[GLT-3652] updates to match MISO v1.43.1 (#111)

Author: djcooke

_config.yml

@@ -16,6 +16,7 @@ miso_url: 'http://miso.gsi.oicr.on.ca'
 
 # Configuration for important site-specific values used in the tutorials. Make
 # sure these match existing items in your MISO instance.
+pipeline: 'Research'
 box_size: '8x12 Storage (scannable)'
 sequencer: 'D00331'
 platform: 'Illumina HiSeq 2500'
@@ -28,6 +29,7 @@ library_type: 'Paired End'
 index_kit: 'Nextera DNA Dual Index'
 flowcell: 'HiSeq PE Flow Cell v4'
 seq_params: 'V4 2×101'
+run_scanner_run: '220120_A00469_0263_AH3YMFDSX3'
 lane_qc_bad: 'Failed: Other problem'
 
 # values only affecting plain sample mode

_includes/libraries-from-samples.md

@@ -23,11 +23,6 @@ In this section, you will use the samples created already to create libraries.
 1. A table will appear. Enter the library information:
     * _Library Name_: Leave blank as this will be filled in automatically after save.
     * _Library Alias_: Leave blank as this will be filled in automatically.
-{% if include.detailed == true %}
-    * _Description_: `Library ((Tissue type)(individual))`, e.g. `Library P1`
-{% else %}
-    * _Description_: `Library (row number)`, e.g. `Library 1`
-{% endif %}
     * _Matrix Barcode_: As before, usually this would be scanned by the hand scanner. In this tutorial, enter matrix
       barcodes in the form `(project {% if include.detailed %}short{% endif %} name)_(row number)_lib`, e.g.
       `PROJ_1_lib`.

_includes/libraries-qc.md

@@ -4,7 +4,7 @@
 
 There are three ways to indicate library quality in MISO: 1)
 Enter quantitative QC values under the _Library QC_ section; 2) The overall
-pre-sequencing quality flag _QC passed_; and 3) The post-sequencing quality
+pre-sequencing quality field _QC Status_; and 3) The post-sequencing quality
 control flag _Low quality library_.
 
 ## 4.1 Library QC

_includes/libraries-receipt.md

@@ -26,22 +26,24 @@ if they match the data entered.
     * _Sample Alias_: Enter a sample alias like `{{ site.plain_sample6_alias }}`, replacing `PROJ` with your project's
       name.
 {% endif %}
-    * _Sample Type_: `GENOMIC`
     * _Project_: Select your project from the drop-down.
 {% if include.detailed %}
     * _Subproject_: Select the subproject you created.
 {% endif %}
+    * _Sample Type_: `GENOMIC`
     * _Sci. Name_: `{{ site.scientific_name }}`{% if include.detailed == true %}
     * _External Name_: Enter `PROJ_ID10`, replacing the `PROJ` with your own project short name. The
       _Identity Alias_ column should change to show `First Receipt (PROJ)`.
     * _Donor Sex_: Select any.
     * _Tissue Origin_: `{{ site.tissue_origin_4 }}`
     * _Tissue Type_: `{{ site.tissue_type_2 }}`
     * _Times Received_: `1`
-    * _Tube Number_: `1`{% endif %}
+    * _Tube Number_: `1`
+    * _Timepoint_: `Week 8`{% endif %}
     * _Date of receipt_: Select today's date
     * _Received From_: Select any lab.
     * _Received By_: Select any group.
+    * _Matrix Barcode_: Enter `PROJ_lib5`, replacing `PROJ` with your own project short name.
 {% if include.detailed == true %}
     * _Design_: Select any.
 {% endif %}

_includes/project-create.md

@@ -18,20 +18,11 @@ display with a number of fields that you can fill in.
 1. Leave the _Short Name_ field blank.
 {% endif %}
 1. In the _Description_ field, enter `MISO training workshop [Date]`
-1. Choose the amount of _Progress_ that your project has accomplished:
-  * Unknown : I was told to enter this data and I does what they tells me.
-  * Active : We are receiving/have received samples and are actively working on
-    this project.
-  * Inactive : Project is not yet done, but waiting for external collaborators,
-    REB approval, papers to be published, etc.
-  * Cancelled : Project was scrapped because we did not get funding/samples/REB
-    approval.
-  * Proposed : Project Initiation form has been received and is awaiting go-ahead
-    by Genomics leadership.
-  * Pending : We are waiting for the project to start.
-  * Approved : Project has been approved by Genomics leadership.
+1. For the _Progress_ field, choose `Active`
 1. Select the _Reference Genome_ `{{ site.reference_genome }}`. This should be the primary species that will be
    sequenced in the course of the project. Xenografts count as human.
+1. Select the _Pipeline_ `{{ site.pipeline }}`. This value identifies the analysis pipeline to put sample data through
+   after sequencing
 1. Click the _Save_ button at the upper right.
-1. MISO will generate an ID and name for the project. The name be 'PRO' followed by the ID (e.g. "PRO123").
+1. MISO will generate an ID and name for the project. The name will be 'PRO' followed by the ID (e.g. "PRO123").
    {% if include.worksheet %}Record this name in your worksheet. <img src="pics/blue_pencil.png">{% endif %}

_includes/project-new.md

@@ -19,21 +19,6 @@ button where you can find basic information about the current page.
 
 {% include project-create.md detailed=include.detailed section=2.1 worksheet=true %}
 
-### 2.1.1 Add a Study (optional)
-
-If you plan to upload your project data to the ENA, you must add a _Study_ to
-your Project.
-
-1. Click on the _Studies_ header to expand the section.
-1. Click the _Add_ button at the top left of the table.
-1. Much like creating a Project, enter:
-    * _Alias_ (letters and numbers only): this can have any name, but make sure
-       it is recognizable as belonging to your Project.
-    * _Description_: any free-text description
-    * _Study Type_: Select an option from the drop-down menu. Unless you are certain
-      of the sequencing type, select `Other`.
-1. Click the _Save_ button at the upper right.
-
 
 ## 2.2 Projects List
 
@@ -63,7 +48,7 @@ searched using the field in the upper right.
 
 ### 2.3.1 Add Project Files
 
-In the _Project Files_ section, you can add attach any necessary documents to the
+In the _Project Files_ section, you can attach any necessary documents to the
 project (e.g. Project Information form, REB).
 
 1. On the Edit Project page, click the _Project Files_ header to expand the section.

_includes/runs-add-pools.md

@@ -24,5 +24,5 @@ _Sequencing Container_.
 
 Now check on the sequencing order.
 
-1. Click on the _Outstanding Sequencing Orders_ page and verify that the _Remaining_ column now shows 1 for the pool you
+1. Click on the _Outstanding Sequencing Orders_ page and verify that the _Running_ column now shows 1 for the pool you
    added to the run.

_includes/runs-auto.md

@@ -11,7 +11,7 @@ about the quality of the run similar to the on-instrument applications like SAV.
 This includes statistics like percent pass filter, the percent of bases with
 Qscores over 30, and cluster density.
 
-1. From the _Sequencing Runs_ page, find the run assigned to you for this tutorial.
+1. From the _Sequencing Runs_ page, find the run `{{ site.run_scanner_run }}`.
    Click on the run alias to go to the run page.
 1. Scroll down to the _Metrics_ section and examine the sequencing metrics for
    this run.

_includes/samples-receiving-bulk.md

@@ -18,20 +18,21 @@ the table.
     * _Time of Receipt_: `9:00 am`
     * _Received From_: Select any lab.
     * _Received By_: Select any group.
-    * _Sample Type_: `GENOMIC`
     * _Project_: Select your project's {% if include.detailed %}short{% endif %} name from the drop-down.
 {% if include.detailed %}
     * _Subproject_: Select the subproject you created.
 {% endif %}
+    * _Sample Type_: `GENOMIC`
     * _Sci. Name_: `{{ site.scientific_name }}`
 {% if include.detailed %}
     * _Donor Sex_: Select any item from the drop-down.
     * _Tissue Origin_: `{{ site.tissue_origin_2 }}`
     * _Tissue Type_: `{{ site.tissue_type_2 }}`
     * _Times Received_: `1`
     * _Tube Number_: `1`
-    * _Secondary ID_: `BioBankID 1`.
+    * _Secondary ID_: `BioBankID 2`.
     * _Material_: Select any item from the drop down.
+    * _Tiempoint_: `T1`
     * _QC Status_: `Ready`
 {% else %}
     * _QC Passed?_: `True`
@@ -53,9 +54,9 @@ Command+V (Mac) on your keyboard to paste into the selected cell(s).
 1. Click the _Date of Receipt_ cell in the first row. A blue square will appear at
    the lower right hand corner of the cell. Double click it to fill in the rest of the
    column with the same date.
-1. Fill in the columns in the same way for: _Time of Receipt_, _Received From_, _Received By_, _Sample Type_, _Project_,
+1. Fill in the columns in the same way for: _Time of Receipt_, _Received From_, _Received By_, _Project_, _Sample Type_,
    _Sci. Name_, {% if include.detailed %} _Subproject_, _Donor Sex_, _Tissue Origin_, _Tissue Type_, _Times Received_,
-   _Tube Number_, _Material_, and _QC Status_ {% else %} _QC Passed?_{% endif %}.
+   _Tube Number_, _Material_, _Timepoint_, and _QC Status_ {% else %} _QC Status_{% endif %}.
 1. Copy text from another program and paste it into the _Description_ cell.
 
 1. _Matrix Barcode_: you would normally use a hand-scanner or copy and paste a list of
@@ -83,7 +84,7 @@ If you have a label with an incrementing number (_e.g._, `1`, `2`), enter two ro
 blue square.
 
 {% if include.detailed %}
-1. _Secondary ID_: enter `BioBankID 2` in the second row. Select the _Secondary Identifier_ fields for rows 1 and 2,
+1. _Secondary ID_: enter `BioBankID 3` in the second row. Select the _Secondary Identifier_ fields for rows 1 and 2,
    then double click the blue square to fill down rows 3 and 4.
 {% else %}
 1. _Alias_: enter `{{ site.plain_sample3_alias }}` in the second row. Select the _Alias_ fields for rows 1 and 2, then

_includes/samples-receiving.md

@@ -22,7 +22,6 @@
        If you weren't given any barcodes to use, enter one like `PROJ-101`,
        replacing `PROJ` with your project's {% if include.detailed == true %}short{% endif %}
        name. Record the barcode on your worksheet. <img src="pics/blue_pencil.png">
-    1. _Sample Type_: select `GENOMIC` from the drop down.
     1. _Project_: Select the {% if include.detailed %}short{% endif %} name of the project you created in the last
        exercise.
 {% if include.detailed %}
@@ -31,4 +30,5 @@
        information. It can sometimes take a few minutes for the new subproject option
        to become available.
 {% endif %}
+    1. _Sample Type_: select `GENOMIC` from the drop down.
     1. _Scientific Name_: `{{ site.scientific_name }}`.

_includes/working_with_tables.md

@@ -126,10 +126,10 @@ Samples, libraries, library aliquots, or pools can be bulk-added to a box from w
 
 # 6. Check QCs (Libraries only)
 
-The _Check QCs_ feature can be used to automatically update the _QC Passed?_ column values based on the values in the _Size (bp)_, _Volume_, or _Conc._ columns.
+The _Check QCs_ feature can be used to automatically update the _QC Status_ column values based on the values in the _Size (bp)_, _Volume_, or _Conc._ columns.
 
 1. Return to your _Create Libraries_ bulk table.
-1. Ensure all _QC Passed?_ cells are set to **Unknown**.
+1. Ensure all _QC Status_ cells are empty.
 1. In the top row, enter the following values:
     * _Size (bp)_: **300**
     * _Volume_: **10**
@@ -144,13 +144,13 @@ The _Check QCs_ feature can be used to automatically update the _QC Passed?_ col
 1. In the _Size_ section, select **=** from the dropdown menu and enter **303** into the input field.
 1. Leave the _Volume_ and _Concentration_ sections set to **ignore**.
 1. Click **Check**.
-    * Note that the _QC Passed?_ values have changed.
+    * Note that the _QC Status_ values have changed.
 1. Click **Check QCs**.
 1. In the _Volume_ section, select **>** from the dropdown menu and enter **10** into the input field.
 1. In the _Concentration_ section, select **<=** from the dropdown menu and enter **4** into the input field.
 1. Leave the _Size_ section set to **ignore**.
 1. Click **Check**.
-    * Note that the _QC Passed?_ values have changed.
+    * Note that the _QC Status_ values have changed.
 
 <a name="export"/>
 
@@ -159,7 +159,7 @@ The _Check QCs_ feature can be used to automatically update the _QC Passed?_ col
 The current state of the bulk table data can be exported at any time. Exports can be saved as Microsoft Excel, Open Document Format, or Comma-delimited Data (CSV) files.
 
 1. Return to your _Create Libraries_ bulk table.
-1. Click **Export Data** at the top of the table.
+1. Click **Export** at the top of the table.
 1. Select **Microsoft Excel** format.
 1. Click **Export**.
     * The spreadsheet will begin downloading.

tutorial-detailed-project-coordination.md

@@ -38,7 +38,7 @@ Sub-projects are an optional feature - a project is not required to have sub-pro
     * Fill in the alias and description.
     * Select the priority from the drop-down. This will cause high-priority items
       to display priority messages in the MISO interface.
-    * Select `{{ site.scientific_name }}` from the Reference Genome dropdown
+    * Select `{{ site.reference_genome }}` from the Reference Genome dropdown
 1. Click _Save_ in the top right corner of the page.
 
 Once a subproject is set up, it can be selected when creating Samples.

tutorial-detailed-samples.md

@@ -91,6 +91,7 @@ donor `PROJ_ID1`.
     1. _Secondary ID_: `BioBankID 1`. This is the Biobank ID or Tube ID. It may also be left
        blank.
     1. _Material_: Select any from the drop-down.
+    1. _Timepoint_: `T1`
     1. _QC Status_: select `Ready` from the drop down.
 1. At the upper right hand side, click _Save_.
 
@@ -168,6 +169,7 @@ In this section, we will 'receive' a single stock DNA tube from the tissue mater
   * _Times Received_: `1`
   * _Tube Number_: `1`
   * _Secondary ID_: `BioBankID 6`.
+  * _Timepoint_: `T1`
   * _STR Status_: select any value from the dropdown menu.
   * _Volume_: `300`
   * _Vol. Units_: `µL`
@@ -215,7 +217,7 @@ created from the tissue.
 
 Create a {{ site.slide_class }} from one of your Tissue samples.
 
-1. On the _Samples_ page, enter your project name in the search box.
+1. On the _Samples_ page, enter your project short name in the search box.
 1. Check the box for the {{ site.tissue_class }} you created in exercise 2.1. It will have tissue origin
    {{ site.tissue_origin_1 }} and tissue type {{ site.tissue_type_1 }}.
 1. Click the _Propagate_ button at the top left of the table.
@@ -239,14 +241,13 @@ Record the alias in your worksheet. <img src="pics/blue_pencil.png">
 For three of the {{ site.tissue_class }} samples created previously (by bulk entry), we will
 create stocks for library preparation.
 
-1. On the _Samples_ page, enter your project name in the search box.
+1. On the _Samples_ page, enter your project short name in the search box.
 1. Check the boxes for any three of the the {{ site.tissue_class }} samples with tissue type {{ site.tissue_type_2 }}
    that you created in section 2.3.
 1. Click the _Propagate_ button at the top left of the table.
 1. Enter `1` replicates to `Stock`.
 1. Click _Propagate_.
 1. Fill out the table:
-  * _Description_: Free text description. In this case, use "Stock (Tissue Type)(Individual)". (e.g. `Stock P2`)
   * _Matrix Barcode_: Choose a barcode for each stock. If you were not given barcodes to use,
     enter the following instead, replacing `PROJ` with your project's short name. Record the
     barcodes on your worksheet. <img src="pics/blue_pencil.png">
@@ -274,7 +275,7 @@ In this case we will update several fields of 4 stock samples. We will use the
 stocks we entered in the previous step as well as the reference stock entered in
 part 2.4 of this tutorial.
 
-1. On the _Samples_ page, enter your project name in the search box.
+1. On the _Samples_ page, enter your project short name in the search box.
 1. Check the boxes for the {{ site.stock_class }} samples (propagated and received) that you created in
    sections 2.4 and 3.2.
 1. Click the _Edit_ button at the top left of the table.
@@ -294,17 +295,14 @@ Propagate again from the 4 _{{ site.stock_class }}_ samples to _{{ site.aliquot_
 
 1. If you are continuing from the end of section **3.3 Bulk Editing**, do not
   navigate away from the page.
-    1. At the top left of the table after saving samples, click the _Propagate_ button.
-    1. Enter `1` for the number of replicates (child samples to be created from each parent)
-       and `Aliquot` for the category of child sample. Continue to step 3.
+    1. At the top left of the table after saving samples, click the _Propagate_ button and continue to step 3.
 1. Otherwise, select samples using the following:
-    1. On the _Samples_ page, enter your project name in the search box.
+    1. On the _Samples_ page, enter your project short name in the search box.
     1. Check the boxes for the {{ site.stock_class }} samples.
     1. Click the _Propagate_ button at the top of the table.
-    1. A dialog will appear. Select `1` replicate to `Aliquot` and click _Propagate_.
+1. A dialog will appear. Select `1` replicate to `Aliquot` and click _Propagate_.
 1. Fill out the table:
     * _Sample Alias_: Skip this field. It will be automatically filled in upon save.
-    * _Description_: Free text description. In this case, use "Aliquot (Tissue Type)(Individual)". (e.g. `Aliquot P2`)
     * _Matrix Barcode_: choose a barcode for each aliquot. If you weren't given barcodes to use, enter the following
       instead, replacing `PROJ` with your project's short name. Record the barcodes on your worksheet.
       <img src="pics/blue_pencil.png">