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Expand help text and replace SVGs for filter empty, failed, and null tools
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
This commit is contained in:
nekrut
committed by
John Davis
John Davis
co-authored by
Claude Opus 4.6
Claude Opus 4.6
parent
8b4c2b92d0
commit
171f783b6d
@@ -42,21 +42,58 @@
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Synopsis
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========
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Removes empty datasets from a collection.
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Removes empty (zero-byte) datasets from a collection.
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===========
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Description
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===========
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This tool takes a dataset collection and filters out (removes) datasets that have no content (zero bytes). This is useful for continuing a multi-sample analysis when downstream tools require datasets to have content.
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This tool takes a dataset collection and filters out elements that have no content. A dataset is considered empty if it contains zero bytes of actual data (including compressed archives that decompress to nothing).
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Optionally, you can provide a replacement dataset. When a replacement is specified, empty elements are replaced with that dataset instead of being removed.
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This is useful when a multi-sample analysis produces some empty outputs — for example, when a filtering step removes all reads for certain samples. Downstream tools often fail on empty inputs, so removing them lets the rest of the analysis proceed.
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Optionally, you can provide a **replacement dataset**. When specified, empty elements are replaced with that dataset instead of being removed. This preserves the collection size, which is important when element-wise pairing with another collection is needed.
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========
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Examples
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========
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**Remove empty elements**
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Given a list collection where one sample produced no output::
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List: "Filtered reads"
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sample1 → reads.fastq (1.2 MB)
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sample2 → reads.fastq (0 bytes)
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sample3 → reads.fastq (800 KB)
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The output keeps only non-empty elements::
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List: "Filtered reads (filtered empty datasets)"
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sample1 → reads.fastq (1.2 MB)
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sample3 → reads.fastq (800 KB)
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-------
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**Replace instead of remove**
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If a replacement dataset is provided, empty elements are swapped rather than dropped, preserving the collection structure::
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List: "Filtered reads (filtered empty datasets)"
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sample1 → reads.fastq (1.2 MB)
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sample2 → replacement.fastq
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sample3 → reads.fastq (800 KB)
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-------
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.. image:: ${static_path}/images/tools/collection_ops/filter_empty.svg
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:alt: Filtering empty datasets
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:alt: Filter empty datasets from collection
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:width: 500
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-----
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-------
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.. class:: infomark
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@@ -53,15 +53,52 @@ Removes datasets in the error (red) state from a collection.
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Description
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===========
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This tool takes a dataset collection and filters out (removes) datasets in the failed (red) state. This is useful for continuing a multi-sample analysis when one or more of the samples fails at some point.
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This tool takes a dataset collection and filters out elements whose datasets are in the failed (red) state. A dataset enters this state when the tool that created it encountered an error during execution.
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Optionally, you can provide a replacement dataset. When a replacement is specified, failed elements are replaced with that dataset instead of being removed.
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This is useful when running a multi-sample analysis and one or more samples fail at some step. Rather than restarting the entire analysis, you can remove the failed elements and continue with the samples that succeeded.
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Optionally, you can provide a **replacement dataset**. When specified, failed elements are replaced with that dataset instead of being removed. This preserves the collection size, which is important when element-wise pairing with another collection is needed.
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========
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Examples
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========
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**Remove failed elements**
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Given a list collection where one sample's alignment failed::
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List: "Aligned reads"
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sample1 → aligned.bam (ok)
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sample2 → aligned.bam (error)
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sample3 → aligned.bam (ok)
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The output keeps only successful elements::
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List: "Aligned reads (filtered failed datasets)"
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sample1 → aligned.bam
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sample3 → aligned.bam
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-------
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**Replace instead of remove**
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If a replacement dataset is provided, failed elements are swapped rather than dropped, preserving the collection structure::
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List: "Aligned reads (filtered failed datasets)"
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sample1 → aligned.bam
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sample2 → replacement.bam
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sample3 → aligned.bam
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-------
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.. image:: ${static_path}/images/tools/collection_ops/filter_error.svg
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:alt: Filter failed datasets
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:alt: Filter failed datasets from collection
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:width: 500
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-----
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-------
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.. class:: infomark
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@@ -44,11 +44,52 @@ Removes null (missing) elements from a collection.
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Description
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===========
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This tool takes a dataset collection and filters out null elements. Null elements can appear when workflows use conditional steps -- if a step is skipped, it may produce a null placeholder instead of a real dataset.
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This tool takes a dataset collection and filters out null elements. A null element is a placeholder that contains no actual dataset — it appears when a workflow uses conditional steps and a step is skipped, or when an expression tool produces a ``null`` value.
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Optionally, you can provide a replacement dataset. When a replacement is specified, null elements are replaced with that dataset instead of being removed.
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This is useful for cleaning up collections produced by conditional workflows. Downstream tools cannot process null elements, so removing them ensures the rest of the analysis can proceed.
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-----
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Optionally, you can provide a **replacement dataset**. When specified, null elements are replaced with that dataset instead of being removed. This preserves the collection size, which is important when element-wise pairing with another collection is needed.
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========
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Examples
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========
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**Remove null elements**
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Given a list collection produced by a conditional workflow where one branch was skipped::
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List: "Workflow outputs"
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sample1 → result.txt (ok)
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sample2 → (null)
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sample3 → result.txt (ok)
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The output keeps only real elements::
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List: "Workflow outputs (without null datasets)"
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sample1 → result.txt
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sample3 → result.txt
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-------
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**Replace instead of remove**
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If a replacement dataset is provided, null elements are swapped rather than dropped, preserving the collection structure::
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List: "Workflow outputs (without null datasets)"
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sample1 → result.txt
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sample2 → replacement.txt
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sample3 → result.txt
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-------
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.. image:: ${static_path}/images/tools/collection_ops/filter_null.svg
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:alt: Filter null elements from collection
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:width: 500
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-------
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.. class:: infomark
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@@ -0,0 +1,54 @@
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<?xml version="1.0" encoding="UTF-8"?>
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<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 620 210" width="620" height="210">
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<defs>
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<filter id="shadow" x="-4%" y="-4%" width="110%" height="110%">
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<feGaussianBlur in="SourceAlpha" stdDeviation="2" result="blur"/>
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<feComponentTransfer in="blur">
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<feFuncA type="linear" slope="0.3"/>
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</feComponentTransfer>
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<feMerge>
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<feMergeNode/>
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<feMergeNode in="SourceGraphic"/>
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</feMerge>
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</filter>
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<marker id="arrowhead" markerWidth="10" markerHeight="7" refX="9" refY="3.5" orient="auto">
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<polygon points="0 0, 10 3.5, 0 7" fill="#555"/>
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</marker>
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</defs>
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<!-- Left: input collection -->
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<rect x="10" y="10" width="210" height="185" rx="8" ry="8" fill="#d9ead3" stroke="#888" stroke-width="1" filter="url(#shadow)"/>
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<text x="115" y="30" text-anchor="middle" font-family="sans-serif" font-size="13" font-weight="bold" fill="#333">List</text>
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<rect x="25" y="42" width="180" height="28" rx="4" ry="4" fill="#fff" stroke="#aaa" stroke-width="0.7"/>
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<text x="115" y="61" text-anchor="middle" font-family="sans-serif" font-size="12" fill="#333">sample1</text>
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<text x="195" y="61" text-anchor="end" font-family="sans-serif" font-size="9" fill="#2e7d32">ok</text>
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<!-- Null element (highlighted gray/dashed) -->
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<rect x="25" y="78" width="180" height="28" rx="4" ry="4" fill="#f0f0f0" stroke="#999" stroke-width="1.2" stroke-dasharray="4,2"/>
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<text x="115" y="97" text-anchor="middle" font-family="sans-serif" font-size="12" fill="#999">sample2</text>
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<text x="195" y="97" text-anchor="end" font-family="sans-serif" font-size="9" fill="#999">null</text>
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<rect x="25" y="114" width="180" height="28" rx="4" ry="4" fill="#fff" stroke="#aaa" stroke-width="0.7"/>
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<text x="115" y="133" text-anchor="middle" font-family="sans-serif" font-size="12" fill="#333">sample3</text>
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<text x="195" y="133" text-anchor="end" font-family="sans-serif" font-size="9" fill="#2e7d32">ok</text>
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<text x="115" y="166" text-anchor="middle" font-family="sans-serif" font-size="10" font-style="italic" fill="#999">sample2 is null</text>
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<!-- Arrow -->
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<line x1="240" y1="92" x2="360" y2="92" stroke="#555" stroke-width="2" marker-end="url(#arrowhead)"/>
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<text x="300" y="82" text-anchor="middle" font-family="sans-serif" font-size="12" font-weight="bold" fill="#555">Filter</text>
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<!-- Right: filtered collection -->
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<rect x="380" y="10" width="220" height="155" rx="8" ry="8" fill="#d9ead3" stroke="#888" stroke-width="1" filter="url(#shadow)"/>
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<text x="490" y="30" text-anchor="middle" font-family="sans-serif" font-size="13" font-weight="bold" fill="#333">List (filtered)</text>
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<rect x="395" y="42" width="190" height="28" rx="4" ry="4" fill="#fff" stroke="#aaa" stroke-width="0.7"/>
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<text x="490" y="61" text-anchor="middle" font-family="sans-serif" font-size="12" fill="#333">sample1</text>
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<rect x="395" y="78" width="190" height="28" rx="4" ry="4" fill="#fff" stroke="#aaa" stroke-width="0.7"/>
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<text x="490" y="97" text-anchor="middle" font-family="sans-serif" font-size="12" fill="#333">sample3</text>
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<text x="490" y="140" text-anchor="middle" font-family="sans-serif" font-size="10" font-style="italic" fill="#666">null element removed</text>
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</svg>
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