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-rw-r--r--autogen.pdfbin0 -> 17464 bytes
-rw-r--r--autogen.svg426
-rw-r--r--config.pdfbin0 -> 14672 bytes
-rw-r--r--config.svg223
-rw-r--r--redcap.pdfbin0 -> 13903 bytes
-rw-r--r--redcap.svg148
-rw-r--r--sfrc01042-gridss.pdfbin0 -> 24223 bytes
-rw-r--r--sfrc01042-gridss.svg3784
-rw-r--r--sfrc01042.pdfbin0 -> 79461 bytes
-rw-r--r--sfrc01042.svg5065
-rw-r--r--slides.tex101
11 files changed, 9726 insertions, 21 deletions
diff --git a/autogen.pdf b/autogen.pdf
new file mode 100644
index 0000000..fa9bb2d
--- /dev/null
+++ b/autogen.pdf
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diff --git a/autogen.svg b/autogen.svg
new file mode 100644
index 0000000..0db0c5a
--- /dev/null
+++ b/autogen.svg
@@ -0,0 +1,426 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<svg
+ xmlns:dc="http://purl.org/dc/elements/1.1/"
+ xmlns:cc="http://creativecommons.org/ns#"
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+ xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd"
+ xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"
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+ sodipodi:docname="autogen.svg">
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+ style="overflow:visible"
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+ <path
+ transform="matrix(-0.8,0,0,-0.8,-10,0)"
+ style="fill:#000000;fill-opacity:1;fill-rule:evenodd;stroke:#000000;stroke-width:1pt;stroke-opacity:1"
+ d="M 0,0 5,-5 -12.5,0 5,5 Z"
+ id="path850" />
+ </marker>
+ <rect
+ x="-200.98668"
+ y="21.381561"
+ width="269.63922"
+ height="253.40543"
+ id="rect18" />
+ <rect
+ x="59.720238"
+ y="16.630953"
+ width="859.45923"
+ height="488.2782"
+ id="rect12" />
+ </defs>
+ <sodipodi:namedview
+ id="base"
+ pagecolor="#ffffff"
+ bordercolor="#666666"
+ borderopacity="1.0"
+ inkscape:pageopacity="0.0"
+ inkscape:pageshadow="2"
+ inkscape:zoom="0.3789018"
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+ units="px" />
+ <metadata
+ id="metadata5">
+ <rdf:RDF>
+ <cc:Work
+ rdf:about="">
+ <dc:format>image/svg+xml</dc:format>
+ <dc:type
+ rdf:resource="http://purl.org/dc/dcmitype/StillImage" />
+ <dc:title></dc:title>
+ </cc:Work>
+ </rdf:RDF>
+ </metadata>
+ <g
+ inkscape:label="Layer 1"
+ inkscape:groupmode="layer"
+ id="layer1"
+ transform="translate(470.13962,-16.998291)">
+ <text
+ xml:space="preserve"
+ id="text10"
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:7.05556px;line-height:1.25;font-family:'TeX Gyre Heros';-inkscape-font-specification:'TeX Gyre Heros, Normal';font-variant-ligatures:normal;font-variant-caps:normal;font-variant-numeric:normal;font-feature-settings:normal;text-align:start;letter-spacing:0px;word-spacing:0px;writing-mode:lr-tb;white-space:pre;shape-inside:url(#rect12);fill:#000000;fill-opacity:1;stroke:none;"
+ transform="matrix(0.59766334,0,0,0.59766334,-205.02948,6.8390357)"><tspan
+ x="59.720703"
+ y="23.044364"><tspan
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'">with import ./milton-slurm.nix { };
+</tspan></tspan><tspan
+ x="59.720703"
+ y="32.103703"><tspan
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'">let
+</tspan></tspan><tspan
+ x="59.720703"
+ y="41.163043"><tspan
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'"> samples = [
+</tspan></tspan><tspan
+ x="59.720703"
+ y="50.22238"><tspan
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'"> {
+</tspan></tspan><tspan
+ x="59.720703"
+ y="59.281722"><tspan
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'"> site = &quot;B1&quot;;
+</tspan></tspan><tspan
+ x="59.720703"
+ y="68.341063"><tspan
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'"> class = &quot;normals&quot;;
+</tspan></tspan><tspan
+ x="59.720703"
+ y="77.400404"><tspan
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'"> pdx = false;
+</tspan></tspan><tspan
+ x="59.720703"
+ y="86.459746"><tspan
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'"> r1 =
+</tspan></tspan><tspan
+ x="59.720703"
+ y="95.519087"><tspan
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'"> &quot;mz/Vf/SHA256E-s23731819040--c650db8ef7fcd00178178fd254970d989b1a964ee68b887f56ae0586683f7c0a.gz/SHA256E-s23731819040--c650db8ef7fcd00178178fd254970d989b1a964ee68b887f56ae0586683f7c0a.gz&quot;;
+</tspan></tspan><tspan
+ x="59.720703"
+ y="104.57843"><tspan
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'"> r2 =
+</tspan></tspan><tspan
+ x="59.720703"
+ y="113.63777"><tspan
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'"> &quot;kz/Zq/SHA256E-s25775609303--bfe116906bddf9799ba78d78be56938b21910812bebcf947f0c56cfbd5fc650a.gz/SHA256E-s25775609303--bfe116906bddf9799ba78d78be56938b21910812bebcf947f0c56cfbd5fc650a.gz&quot;;
+</tspan></tspan><tspan
+ x="59.720703"
+ y="122.69711"><tspan
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'"> }
+</tspan></tspan><tspan
+ x="59.720703"
+ y="131.75645"><tspan
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'"> {
+</tspan></tspan><tspan
+ x="59.720703"
+ y="140.81579"><tspan
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'"> site = &quot;B1&quot;;
+</tspan></tspan><tspan
+ x="59.720703"
+ y="149.87513"><tspan
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'"> class = &quot;normals&quot;;
+</tspan></tspan><tspan
+ x="59.720703"
+ y="158.93447"><tspan
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'"> pdx = false;
+</tspan></tspan><tspan
+ x="59.720703"
+ y="167.99381"><tspan
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'"> r1 =
+</tspan></tspan><tspan
+ x="59.720703"
+ y="177.05315"><tspan
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'"> &quot;V4/Wj/SHA256E-s17295801172--19e79e9018a60ea5715481973ff92194f6a218e5f04418303d99a2eafbaac7d9.gz/SHA256E-s17295801172--19e79e9018a60ea5715481973ff92194f6a218e5f04418303d99a2eafbaac7d9.gz&quot;;
+</tspan></tspan><tspan
+ x="59.720703"
+ y="186.11249"><tspan
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'"> r2 =
+</tspan></tspan><tspan
+ x="59.720703"
+ y="195.17184"><tspan
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'"> &quot;j7/z8/SHA256E-s18960756093--07bdcea8a80adfbf021c9082b1de5dd9a27d7325ecbff0122b82d8654245ed20.gz/SHA256E-s18960756093--07bdcea8a80adfbf021c9082b1de5dd9a27d7325ecbff0122b82d8654245ed20.gz&quot;;
+</tspan></tspan><tspan
+ x="59.720703"
+ y="204.23118"><tspan
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'"> }
+</tspan></tspan><tspan
+ x="59.720703"
+ y="213.29052"><tspan
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'"> {
+</tspan></tspan><tspan
+ x="59.720703"
+ y="222.34986"><tspan
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'"> site = &quot;S1&quot;;
+</tspan></tspan><tspan
+ x="59.720703"
+ y="231.4092"><tspan
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'"> class = &quot;tumours&quot;;
+</tspan></tspan><tspan
+ x="59.720703"
+ y="240.46854"><tspan
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'"> pdx = false;
+</tspan></tspan><tspan
+ x="59.720703"
+ y="249.52788"><tspan
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'"> r1 =
+</tspan></tspan><tspan
+ x="59.720703"
+ y="258.58723"><tspan
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'"> &quot;Fm/94/SHA256E-s4503271082--528808192a494d4e8dc98c0596ee8d04e45cd65c70957993ffdf6a8c2294dd51.gz/SHA256E-s4503271082--528808192a494d4e8dc98c0596ee8d04e45cd65c70957993ffdf6a8c2294dd51.gz&quot;;
+</tspan></tspan><tspan
+ x="59.720703"
+ y="267.64657"><tspan
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'"> r2 =
+</tspan></tspan><tspan
+ x="59.720703"
+ y="276.70589"><tspan
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'"> &quot;q2/Zk/SHA256E-s4582653633--d32ee809bd7d19ed497938a7a5ee36117b8f3f1b43109482da174555bcb1a45e.gz/SHA256E-s4582653633--d32ee809bd7d19ed497938a7a5ee36117b8f3f1b43109482da174555bcb1a45e.gz&quot;;
+</tspan></tspan><tspan
+ x="59.720703"
+ y="285.76522"><tspan
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'"> }
+</tspan></tspan><tspan
+ x="59.720703"
+ y="294.82455"><tspan
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'"> {
+</tspan></tspan><tspan
+ x="59.720703"
+ y="303.88387"><tspan
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'"> site = &quot;S1&quot;;
+</tspan></tspan><tspan
+ x="59.720703"
+ y="312.9432"><tspan
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'"> class = &quot;tumours&quot;;
+</tspan></tspan><tspan
+ x="59.720703"
+ y="322.00252"><tspan
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'"> pdx = false;
+</tspan></tspan><tspan
+ x="59.720703"
+ y="331.06185"><tspan
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'"> r1 =
+</tspan></tspan><tspan
+ x="59.720703"
+ y="340.12118"><tspan
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'"> &quot;Kf/w5/SHA256E-s34952768707--cc01c16aea8cdf162e439c8c7cb419bcb381efe95c071b9e6b97771b40f1eff8.gz/SHA256E-s34952768707--cc01c16aea8cdf162e439c8c7cb419bcb381efe95c071b9e6b97771b40f1eff8.gz&quot;;
+</tspan></tspan><tspan
+ x="59.720703"
+ y="349.1805"><tspan
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'"> r2 =
+</tspan></tspan><tspan
+ x="59.720703"
+ y="358.23983"><tspan
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'"> &quot;Gg/gk/SHA256E-s37880355076--e10fc22839c91f8900ef98afd473361ef0dcb1882b92f87140a9000237fac0e6.gz/SHA256E-s37880355076--e10fc22839c91f8900ef98afd473361ef0dcb1882b92f87140a9000237fac0e6.gz&quot;;
+</tspan></tspan><tspan
+ x="59.720703"
+ y="367.29915"><tspan
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'"> }
+</tspan></tspan><tspan
+ x="59.720703"
+ y="376.35848"><tspan
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'"> {
+</tspan></tspan><tspan
+ x="59.720703"
+ y="385.41781"><tspan
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'"> site = &quot;S1&quot;;
+</tspan></tspan><tspan
+ x="59.720703"
+ y="394.47713"><tspan
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'"> class = &quot;tumours&quot;;
+</tspan></tspan><tspan
+ x="59.720703"
+ y="403.53646"><tspan
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'"> pdx = false;
+</tspan></tspan><tspan
+ x="59.720703"
+ y="412.59579"><tspan
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'"> r1 =
+</tspan></tspan><tspan
+ x="59.720703"
+ y="421.65511"><tspan
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'"> &quot;xM/Q9/SHA256E-s38656117968--04dc46ef77fef4a5578d00d073682d433dfeb6337b905a2cc822b685e0cf61ea.gz/SHA256E-s38656117968--04dc46ef77fef4a5578d00d073682d433dfeb6337b905a2cc822b685e0cf61ea.gz&quot;;
+</tspan></tspan><tspan
+ x="59.720703"
+ y="430.71444"><tspan
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'"> r2 =
+</tspan></tspan><tspan
+ x="59.720703"
+ y="439.77376"><tspan
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'"> &quot;Jq/6j/SHA256E-s42454148279--ec5c092b13b76197e2659c51f11bf17c78b2caa44789c4fe006844f8bd15561e.gz/SHA256E-s42454148279--ec5c092b13b76197e2659c51f11bf17c78b2caa44789c4fe006844f8bd15561e.gz&quot;;
+</tspan></tspan><tspan
+ x="59.720703"
+ y="448.83309"><tspan
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'"> }
+</tspan></tspan><tspan
+ x="59.720703"
+ y="457.89242"><tspan
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'"> ];
+</tspan></tspan><tspan
+ x="59.720703"
+ y="466.95174"><tspan
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'">in import ./multisample.nix {
+</tspan></tspan><tspan
+ x="59.720703"
+ y="476.01107"><tspan
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'"> inherit bionix samples fetch;
+</tspan></tspan><tspan
+ x="59.720703"
+ y="485.0704"><tspan
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'"> name = &quot;SFRC01247&quot;;
+</tspan></tspan><tspan
+ x="59.720703"
+ y="494.12972"><tspan
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'">}
+</tspan></tspan><tspan
+ x="59.720703"
+ y="503.18905"><tspan
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'">
+</tspan></tspan></text>
+ <text
+ xml:space="preserve"
+ id="text16"
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:7.05556px;line-height:1.25;font-family:'TeX Gyre Heros';-inkscape-font-specification:'TeX Gyre Heros, Normal';font-variant-ligatures:normal;font-variant-caps:normal;font-variant-numeric:normal;font-feature-settings:normal;text-align:start;letter-spacing:0px;word-spacing:0px;writing-mode:lr-tb;white-space:pre;shape-inside:url(#rect18);fill:#000000;fill-opacity:1;stroke:none;"
+ transform="matrix(0.59766334,0,0,0.59766334,-350.2056,73.998447)"><tspan
+ x="-200.98633"
+ y="27.794364"><tspan
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'">SBJ00237,MDX190227,L1901038,SFRC01247,SFRC01247-B1
+</tspan></tspan><tspan
+ x="-200.98633"
+ y="36.853703"><tspan
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'">SBJ00237,MDX190227,L1901038_topup,SFRC01247,SFRC01247-B1
+</tspan></tspan><tspan
+ x="-200.98633"
+ y="45.913043"><tspan
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+</tspan></tspan><tspan
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+</tspan></tspan><tspan
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+</tspan></tspan><tspan
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+</tspan></tspan></text>
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+ style="fill:#000000;fill-opacity:1;stroke:#000000;stroke-width:0.597664;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1;marker-end:url(#Arrow1Lend)"
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+ sodipodi:role="line"
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+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code';stroke-width:0.264583"
+ id="tspan8687">, speed ? &quot;normal&quot;</tspan><tspan
+ sodipodi:role="line"
+ x="-144.16017"
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+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code';stroke-width:0.264583"
+ id="tspan8689">, max-genotypes ? 0</tspan><tspan
+ sodipodi:role="line"
+ x="-144.16017"
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+ id="tspan8691">, targets ? [] }:</tspan></text>
+ <path
+ style="fill:none;stroke:#000000;stroke-width:0.5;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1;marker-end:url(#Arrow1Lend)"
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+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'"> options.octopus.call = {
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+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'"> speed = mkOption {
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+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'"> type = types.enum [ &quot;normal&quot; &quot;fast&quot; &quot;very-fast&quot; ];
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+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'"> max-genotypes = mkOption {
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+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'"> type = types.int;
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+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'"> default = 0;
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+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'"> description = &quot;Maximum number of candidate genotypes. If </tspan></tspan><tspan
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+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'">zero then flag is not passed to octopus.&quot;
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+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'"> };
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+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'"> targets = mkOption {
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+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'"> type = types.either (types.listOf types.str) types.path;
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+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'"> default = [];
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+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'"> description = &quot;either a list of genomic regions to call or a </tspan></tspan><tspan
+ x="-21.242188"
+ y="124.65156"><tspan
+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'">file containing a list of genomic regions to call&quot;;
+</tspan></tspan><tspan
+ x="-21.242188"
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+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'"> example = ''
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+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'"> targets = [ &quot;chr1&quot; &quot;chr2:0-1,000&quot; ];
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+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'"> '';
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+ style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-family:'Fira Code';-inkscape-font-specification:'Fira Code'">...</tspan></tspan></text>
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diff --git a/redcap.pdf b/redcap.pdf
new file mode 100644
index 0000000..a3be593
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+++ b/redcap.pdf
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diff --git a/sfrc01042-gridss.pdf b/sfrc01042-gridss.pdf
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diff --git a/slides.tex b/slides.tex
index c51f1e5..04ed327 100644
--- a/slides.tex
+++ b/slides.tex
@@ -20,7 +20,7 @@
\author{Justin Bed\H{o}\\WEHI}
\title{\includegraphics[width=.7\linewidth]{logo}\\functional, reproducible bioinformatics workflows}
-\date{November 10, 2020}
+\date{December 8th, 2020}
\begin{document}
@@ -40,7 +40,7 @@
\item More complex than a straight chain
\end{enumerate}
\begin{center}
- $\Rightarrow$ tooling needed for reproducibility
+ $\Rightarrow$ tooling needed for reproducibility\footnote{generate bit-identical output from an analysis specification on any machine with sufficient resources}
\end{center}
\end{frame}
@@ -169,8 +169,6 @@
\begin{minipage}{.55\textwidth}
\begin{overprint}
\onslide<1>\includegraphics[width=\linewidth]{pipeline}
- \onslide<2>\includegraphics[width=.75\linewidth]{bwa-stage}
- \onslide<3>\includegraphics[width=\linewidth]{bwa-drv}
\end{overprint}
\end{minipage}
\end{frame}
@@ -199,30 +197,91 @@
\end{frame}
\begin{frame}
- \frametitle{NextFlow example translation}
- \begin{minipage}{.5\textwidth}
- \begin{block}{BioNix}
- \vspace{.25cm}
- \includegraphics[height=.65\textheight]{nextflow-nix}
- \end{block}
- \end{minipage}
- \begin{minipage}{.4\textwidth}
- \begin{block}{NextFlow}
- \vspace{.25cm}
- \includegraphics[height=.65\textheight]{nextflow}
- \end{block}
- \end{minipage}
+ \frametitle{Stafford Fox Rare Cancer Project}
+ \begin{enumerate}
+ \item $\geq100$ WGS/WES samples totalling 20 TiB of primary data
+ \item Clinical \& research driven
+ \item Timely reporting to requesting clinicians
+ \item Flexibility required to respond to research questions
+ \item Cohort requires consistent processing
+ \item Reproducibility throughout time
+ \end{enumerate}
\end{frame}
\begin{frame}
- \frametitle{Real-world usage at WEHI}
+ \frametitle{Stafford Fox Rare Cancer Project}
\begin{enumerate}
- \item Stafford Fox Rare Cancer Project
- \item $\geq100$ WGS/WES samples totalling 20 TiB of primary data
+ \item Reproducible workflow via BioNix, with version control provided by git
\item SNV calling, neoantigen prediction, structural variants, copy number, mutational signatures, and report generation with embedded revision hash
- \item CI ensures reports are always up to date and consistent across the cohort
+ \item Handles WES, WGS, comprehensive cancer panel, PDX
+ \item Continuous integration ensures reports are always up to date and consistent across the cohort
\item Processed at Pawsey (Slurm) and WEHI (PBS \& Slurm)
+ \item Almost completely automated handling of new data
+ \end{enumerate}
+\end{frame}
+
+\begin{frame}
+ \frametitle{Example report}
+\end{frame}
+
+\begin{frame}
+ \frametitle{Stafford Fox Rare Cancer Workflow}
+ \includegraphics[width=\linewidth]{sfrc01042}
+\end{frame}
+
+\begin{frame}
+ \frametitle{Stafford Fox Rare Cancer Workflow}
+ \includegraphics[width=\linewidth]{sfrc01042-gridss}
+\end{frame}
+
+\begin{frame}
+ \frametitle{Generating expressions for new data}
+ \includegraphics[width=.9\linewidth]{autogen}
+\end{frame}
+
+\begin{frame}
+ \frametitle{Integrating RedCap information reproducibly}
+ \begin{minipage}{.3\textwidth}
+ \includegraphics[width=\linewidth]{redcap}
+ \end{minipage}
+ \begin{minipage}{.68\textwidth}
+ \begin{enumerate}
+ \item Difficult, live database without a release schedule
+ \item Solution: store the relevant annotations in the expressions
+ \item Git version control then also applies to the DB content
+ \item Sync script to update annotations
\end{enumerate}
+ \end{minipage}
+\end{frame}
+
+\begin{frame}
+ \frametitle{Benefits from using BioNix}
+ \begin{enumerate}
+ \item Guarantees a high degree of reproducibility and portability
+ \item Easy to modify workflow and add components
+ \item Small continuous integration implementation
+ \item Inbuilt consistency checking via hash verification
+ \end{enumerate}
+\end{frame}
+
+\begin{frame}
+ \frametitle{Issues with BioNix}
+ \begin{enumerate}
+ \item Steep learning curve
+ \begin{enumerate}
+ \item Nix the language
+ \item BioNix/nixpkgs abstractions
+ \item Stafford Fox workflow particulars
+ \end{enumerate}
+ \item Low discoverability
+ \item Modest collection of bioinformatics software in nixpkgs
+ \item Nix evaluation isn't hermetic (fixed with flakes)
+ \end{enumerate}
+\end{frame}
+
+\begin{frame}
+ \frametitle{Alternative configuration structure}
+ \includegraphics[width=\linewidth]{config}
\end{frame}
\begin{frame}
generated by cgit v1.3 (git 2.53.0) at 2026-05-15 13:13:07 +0000