diff --git a/topics/sequence-analysis/tutorials/mapping/tutorial.md b/topics/sequence-analysis/tutorials/mapping/tutorial.md index 718df778b449ac..b5b2ed18580b9e 100644 --- a/topics/sequence-analysis/tutorials/mapping/tutorial.md +++ b/topics/sequence-analysis/tutorials/mapping/tutorial.md @@ -33,10 +33,17 @@ follow_up_training: level: Introductory edam_ontology: - topic_0102 -contributors: -- joachimwolff -- bebatut -- hexylena +contributions: + authorship: + - joachimwolff + - bebatut + - hexylena + editing: + - tflowers15 + funding: + - unimelb + - melbournebioinformatics + - AustralianBioCommons recordings: - captioners: - shiltemann @@ -114,6 +121,10 @@ In the following, we will process a dataset with the mapper **Bowtie2** and we w > > {% snippet faqs/galaxy/datasets_rename.md %} > +> 4. Create a paired collection named `Paired Reads` +> +> {% snippet faqs/galaxy/collections_build_list_paired.md %} +> {: .hands_on} We just imported in Galaxy FASTQ files corresponding to paired-end data as we could get directly from a sequencing facility. @@ -135,10 +146,9 @@ We need a reference genome to map the reads on. Currently, there are over 60 different mappers, and their number is growing. In this tutorial, we will use [Bowtie2](http://bowtie-bio.sourceforge.net/bowtie2/), a fast and memory-efficient open-source tool particularly good at aligning sequencing reads of about 50 up to 1,000s of bases to relatively long genomes. > Mapping with Bowtie2 -> 1. {% tool [Bowtie2](toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.2+galaxy0) %} with the following parameters +> 1. {% tool [Bowtie2](toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.4+galaxy0) %} with the following parameters > - *"Is this single or paired library"*: `Paired-end` -> - {% icon param-file %} *"FASTA/Q file #1"*: `reads_1` -> - {% icon param-file %} *"FASTA/Q file #2"*: `reads_2` +> - {% icon param-collection %} *"FASTQ Paired Dataset"*: `Paired Reads` > - *"Do you want to set paired-end options?"*: `No` > > You should have a look at the parameters there, specially the mate orientation if you know it. They can improve the quality of the paired-end mapping. diff --git a/topics/sequence-analysis/tutorials/mapping/workflows/mapping-test.yml b/topics/sequence-analysis/tutorials/mapping/workflows/mapping-test.yml deleted file mode 100644 index b7164ce47eb70c..00000000000000 --- a/topics/sequence-analysis/tutorials/mapping/workflows/mapping-test.yml +++ /dev/null @@ -1,16 +0,0 @@ ---- -- doc: "Test sample data for Sequence analysis:Mapping" - job: mapping-job.yml - outputs: - bowtie2_mapping_stats: - asserts: - has_text: - text: '43652 (90.26%) aligned concordantly exactly 1 time' - bam_stats_1: - asserts: - has_text: - text: '4819009' - bam_stats_2: - asserts: - has_text: - text: '4466767' diff --git a/topics/sequence-analysis/tutorials/mapping/workflows/mapping-tests.yml b/topics/sequence-analysis/tutorials/mapping/workflows/mapping-tests.yml new file mode 100644 index 00000000000000..d59b448af72fd6 --- /dev/null +++ b/topics/sequence-analysis/tutorials/mapping/workflows/mapping-tests.yml @@ -0,0 +1,29 @@ +- doc: "Test sample data for Sequence analysis: Mapping" + job: + null: + class: Collection + collection_type: list:paired + elements: + - class: Collection + type: paired + identifier: wt_H3K4me3 + elements: + - class: File + identifier: forward + location: https://zenodo.org/record/1324070/files/wt_H3K4me3_read1.fastq.gz + - class: File + identifier: reverse + location: https://zenodo.org/record/1324070/files/wt_H3K4me3_read2.fastq.gz + outputs: + bowtie2_mapping_stats: + asserts: + has_text: + text: '43652 (90.26%) aligned concordantly exactly 1 time' + bam_stats_1: + asserts: + has_text: + text: '4819009' + bam_stats_2: + asserts: + has_text: + text: '4466767' diff --git a/topics/sequence-analysis/tutorials/mapping/workflows/mapping.ga b/topics/sequence-analysis/tutorials/mapping/workflows/mapping.ga index f4046a16f515a8..f5b4c8f2da204e 100644 --- a/topics/sequence-analysis/tutorials/mapping/workflows/mapping.ga +++ b/topics/sequence-analysis/tutorials/mapping/workflows/mapping.ga @@ -1,8 +1,20 @@ { "a_galaxy_workflow": "true", "annotation": "Mapping", + "comments": [], + "creator": [ + { + "class": "Person", + "identifier": "0000-0002-6606-5953", + "name": "Tristan Reynolds" + } + ], "format-version": "0.1", - "name": "GTN - Sequence Analyses - Mapping (imported from uploaded file)", + "license": "CC-BY-4.0", + "name": "GTN - Sequence Analyses - Mapping", + "report": { + "markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n" + }, "steps": { "0": { "annotation": "", @@ -10,138 +22,108 @@ "errors": null, "id": 0, "input_connections": {}, - "inputs": [ - { - "description": "", - "name": "reads_1" - } - ], - "label": "reads_1", - "name": "Input dataset", + "inputs": [], + "label": null, + "name": "Input dataset collection", "outputs": [], "position": { - "bottom": -18, - "height": 61, - "left": -85, - "right": 115, - "top": -79, - "width": 200, - "x": -85, - "y": -79 + "left": 0, + "top": 192.23747731820447 }, "tool_id": null, - "tool_state": "{\"optional\": false}", + "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list:paired\", \"fields\": null}", "tool_version": null, - 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