description": "Alternate assembly generated by contiging workflow in fasta format.", "name": "Hifiasm Alternate assembly" } ], @@ -87,8 +87,8 @@ "name": "Input dataset", "outputs": [], "position": { - "left": 52.071868896484375, - "top": 200.32501220703125 + "left": 52.028900146484375, + "top": 200.42266845703125 }, "tool_id": null, "tool_state": "{\"optional\": false, \"format\": [\"fasta\"], \"tag\": \"hifiasm_hic_hap2\"}", @@ -99,14 +99,14 @@ "workflow_outputs": [] }, "3": { - "annotation": "", + "annotation": "Meryl database generated by K-mer profiling workflow.\n", "content_id": null, "errors": null, "id": 3, "input_connections": {}, "inputs": [ { - "description": "", + "description": "Meryl database generated by K-mer profiling workflow.\n", "name": "Meryl Database" } ], @@ -114,8 +114,8 @@ "name": "Input dataset", "outputs": [], "position": { - "left": 101.93851725260417, - "top": 297.89164225260447 + "left": 101.96484375, + "top": 297.9609375 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": \"meryl_db\"}", @@ -126,14 +126,14 @@ "workflow_outputs": [] }, "4": { - "annotation": "", + "annotation": "GenomeScope model parameters generated by K-mer profiling workflow.\n", "content_id": null, "errors": null, "id": 4, "input_connections": {}, "inputs": [ { - "description": "", + "description": "GenomeScope model parameters generated by K-mer profiling workflow.\n", "name": "Genomescope model parameters" } ], @@ -141,8 +141,8 @@ "name": "Input dataset", "outputs": [], "position": { - "left": 145.4510498046875, - "top": 390.25838216145866 + "left": 145.4080810546875, + "top": 390.35603841145866 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": \"genomescope_params\"}", @@ -153,14 +153,14 @@ "workflow_outputs": [] }, "5": { - "annotation": "", + "annotation": "Estimated genome size generated by contiging workflows. ", "content_id": null, "errors": null, "id": 5, "input_connections": {}, "inputs": [ { - "description": "", + "description": "Estimated genome size generated by contiging workflows. 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"top": 1420.140625 + "left": 4745.81640625, + "top": 1420.23828125 }, "post_job_actions": { "HideDatasetActionlog_file": { @@ -2364,8 +2364,8 @@ } ], "position": { - "left": 5040.299957275391, - "top": 1348.9125366210938 + "left": 5040.296875, + "top": 1349.00390625 }, "post_job_actions": { "TagDatasetActionoutput": { @@ -2417,8 +2417,8 @@ } ], "position": { - "left": 5253.46875, - "top": 708.5 + "left": 5253.42578125, + "top": 708.59765625 }, "post_job_actions": { "HideDatasetActionoutfile": { @@ -2456,8 +2456,8 @@ "name": "gfastats_data_prep", "outputs": [], "position": { - "left": 5760.3125, - "top": 526.78125 + "left": 5760.26953125, + "top": 526.87890625 }, "subworkflow": { "a_galaxy_workflow": "true", @@ -2842,8 +2842,8 @@ } ], "position": { - "left": 5646.484375, - "top": 850.46875 + "left": 5646.44140625, + "top": 850.56640625 }, "post_job_actions": { "TagDatasetActionoutput": { @@ -2904,8 +2904,8 @@ "name": "gfastats_plot", "outputs": [], "position": { - "left": 6121.640625, - "top": 374.140625 + "left": 6121.59765625, + "top": 374.23828125 }, "subworkflow": { "a_galaxy_workflow": "true", @@ -3415,6 +3415,6 @@ "tags": [ "VGP_curated" ], - "uuid": "80fccf94-4f19-400d-9921-f7d8db0cfbc5", - "version": 2 + "uuid": "a6c2fa10-d553-47a1-813f-12173d435709", + "version": 4 } \ No newline at end of file diff --git a/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/CHANGELOG.md b/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/CHANGELOG.md index 9eb190948..59c941819 100644 --- a/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/CHANGELOG.md +++ b/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/CHANGELOG.md @@ -1,5 +1,11 @@ # Changelog +## [0.2] - 2023-11-15 + +### Added + +- more descriptive labels for inputs + ## [0.1.2] 2023-11-14 ### Automatic update @@ -17,3 +23,4 @@ Added tags for better visibility of outputs in the history, and exposure of the ## [0.1] - 2023-09-27 Creation of the workflow and tests + diff --git a/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/Scaffolding-HiC-VGP8-tests.yml b/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/Scaffolding-HiC-VGP8-tests.yml index a5190fdba..638d990be 100644 --- a/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/Scaffolding-HiC-VGP8-tests.yml +++ b/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/Scaffolding-HiC-VGP8-tests.yml @@ -1,6 +1,6 @@ - doc: Test outline for Scaffolding-HiC-VGP8 job: - input GFA: + Input GFA: class: File location: https://zenodo.org/records/10037496/files/input%20GFA.gfa1?download=1 filetype: gfa1 diff --git a/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/Scaffolding-HiC-VGP8.ga b/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/Scaffolding-HiC-VGP8.ga index ba9a066e8..67db8e530 100644 --- a/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/Scaffolding-HiC-VGP8.ga +++ b/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/Scaffolding-HiC-VGP8.ga @@ -13,34 +13,34 @@ } ], "format-version": "0.1", - "release": "0.1.2", "license": "CC-BY-4.0", + "release": "0.2", "name": "Scaffolding-HiC-VGP8", "steps": { "0": { - "annotation": "The input GFA must conform to gfa1.2 standards, i.e. should have 'P' lines defined. Output GFAs from assemblers can be run through a GFA->GFA conversion using gfastats to ensure this. ", + "annotation": "The input GFA must conform to gfa1.2 standards, i.e. should have 'P' lines defined. Output GFAs from assemblers can be run through a GFA->GFA conversion using gfastats to ensure this. \n", "content_id": null, "errors": null, "id": 0, "input_connections": {}, "inputs": [ { - "description": "The input GFA must conform to gfa1.2 standards, i.e. should have 'P' lines defined. Output GFAs from assemblers can be run through a GFA->GFA conversion using gfastats to ensure this. ", - "name": "input GFA" + "description": "The input GFA must conform to gfa1.2 standards, i.e. should have 'P' lines defined. Output GFAs from assemblers can be run through a GFA->GFA conversion using gfastats to ensure this. \n", + "name": "Input GFA" } ], - "label": "input GFA", + "label": "Input GFA", "name": "Input dataset", "outputs": [], "position": { "left": 0, - "top": 218.015625 + "top": 163.55078125 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": \"\"}", "tool_version": null, "type": "data_input", - "uuid": "48622cc7-df63-4c71-8a1c-f0d2d326504d", + "uuid": "0c6a3af4-d5fc-442d-abc2-dc28c043abad", "when": null, "workflow_outputs": [] }, @@ -60,8 +60,8 @@ "name": "Input dataset", "outputs": [], "position": { - "left": 36.390625, - "top": 392.96875 + "left": 2.48046875, + "top": 320.09375 }, "tool_id": null, "tool_state": "{\"optional\": true, \"tag\": \"\"}", @@ -69,17 +69,23 @@ "type": "data_input", "uuid": "6b5dfbf0-36da-4489-9f50-23c55ae5762f", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "4a853203-87b2-4ed0-b300-731e7a1aaff1" + } + ] }, "2": { - "annotation": "Provide lineage for BUSCO (e.g. Vertebrata)", + "annotation": "Taxonomic lineage for the organism being assembled for Busco analysis\n", "content_id": null, "errors": null, "id": 2, "input_connections": {}, "inputs": [ { - "description": "Provide lineage for BUSCO (e.g. Vertebrata)", + "description": "Taxonomic lineage for the organism being assembled for Busco analysis\n", "name": "Lineage" } ], @@ -87,7 +93,7 @@ "name": "Input parameter", "outputs": [], "position": { - "left": 28.5, + "left": 89.68318337500133, "top": 487.5 }, "tool_id": null, @@ -96,17 +102,23 @@ "type": "parameter_input", "uuid": "e76f50b3-d497-4f51-884c-0dc181592f8f", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "cb5e2420-90a2-4609-8e4d-d3b0ef520376" + } + ] }, "3": { - "annotation": "", + "annotation": "Forward reads as a single dataset in fastq format", "content_id": null, "errors": null, "id": 3, "input_connections": {}, "inputs": [ { - "description": "", + "description": "Forward reads as a single dataset in fastq format", "name": "HiC Forward reads" } ], @@ -114,11 +126,11 @@ "name": "Input dataset", "outputs": [], "position": { - "left": 24.828125, + "left": 86.05427712500133, "top": 566.625 }, "tool_id": null, - "tool_state": "{\"optional\": false, \"format\": [\"fastqsanger\"], \"tag\": \"\"}", + "tool_state": "{\"optional\": false, \"format\": [\"fastqsanger\", \"fastqsanger.gz\"], \"tag\": \"\"}", "tool_version": null, "type": "data_input", "uuid": "89a3dfc3-42c4-4c08-a221-7f3f844af0a4", @@ -126,14 +138,14 @@ "workflow_outputs": [] }, "4": { - "annotation": "", + "annotation": "Reverse reads as a single dataset in fastq format", "content_id": null, "errors": null, "id": 4, "input_connections": {}, "inputs": [ { - "description": "", + "description": "Reverse reads as a single dataset in fastq format", "name": "HiC reverse reads" } ], @@ -141,11 +153,11 @@ "name": "Input dataset", "outputs": [], "position": { - "left": 25.359375, + "left": 86.54255837500133, "top": 673.9453125 }, "tool_id": null, - "tool_state": "{\"optional\": false, \"format\": [\"fastqsanger\"], \"tag\": \"\"}", + "tool_state": "{\"optional\": false, \"format\": [\"fastqsanger\", \"fastqsanger.gz\"], \"tag\": \"\"}", "tool_version": null, "type": "data_input", "uuid": "3128533f-206a-41f0-9911-98b88e4f8714", @@ -153,14 +165,14 @@ "workflow_outputs": [] }, "5": { - "annotation": "", + "annotation": "Restriction enzymes used in preparation of Hi-C libraries.", "content_id": null, "errors": null, "id": 5, "input_connections": {}, "inputs": [ { - "description": "", + "description": "Restriction enzymes used in preparation of Hi-C libraries.", "name": "Restriction enzymes" } ], @@ -168,8 +180,8 @@ "name": "Input parameter", "outputs": [], "position": { - "left": 34.3125, - "top": 786.015625 + "left": 95.12778237364729, + "top": 786.2561485229093 }, "tool_id": null, "tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}", @@ -177,17 +189,23 @@ "type": "parameter_input", "uuid": "68e8d6b9-f48f-4c78-a603-0623af75111e", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "2fc1e833-68f1-42d7-8246-55119940d36d" + } + ] }, "6": { - "annotation": "", + "annotation": "Estimated genome size from contiging workflow", "content_id": null, "errors": null, "id": 6, "input_connections": {}, "inputs": [ { - "description": "", + "description": "Estimated genome size from contiging workflow", "name": "Estimated genome size - Parameter File" } ], @@ -195,11 +213,11 @@ "name": "Input dataset", "outputs": [], "position": { - "left": 51.203125, - "top": 915.09375 + "left": 112.3863140301566, + "top": 915.1585681126172 }, "tool_id": null, - "tool_state": "{\"optional\": false, \"tag\": \"\"}", + "tool_state": "{\"optional\": false, \"tag\": \"estimated_genome_size\"}", "tool_version": null, "type": "data_input", "uuid": "b9768cf7-430a-4465-adc8-45497954f036", @@ -222,7 +240,7 @@ "name": "Input dataset", "outputs": [], "position": { - "left": 61.953125, + "left": 123.13630837500133, "top": 1019.3125 }, "tool_id": null, @@ -231,88 +249,93 @@ "type": "data_input", "uuid": "6067a21b-a403-4fef-9c9a-184b219a2924", "when": null, - 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"id": 8, + "id": 9, "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool BWA-MEM2", + "name": "fastq_input" + }, + { + "description": "runtime parameter for tool BWA-MEM2", + "name": "reference_source" + } + ], "label": null, "name": "BWA-MEM2", "outputs": [ @@ -341,8 +373,8 @@ } ], "position": { - "left": 1397.067374745586, - "top": 515.859375 + "left": 1457.9766031901042, + "top": 515.8124593098959 }, "post_job_actions": { "HideDatasetActionbam_output": { @@ -376,11 +408,20 @@ "output_name": "output" }, "reference_source|ref_file": { - "id": 8, + "id": 9, "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool BWA-MEM2", + "name": "fastq_input" + }, + { + "description": "runtime parameter for tool BWA-MEM2", + "name": "reference_source" + } + ], "label": null, "name": "BWA-MEM2", "outputs": [ @@ -390,8 +431,8 @@ } ], "position": { - "left": 1306.239249745586, - "top": 956.0625 + "left": 1367.45654296875, + "top": 956.0625208281244 }, "post_job_actions": { "HideDatasetActionbam_output": { @@ -406,7 +447,7 @@ "name": "bwa_mem2", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" - 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"id": 8, + "id": 9, "output_name": "output" } }, @@ -565,7 +606,7 @@ } ], "position": { - "left": 2423.5204997455858, + "left": 2484.703683120587, "top": 0 }, "post_job_actions": { @@ -632,7 +673,7 @@ } ], "position": { - "left": 2167.5204997455858, + "left": 2228.703683120587, "top": 971.375 }, "post_job_actions": { @@ -670,7 +711,7 @@ "id": 16, "input_connections": { "input_file": { - "id": 8, + "id": 9, "output_name": "output" }, "mode_condition|agp_to_path": { @@ -688,8 +729,8 @@ } ], "position": { - "left": 2766.6454997455858, - "top": 128.703125 + "left": 2827.99169921875, + "top": 128.21483406054637 }, "post_job_actions": { "RenameDatasetActionoutput": { @@ -748,7 +789,7 @@ } ], "position": { - "left": 2537.7392497455858, + "left": 2598.922433120587, "top": 1090.8125 }, "post_job_actions": { @@ -799,7 +840,7 @@ } ], "position": { - "left": 3191.0048747455858, + "left": 3252.188058120587, "top": 324.421875 }, "post_job_actions": { @@ -842,7 +883,7 @@ "output_name": "output" }, "mode_condition|statistics_condition|expected_genomesize": { - "id": 9, + "id": 8, "output_name": "integer_param" } }, @@ -856,7 +897,7 @@ } ], "position": { - "left": 3650.5361247455858, + "left": 3711.719308120587, "top": 1761.203125 }, "post_job_actions": { @@ -909,7 +950,7 @@ } ], "position": { - "left": 3778.1923747455858, + "left": 3839.375558120587, "top": 1568.171875 }, "post_job_actions": { @@ -966,7 +1007,7 @@ } ], "position": { - "left": 3437.8954997455858, + "left": 3499.078683120587, "top": 550.453125 }, "post_job_actions": { @@ -1015,7 +1056,7 @@ } ], "position": { - "left": 3436.7392497455858, + "left": 3497.922433120587, "top": 828.171875 }, "post_job_actions": { @@ -1076,7 +1117,7 @@ } ], "position": { - "left": 3723.53125, + "left": 3784.714433375001, "top": 276.07421875 }, "post_job_actions": { @@ -1122,15 +1163,15 @@ "uuid": "9e1fe0cc-77a8-4239-a139-14900a5fcc94", "when": null, "workflow_outputs": [ - { - "label": "Busco Summary image", - "output_name": "summary_image", - "uuid": "5e1fe01a-5d84-4deb-a30b-c2a2d4b46b61" - }, { "label": "Busco Summary", "output_name": "busco_sum", "uuid": "b9937b4e-aed2-4fcf-aad2-1b56d65bed84" + }, + { + "label": "Busco Summary image", + "output_name": "summary_image", + "uuid": "5e1fe01a-5d84-4deb-a30b-c2a2d4b46b61" } ] }, @@ -1149,7 +1190,7 @@ "name": "gfastats_data_prep", "outputs": [], "position": { - "left": 4311.051749745586, + "left": 4372.234933120587, "top": 1677.609375 }, "subworkflow": { @@ -1529,7 +1570,7 @@ } ], "position": { - "left": 3740.7236247455858, + "left": 3801.906808120587, "top": 827.390625 }, "post_job_actions": { @@ -1576,7 +1617,7 @@ } ], "position": { - "left": 4874.457999745586, + "left": 4935.641183120587, "top": 1404.421875 }, "post_job_actions": {}, @@ -1609,7 +1650,7 @@ } ], "position": { - "left": 4876.489249745586, + "left": 4937.672433120587, "top": 1545.40625 }, "post_job_actions": { @@ -1648,7 +1689,7 @@ } ], "position": { - "left": 4079.5829997455858, + "left": 4140.766183120587, "top": 961.375 }, "post_job_actions": { @@ -1695,7 +1736,7 @@ } ], "position": { - "left": 4221.770499745586, + "left": 4282.953683120587, "top": 721.03125 }, "post_job_actions": { @@ -1740,7 +1781,7 @@ } ], "position": { - "left": 5153.832999745586, + "left": 5215.016183120587, "top": 1327.078125 }, "post_job_actions": { @@ -1800,7 +1841,7 @@ } ], "position": { - "left": 5145.551749745586, + "left": 5206.734933120587, "top": 1561.296875 }, "post_job_actions": { @@ -1860,7 +1901,7 @@ } ], "position": { - "left": 4447.950301082095, + "left": 4509.1334844570965, "top": 1064.8994221213547 }, "post_job_actions": { @@ -1912,7 +1953,7 @@ } ], "position": { - "left": 4535.075132770334, + "left": 4596.258316145335, "top": 390.1009386788954 }, "post_job_actions": { @@ -1959,7 +2000,7 @@ } ], "position": { - "left": 4712.270499745586, + "left": 4773.453683120587, "top": 1125.96875 }, "post_job_actions": { @@ -1989,6 +2030,6 @@ "tags": [ "VGP_curated" ], - "uuid": "2551cf72-6739-4ff1-a5ac-8f5061121fda", - "version": 3 -} + "uuid": "434ddf40-c218-42d1-8c7b-a7c5fcd18736", + "version": 14 +} \ No newline at end of file diff --git a/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/CHANGELOG.md b/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/CHANGELOG.md index e5752b6d6..afaed9a2a 100644 --- a/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/CHANGELOG.md +++ b/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/CHANGELOG.md @@ -1,5 +1,11 @@ # Changelog +## [0.1.4] 2023-11-15 + +### Added + +- more descriptive labels for inputs + ## [0.1.3] 2023-11-09 ### Automatic update - `toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy2` diff --git a/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/kmer-profiling-hifi-VGP1.ga b/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/kmer-profiling-hifi-VGP1.ga index e1585dbec..1fbeff580 100644 --- a/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/kmer-profiling-hifi-VGP1.ga +++ b/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/kmer-profiling-hifi-VGP1.ga @@ -14,18 +14,18 @@ ], "format-version": "0.1", "license": "CC-BY-4.0", - "release": "0.1.3", + "release":"0.1.4", "name": "kmer-profiling-hifi-VGP1", "steps": { "0": { - "annotation": "", + "annotation": "A simple list collection containing PacBio data in either fastq or fasta format", "content_id": null, "errors": null, "id": 0, "input_connections": {}, "inputs": [ { - "description": "", + "description": "A simple list collection containing PacBio data in either fastq or fasta format", "name": "Collection of Pacbio Data" } ], @@ -33,8 +33,8 @@ "name": "Input dataset collection", "outputs": [], "position": { - "left": 0, - "top": 15.427657616021285 + "left": 0.0, + "top": 86.5078125 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": \"\", \"collection_type\": \"list\"}", @@ -60,8 +60,8 @@ "name": "Input parameter", "outputs": [], "position": { - "left": 22.121832152706936, - "top": 151.04017592656817 + "left": 17.57421875, + "top": 226.734375 }, "tool_id": null, "tool_state": "{\"default\": 21, \"parameter_type\": \"integer\", \"optional\": true}", @@ -69,17 +69,23 @@ "type": "parameter_input", "uuid": "946bcadd-8ab0-4595-9985-abb574539844", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "18b69ad3-4c09-46f5-9a4c-bf4097b37fef" + } + ] }, "2": { - "annotation": "", + "annotation": "Ploidy for the organism being assembled", "content_id": null, "errors": null, "id": 2, "input_connections": {}, "inputs": [ { - "description": "", + "description": "Ploidy for the organism being assembled", "name": "Ploidy" } ], @@ -87,8 +93,8 @@ "name": "Input parameter", "outputs": [], "position": { - "left": 65.68433215270693, - "top": 283.0276637195369 + "left": 50.12890625, + "top": 342.609375 }, "tool_id": null, "tool_state": "{\"default\": 2, \"parameter_type\": \"integer\", \"optional\": true}", @@ -96,7 +102,13 @@ "type": "parameter_input", "uuid": "e3848560-55a2-42a5-ac1a-487ccf084d92", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "1fea95fa-67d6-408d-94b6-264107cc19a1" + } + ] }, "3": { "annotation": "", @@ -123,8 +135,8 @@ } ], "position": { - "left": 300.9374263897614, - "top": 16.412041203882488 + "left": 296.8668759977911, + "top": 27 }, "post_job_actions": { "HideDatasetActionread_db": { @@ -168,8 +180,8 @@ } ], "position": { - "left": 569.718710741206, - "top": 143.25579365755715 + "left": 576.8668759977911, + "top": 0 }, "post_job_actions": { "TagDatasetActionread_db": { @@ -221,8 +233,8 @@ } ], "position": { - "left": 859.375, - "top": 92.34016036987308 + "left": 856.8668759977911, + "top": 42 }, "post_job_actions": { "HideDatasetActionread_db_hist": { @@ -298,8 +310,8 @@ } ], "position": { - "left": 1198.9374694824219, - "top": 0.0 + "left": 1136.866875997791, + "top": 15 }, "post_job_actions": { "TagDatasetActionlinear_plot": { @@ -365,6 +377,11 @@ "uuid": "955de351-ef19-42dc-89d7-ca213994515a", "when": null, "workflow_outputs": [ + { + "label": "GenomeScope linear plot", + "output_name": "linear_plot", + "uuid": "57230be4-36d5-4307-b4b0-b8a73f6800ce" + }, { "label": "GenomeScope transformed linear plot", "output_name": "transformed_linear_plot", @@ -389,11 +406,6 @@ "label": "GenomeScope log plot", "output_name": "log_plot", "uuid": "988e2189-d5f2-4e9e-8fc2-4434e68e8501" - }, - { - "label": "GenomeScope linear plot", - "output_name": "linear_plot", - "uuid": "57230be4-36d5-4307-b4b0-b8a73f6800ce" } ] } @@ -402,6 +414,6 @@ "Reviewed", "VGP" ], - "uuid": "a3ef9c73-c661-46af-bfde-3daa97d8b473", - "version": 2 + "uuid": "7542ffba-d083-415e-b745-08d9503debc4", + "version": 4 } \ No newline at end of file diff --git a/workflows/data-fetching/parallel-accession-download/CHANGELOG.md b/workflows/data-fetching/parallel-accession-download/CHANGELOG.md index e27378f3a..5bb1e09fe 100644 --- a/workflows/data-fetching/parallel-accession-download/CHANGELOG.md +++ b/workflows/data-fetching/parallel-accession-download/CHANGELOG.md @@ -1,5 +1,10 @@ # Changelog +## [0.1.8] 2023-11-20 + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.0.8+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.0.8+galaxy1` + ## [0.1.7] 2023-11-10 ### Automatic update diff --git a/workflows/data-fetching/parallel-accession-download/parallel-accession-download-tests.yml b/workflows/data-fetching/parallel-accession-download/parallel-accession-download-tests.yml index c750457a7..34a0291c4 100644 --- a/workflows/data-fetching/parallel-accession-download/parallel-accession-download-tests.yml +++ b/workflows/data-fetching/parallel-accession-download/parallel-accession-download-tests.yml @@ -8,24 +8,5 @@ element_tests: SRR044777: file: test-data/SRR044777_head.fastq - decompress: true + decompress: false compare: contains - -- doc: Test download of single and paired end accession - job: - Run accessions: - class: File - path: test-data/input_accession_paired_end.txt - outputs: - Paired End Reads: - element_tests: - SRR11953971: - elements: - forward: - file: test-data/SRR11953971_1_head.fastq - decompress: true - compare: contains - reverse: - file: test-data/SRR11953971_2_head.fastq - decompress: true - compare: contains 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 1aefcd3b2..81cb2cc5e 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": "0.1.7", + "release": "0.1.8", "name": "Parallel Accession Download", "steps": { "0": { @@ -131,7 +131,7 @@ }, "3": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.0.8+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.0.8+galaxy1", "errors": null, "id": 3, "input_connections": { @@ -187,15 +187,15 @@ "output_name": "output_collection_other" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.0.8+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.0.8+galaxy1", "tool_shed_repository": { - "changeset_revision": "6591f049cf7e", + "changeset_revision": "e407b9da183a", "name": "sra_tools", "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_version": "3.0.8+galaxy0", + "tool_version": "3.0.8+galaxy1", "type": "tool", "uuid": "4d328e7b-df7d-4d3e-a60f-1ea12925f317", "when": null, diff --git a/workflows/data-fetching/sra-manifest-to-concatenated-fastqs/CHANGELOG.md b/workflows/data-fetching/sra-manifest-to-concatenated-fastqs/CHANGELOG.md index a3935d194..ad99cf293 100644 --- a/workflows/data-fetching/sra-manifest-to-concatenated-fastqs/CHANGELOG.md +++ b/workflows/data-fetching/sra-manifest-to-concatenated-fastqs/CHANGELOG.md @@ -1,5 +1,10 @@ # Changelog +## [0.2.1] 2023-11-20 + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.0.8+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.0.8+galaxy1` + ## [0.2] 2023-11-10 ### Automatic update diff --git a/workflows/data-fetching/sra-manifest-to-concatenated-fastqs/sra-manifest-to-concatenated-fastqs.ga b/workflows/data-fetching/sra-manifest-to-concatenated-fastqs/sra-manifest-to-concatenated-fastqs.ga index fc85f267e..b774725c4 100644 --- a/workflows/data-fetching/sra-manifest-to-concatenated-fastqs/sra-manifest-to-concatenated-fastqs.ga +++ b/workflows/data-fetching/sra-manifest-to-concatenated-fastqs/sra-manifest-to-concatenated-fastqs.ga @@ -19,7 +19,7 @@ } ], "format-version": "0.1", - "release": "0.2", + "release": "0.2.1", "license": "MIT", "name": "sra_manifest_to_concatenated_fastqs_parallel", "steps": { @@ -360,7 +360,7 @@ }, "9": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.0.8+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.0.8+galaxy1", "errors": null, "id": 9, "input_connections": { @@ -416,15 +416,15 @@ "output_name": "output_collection_other" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.0.8+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.0.8+galaxy1", "tool_shed_repository": { - "changeset_revision": "6591f049cf7e", + "changeset_revision": "e407b9da183a", "name": "sra_tools", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "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__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "3.0.8+galaxy0", + "tool_version": "3.0.8+galaxy1", "type": "tool", "uuid": "fa409017-1eea-4426-83f6-22a10b9f762c", "when": null,