Gigascience_Indels_SAV_non-normal_demonstration_STS26T-Gent_Workflow

Run Workflow in Galaxy

• Galaxy Europe
• Galaxy France
• Galaxy Australia
• Galaxy Main
• Import to another server (≥23.0+ only!)

flowchart TD
  0["ℹ️ Input Dataset\nHomo_sapiens.GRCh38_canon.106.gtf"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nRNA-Seq_Reads_2.fastq"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nRNA-Seq_Reads_1.fastq"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\nHUMAN-Uniprot-and-isoforms_and_cRAP-FASTA-Database"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["Uncompressed_RNA_Seq_Reads_2"];
  1 -->|output| 4;
  5983317a-db25-4f0f-8a0b-290d15aafd14["Output\nUncompressed_RNA_Seq_Reads_2"];
  4 --> 5983317a-db25-4f0f-8a0b-290d15aafd14;
  style 5983317a-db25-4f0f-8a0b-290d15aafd14 stroke:#2c3143,stroke-width:4px;
  5["Uncompressed_RNA_Seq_Reads_1"];
  2 -->|output| 5;
  d6f2044c-cd3b-4fde-901a-2c6c7db5db4f["Output\nUncompressed_RNA_Seq_Reads_1"];
  5 --> d6f2044c-cd3b-4fde-901a-2c6c7db5db4f;
  style d6f2044c-cd3b-4fde-901a-2c6c7db5db4f stroke:#2c3143,stroke-width:4px;
  6["Convert_HUMAN_Uniprot_and_CRAP_FASTA_to_tabular"];
  3 -->|output| 6;
  067e8f48-59d2-4f9c-bce9-13d1dca9d74e["Output\nHUMAN_Uniprot_and_CRAP.tabular"];
  6 --> 067e8f48-59d2-4f9c-bce9-13d1dca9d74e;
  style 067e8f48-59d2-4f9c-bce9-13d1dca9d74e stroke:#2c3143,stroke-width:4px;
  7["HISAT2_Alignment_BAM"];
  5 -->|output1| 7;
  4 -->|output1| 7;
  0137dcb5-9d02-427f-82da-995723a93c85["Output\nHISAT2_Alignment_BAM"];
  7 --> 0137dcb5-9d02-427f-82da-995723a93c85;
  style 0137dcb5-9d02-427f-82da-995723a93c85 stroke:#2c3143,stroke-width:4px;
  8["Filtering_HUMAN_Uniprot_and_cRAP_Accessions_tabular"];
  6 -->|output| 8;
  4a2dbdd0-8e12-418c-a8f9-38256a760be8["Output\nFiltering_HUMAN_Uniprot_and_cRAP_Accessions_tabular"];
  8 --> 4a2dbdd0-8e12-418c-a8f9-38256a760be8;
  style 4a2dbdd0-8e12-418c-a8f9-38256a760be8 stroke:#2c3143,stroke-width:4px;
  9["StringTie_Alignment_GTF"];
  0 -->|output| 9;
  7 -->|output_alignments| 9;
  a4ff5eba-c73a-424b-8a9e-cfe76a0fe77f["Output\nStringTie_Alignment_GTF"];
  9 --> a4ff5eba-c73a-424b-8a9e-cfe76a0fe77f;
  style a4ff5eba-c73a-424b-8a9e-cfe76a0fe77f stroke:#2c3143,stroke-width:4px;
  10["FreeBayes_variants_VCF"];
  7 -->|output_alignments| 10;
  b4ebb058-327d-4284-b96e-f7491262912e["Output\nFreeBayes_variants_VCF"];
  10 --> b4ebb058-327d-4284-b96e-f7491262912e;
  style b4ebb058-327d-4284-b96e-f7491262912e stroke:#2c3143,stroke-width:4px;
  11["GffCompare_Annotated_Transcripts_GTF"];
  0 -->|output| 11;
  9 -->|output_gtf| 11;
  72c73a0b-6677-4701-ab52-4d296c553df9["Output\nGffCompare_Annotated_Transcripts_GTF"];
  11 --> 72c73a0b-6677-4701-ab52-4d296c553df9;
  style 72c73a0b-6677-4701-ab52-4d296c553df9 stroke:#2c3143,stroke-width:4px;
  12["CustomProDB_protein_FASTAs_from_BAM_and_VCF"];
  7 -->|output_alignments| 12;
  10 -->|output_vcf| 12;
  8ce883fd-1961-47f6-b7b0-8153b7d1b4be["Output\nCustomProDB_INDEL_FASTA"];
  12 --> 8ce883fd-1961-47f6-b7b0-8153b7d1b4be;
  style 8ce883fd-1961-47f6-b7b0-8153b7d1b4be stroke:#2c3143,stroke-width:4px;
  b31fbd26-fec0-42d9-a079-a28ae64ec009["Output\nCustomProDB_VARIANT_ANNOTATION_RDATA"];
  12 --> b31fbd26-fec0-42d9-a079-a28ae64ec009;
  style b31fbd26-fec0-42d9-a079-a28ae64ec009 stroke:#2c3143,stroke-width:4px;
  b7944440-cbca-4fb5-96fd-03e952854728["Output\nCustomProDB_Genomic_SQLlite"];
  12 --> b7944440-cbca-4fb5-96fd-03e952854728;
  style b7944440-cbca-4fb5-96fd-03e952854728 stroke:#2c3143,stroke-width:4px;
  9cee39b1-2766-43b0-b002-697e496a11d7["Output\nCustomProDB_VARIANT_ANNOTATION_SQLite"];
  12 --> 9cee39b1-2766-43b0-b002-697e496a11d7;
  style 9cee39b1-2766-43b0-b002-697e496a11d7 stroke:#2c3143,stroke-width:4px;
  8258d64c-c755-4b49-b417-32ea722773bd["Output\nCustomProDB_RPKM_FASTA"];
  12 --> 8258d64c-c755-4b49-b417-32ea722773bd;
  style 8258d64c-c755-4b49-b417-32ea722773bd stroke:#2c3143,stroke-width:4px;
  9ce1b014-b001-4ed8-9144-5890bb8cdbd5["Output\nCustomProDB_SNV_FASTA"];
  12 --> 9ce1b014-b001-4ed8-9144-5890bb8cdbd5;
  style 9ce1b014-b001-4ed8-9144-5890bb8cdbd5 stroke:#2c3143,stroke-width:4px;
  13["GffCompare_Annotated_GTF_to_BED"];
  11 -->|transcripts_annotated| 13;
  751c3898-45a0-4836-bd33-44affbe9748a["Output\nGffCompare_Annotated_GTF_to_BED"];
  13 --> 751c3898-45a0-4836-bd33-44affbe9748a;
  style 751c3898-45a0-4836-bd33-44affbe9748a stroke:#2c3143,stroke-width:4px;
  14["Convert_INDEL_FASTA_to_tabular"];
  12 -->|output_indel| 14;
  dc1bb9c3-0f77-4f30-a0ea-d164563269d8["Output\nCustomProDB_INDEL.tabular"];
  14 --> dc1bb9c3-0f77-4f30-a0ea-d164563269d8;
  style dc1bb9c3-0f77-4f30-a0ea-d164563269d8 stroke:#2c3143,stroke-width:4px;
  15["Convert-SNV_FASTA_to_tabular"];
  12 -->|output_snv| 15;
  0d8682f5-66fa-40db-b280-d6f1bb4a5717["Output\nCustomProDB_SNV.tabular"];
  15 --> 0d8682f5-66fa-40db-b280-d6f1bb4a5717;
  style 0d8682f5-66fa-40db-b280-d6f1bb4a5717 stroke:#2c3143,stroke-width:4px;
  16["Convert-RPKM_FASTA_to_tabular"];
  12 -->|output_rpkm| 16;
  88cfd137-3b8e-4c69-b38a-0b9ea8fea7fc["Output\nCustomProDB_RPKM.tabular"];
  16 --> 88cfd137-3b8e-4c69-b38a-0b9ea8fea7fc;
  style 88cfd137-3b8e-4c69-b38a-0b9ea8fea7fc stroke:#2c3143,stroke-width:4px;
  17["Converting_Genomic_SQLite_to_database_mode"];
  12 -->|output_genomic_mapping_sqlite| 17;
  91eaaad0-e93e-434b-b87c-2de0f9c232ef["Output\nConvert_Genomic_SQLite_to_tabular"];
  17 --> 91eaaad0-e93e-434b-b87c-2de0f9c232ef;
  style 91eaaad0-e93e-434b-b87c-2de0f9c232ef stroke:#2c3143,stroke-width:4px;
  18["Converting_CustomProDB_FASTA_to_tabular"];
  12 -->|output_rpkm| 18;
  6bcf6e52-85a8-439e-83cc-50de2cc8749d["Output\nCustomProDB_FASTA_to_tabular"];
  18 --> 6bcf6e52-85a8-439e-83cc-50de2cc8749d;
  style 6bcf6e52-85a8-439e-83cc-50de2cc8749d stroke:#2c3143,stroke-width:4px;
  19["Converting_Variant_SQLite_to_database_mode"];
  12 -->|output_variant_annotation_sqlite| 19;
  7698d1f1-7979-4deb-9ac2-0f1541d905ce["Output\nConvert_Variant_SQLite_to_tabular"];
  19 --> 7698d1f1-7979-4deb-9ac2-0f1541d905ce;
  style 7698d1f1-7979-4deb-9ac2-0f1541d905ce stroke:#2c3143,stroke-width:4px;
  20["Translate_BED_Transcripts"];
  13 -->|output| 20;
  9510c804-d13e-4cd6-b08e-1c670623e296["Output\nTranslation_FASTA"];
  20 --> 9510c804-d13e-4cd6-b08e-1c670623e296;
  style 9510c804-d13e-4cd6-b08e-1c670623e296 stroke:#2c3143,stroke-width:4px;
  4ebcd87a-1526-4c05-914d-6051b996201d["Output\nTranslate_BED_Transcripts"];
  20 --> 4ebcd87a-1526-4c05-914d-6051b996201d;
  style 4ebcd87a-1526-4c05-914d-6051b996201d stroke:#2c3143,stroke-width:4px;
  21["Annotating-INDEL"];
  14 -->|output| 21;
  aff83bc0-c7af-4257-a51c-93dfe90ae6c0["Output\nAnnotating-INDEL"];
  21 --> aff83bc0-c7af-4257-a51c-93dfe90ae6c0;
  style aff83bc0-c7af-4257-a51c-93dfe90ae6c0 stroke:#2c3143,stroke-width:4px;
  22["Annotating-SNV"];
  15 -->|output| 22;
  960e7c54-1a91-4b92-b75c-0da23fe1650a["Output\nAnnotating-SNV"];
  22 --> 960e7c54-1a91-4b92-b75c-0da23fe1650a;
  style 960e7c54-1a91-4b92-b75c-0da23fe1650a stroke:#2c3143,stroke-width:4px;
  23["Annotating-RPKM"];
  16 -->|output| 23;
  ef203c53-9e5b-4120-a508-a0dcbbfaec3b["Output\nAnnotating-RPKM"];
  23 --> ef203c53-9e5b-4120-a508-a0dcbbfaec3b;
  style ef203c53-9e5b-4120-a508-a0dcbbfaec3b stroke:#2c3143,stroke-width:4px;
  24["Annotating_Genomic_SQLite"];
  17 -->|query_results| 24;
  045776fe-4fc9-4da1-b808-4ab674dcced4["Output\nAnnotating_Genomic_SQLite"];
  24 --> 045776fe-4fc9-4da1-b808-4ab674dcced4;
  style 045776fe-4fc9-4da1-b808-4ab674dcced4 stroke:#2c3143,stroke-width:4px;
  25["Filtering_RPKM_accessions"];
  18 -->|output| 25;
  d23ae9b0-374f-4668-831c-c08217161834["Output\nFiltering_RPKM_accessions"];
  25 --> d23ae9b0-374f-4668-831c-c08217161834;
  style d23ae9b0-374f-4668-831c-c08217161834 stroke:#2c3143,stroke-width:4px;
  26["Annotating_Variant_SQLite"];
  19 -->|query_results| 26;
  0238c405-dbcb-40a0-b9ce-6bc091cc01c5["Output\nAnnotating_Variant_SQLite"];
  26 --> 0238c405-dbcb-40a0-b9ce-6bc091cc01c5;
  style 0238c405-dbcb-40a0-b9ce-6bc091cc01c5 stroke:#2c3143,stroke-width:4px;
  27["Convert_Translation_BED_to_tabular_for_protein_map"];
  20 -->|translation_bed| 27;
  873fc597-ac53-4dfa-8f5a-d5532af8886c["Output\nTranslation_tabular_for_protein_map"];
  27 --> 873fc597-ac53-4dfa-8f5a-d5532af8886c;
  style 873fc597-ac53-4dfa-8f5a-d5532af8886c stroke:#2c3143,stroke-width:4px;
  28["Converting_Annotated_Indel_to_FASTA"];
  21 -->|out_file1| 28;
  ae642819-14c2-46d9-a31f-0b142c074a8c["Output\nConverting_Annotated_Indel_to_FASTA"];
  28 --> ae642819-14c2-46d9-a31f-0b142c074a8c;
  style ae642819-14c2-46d9-a31f-0b142c074a8c stroke:#2c3143,stroke-width:4px;
  29["Converting_Annotated_SNV_to_FASTA"];
  22 -->|out_file1| 29;
  49e24e6a-ae3e-463c-915b-65f895a471e4["Output\nConverting_Annotated_SNV_to_FASTA"];
  29 --> 49e24e6a-ae3e-463c-915b-65f895a471e4;
  style 49e24e6a-ae3e-463c-915b-65f895a471e4 stroke:#2c3143,stroke-width:4px;
  30["Converting_Annotated_RPKM_to_FASTA"];
  23 -->|out_file1| 30;
  0969ba6f-4bd8-4464-94cc-c990cf395507["Output\nConverting_Annotated_RPKM_to_FASTA"];
  30 --> 0969ba6f-4bd8-4464-94cc-c990cf395507;
  style 0969ba6f-4bd8-4464-94cc-c990cf395507 stroke:#2c3143,stroke-width:4px;
  31["Concatenate_HUMAN_Crap_protein-accessions"];
  8 -->|output| 31;
  25 -->|output| 31;
  e3f2a023-888a-4d80-b16c-ea87adbc6588["Output\nConcatenate_HUMAN_Crap_protein-accessions"];
  31 --> e3f2a023-888a-4d80-b16c-ea87adbc6588;
  style e3f2a023-888a-4d80-b16c-ea87adbc6588 stroke:#2c3143,stroke-width:4px;
  32["Variant_input_for_MVP"];
  26 -->|out_file1| 32;
  ef638bf1-2cd7-4c4f-acc7-0fc5ce771756["Output\nVariant_input_for_MVP"];
  32 --> ef638bf1-2cd7-4c4f-acc7-0fc5ce771756;
  style ef638bf1-2cd7-4c4f-acc7-0fc5ce771756 stroke:#2c3143,stroke-width:4px;
  33["Concatenate_databases_from_Genomic_SQlite_and_translation_BED_file"];
  24 -->|out_file1| 33;
  27 -->|output| 33;
  77671f49-26c7-4eeb-b38c-62f09933e99b["Output\nConcatenate_databases_from_Genomic_SQlite_and_translation_BED_file"];
  33 --> 77671f49-26c7-4eeb-b38c-62f09933e99b;
  style 77671f49-26c7-4eeb-b38c-62f09933e99b stroke:#2c3143,stroke-width:4px;
  34["Merge_Indel_SNV_RPKM_to_make_Non_normal_CustomProDB_FASTA"];
  30 -->|output| 34;
  29 -->|output| 34;
  28 -->|output| 34;
  81e3ae85-7111-4517-a9fe-64f245654ad4["Output\nNon-normal_CustomProDB_FASTA"];
  34 --> 81e3ae85-7111-4517-a9fe-64f245654ad4;
  style 81e3ae85-7111-4517-a9fe-64f245654ad4 stroke:#2c3143,stroke-width:4px;
  35["Genomic_input_for_MVP"];
  33 -->|out_file1| 35;
  d72ce75b-6ee3-4bcb-b829-f3c85b3c5a65["Output\nGenomic_input_for_MVP"];
  35 --> d72ce75b-6ee3-4bcb-b829-f3c85b3c5a65;
  style d72ce75b-6ee3-4bcb-b829-f3c85b3c5a65 stroke:#2c3143,stroke-width:4px;
  36["Human_cRAP_Non_normal_transcripts_dB generation"];
  3 -->|output| 36;
  34 -->|output| 36;
  20 -->|translation_fasta| 36;
  400380de-2047-4c30-a9e4-320a19489be4["Output\nHuman_cRAP_Non_normal_transcripts_dB generation"];
  36 --> 400380de-2047-4c30-a9e4-320a19489be4;
  style 400380de-2047-4c30-a9e4-320a19489be4 stroke:#2c3143,stroke-width:4px;

Inputs

Outputs

Tools

To use these workflows in Galaxy you can either click the links to download the workflows, or you can right-click and copy the link to the workflow which can be used in the Galaxy form to import workflows.

Importing into Galaxy

Hands-on: Importing a workflow

• Click on Workflow on the top menu bar of Galaxy. You will see a list of all your workflows.
• Click on galaxy-upload Import at the top-right of the screen
• Provide your workflow
  • Option 1: Paste the URL of the workflow into the box labelled “Archived Workflow URL”
  • Option 2: Upload the workflow file in the box labelled “Archived Workflow File”
• Click the Import workflow button

Below is a short video demonstrating how to import a workflow from GitHub using this procedure:

Version History

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/neoantigen-2-non-normal-database-generation/workflows/main_workflow.ga -O workflow.ga
workflow-to-tools -w workflow.ga -o tools.yaml
shed-tools install -g GALAXY -a API_KEY -t tools.yaml
workflow-install -g GALAXY -a API_KEY -w workflow.ga --publish-workflows