New module: Seqera Platform CLI (#2151)

* New module: seqera-cli * [automated] Update CHANGELOG.md * Add barplot, version, parse uncompressed * Fix * Update docs * Support custom header["to_float"] function, use it for duration. Meaninful colors for barplot * Shorter repo name * remove mention of table sorting * Update multiqc/modules/seqera_cli/seqera_cli.py Co-authored-by: Robert Syme <rob.syme@gmail.com> * Update multiqc/modules/seqera_cli/seqera_cli.py Co-authored-by: Robert Syme <rob.syme@gmail.com> * Update multiqc/modules/seqera_cli/seqera_cli.py Co-authored-by: Phil Ewels <phil.ewels@seqera.io> * Remove to_float, support format callable instead. Add humanize for dates and gb * nbsp * Fix * Address review, fixes * Add nextflow and platform versions, use color badges, use deterministic hash for categorical Bscale * Fix lint * Fix order * Rename search pattern * Add simple barplots * Simple barplots: show if no data * Update multiqc/modules/seqera_cli/seqera_cli.py Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update multiqc/modules/seqera_cli/seqera_cli.py Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update multiqc/modules/seqera_cli/seqera_cli.py Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update multiqc/modules/seqera_cli/seqera_cli.py Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update multiqc/modules/seqera_cli/seqera_cli.py Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update multiqc/modules/seqera_cli/seqera_cli.py Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update multiqc/modules/seqera_cli/seqera_cli.py Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update multiqc/modules/seqera_cli/seqera_cli.py Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update multiqc/modules/seqera_cli/seqera_cli.py Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update multiqc/modules/seqera_cli/seqera_cli.py Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> --------- Co-authored-by: MultiQC Bot <multiqc-bot@seqera.io> Co-authored-by: Phil Ewels <phil.ewels@seqera.io> Co-authored-by: Robert Syme <rob.syme@gmail.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
MultiQC · Nov 2, 2023 · 17bc033 · 17bc033
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diff --git a/.github/workflows/multiqc.yml b/.github/workflows/multiqc.yml
@@ -99,7 +99,7 @@ jobs:
         run: |
           multiqc ${{ needs.changes.outputs.single_module }} test_data/data/modules/ --filename all_ignored.html --ignore-samples '*'
           if [[ -f all_ignored.html ]]; then
-            echo "No report should have been generated! Likely due to a module missing self.ignore_samples() or UserWarning when no matching files are found" >&2
+            echo "No report should have been generated! Likely due to a module missing self.ignore_samples() or ModuleNoSamplesFound when no matching files are found" >&2
             exit 1
           fi
 

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -8,6 +8,9 @@
 
 ### New Modules
 
+- [**Seqera Platform CLI**](https://github.com/seqeralabs/tower-cli) ([#2151](https://github.com/ewels/MultiQC/pull/2151))
+  - Seqera Platform CLI reports statistics generated by the Seqera Platform CLI.
+
 ### Module updates
 
 - **fastp**: correctly parse sample name from --in1/--in2 command. Prefer file name if not `fastp.json`; fallback to file name when error ([#2139](https://github.com/ewels/MultiQC/pull/2139))

diff --git a/CSP.txt b/CSP.txt
@@ -2,6 +2,8 @@
 # (Content Security Policy), you will need the following scripts allowlisted:
 
 script-src 'self'
+    # 1.18
+    'sha256-W6HVWfJ0uI4smLSf8gzVvnrHUJaXGP/HEeBvr0SYfyk=' # multiqc/templates/default/assets/js/multiqc_tables.js
 
     # 1.17
     'sha256-krKzkLmKjisEgw0YGKglUFqLmEh6sK08Qw6xPmmo/10=' # ////////////////////////////////////////////////// Base JS for MultiQC Reports//

diff --git a/docs/core/development/modules.md b/docs/core/development/modules.md
@@ -792,8 +792,8 @@ headers['name'] = {
     'min': None,                    # Maximum value in range, for bar / colour coding
     'scale': 'GnBu',                # Colour scale for colour coding. Set to False to disable.
     'suffix': None,                 # Suffix for value (eg. '%')
-    'format': '{:,.1f}',            # Output format() string
-    'shared_key': None              # See below for description
+    'format': '{:,.1f}',            # Output format() string. Can also be a lambda function.
+    'shared_key': None,             # See below for description
     'modify': None,                 # Lambda function to modify values
     'hidden': False,                # Set to True to hide the column on page load
     'placement' : 1000.0,           # Alter the default ordering of columns in the table
@@ -817,13 +817,16 @@ headers['name'] = {
 - `modify`
   - A python `lambda` function to change the data in some way when it is
     inserted into the table.
+- `format`
+  - A format string or a python `lambda` function to format the data to display
+    on screen.
 - `hidden`
   - Setting this to `True` will hide the column when the report loads. It can
     then be shown through the _Configure Columns_ modal in the report. This can
     be useful when data could be sometimes useful. For example, some modules
     show "percentage aligned" on page load but hide "number of reads aligned".
 - `placement`
-  - If you feel that the results from your module should appear at the left side
+  - If you feel that the results from your module should appear on the left side
     of the table set this value less than 1000. Or to move the column right, set
     it greater than 1000. This value can be any float.
 

diff --git a/docs/core/development/plots.md b/docs/core/development/plots.md
@@ -105,7 +105,7 @@ config = {
     'cpswitch': True,                       # Show the 'Counts / Percentages' switch?
     'cpswitch_c_active': True,              # Initial display with 'Counts' specified? False for percentages.
     'cpswitch_counts_label': 'Counts',      # Label for 'Counts' button
-    'cpswitch_percent_label': 'Percentages' # Label for 'Percentages' button
+    'cpswitch_percent_label': 'Percentages',# Label for 'Percentages' button
     'logswitch': False,                     # Show the 'Log10' switch?
     'logswitch_active': False,              # Initial display with 'Log10' active?
     'logswitch_label': 'Log10',             # Label for 'Log10' button

diff --git a/docs/modules/seqera_cli.md b/docs/modules/seqera_cli.md
@@ -0,0 +1,24 @@
+---
+name: Seqera Platform CLI
+url: https://github.com/seqeralabs/tower-cli
+description: Reports statistics generated by the Seqera Platform CLI.
+---
+
+Parses a tar-gz dump containing logs and stats from a Seqera Platform run, that is,
+the `runs_SmUkr43Nul49G.tar.gz` file generated by the following command:
+
+```sh
+tw runs dump -id=SmUkr43Nul49G --workspace=seqeralabs/benchmarks --output=runs_SmUkr43Nul49G.tar.gz
+```
+
+Expects the dump to contain a `workflow.json` file, along with `workflow-load.json`.
+
+Can also parse an uncompressed version of the dump, that is, a `workflow.json` file
+and a `workflow-load.json` sitting together in a directory.
+
+To allow reading the tar-gz archives, run with `ignore_images: false`
+in the config, e.g.:
+
+```sh
+multiqc . --cl-config 'ignore_images: false'
+```
diff --git a/multiqc/modules/seqera_cli/__init__.py b/multiqc/modules/seqera_cli/__init__.py
@@ -0,0 +1 @@
+from .seqera_cli import MultiqcModule