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Commit d60fefdc authored by Alex Kanitz's avatar Alex Kanitz
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Merge branch 'subpipelines' into 'master' 

Wire all available rules

See merge request zavolan_group/pipelines/rnaseqpipeline!15
parents d5c96d88 ca9a2bb4
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1 merge request!15Wire all available rules
Pipeline #10184 passed
Stage: test
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.gitignore
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View file @ d60fefdc
...@@ -326,7 +326,9 @@ pip-selfcheck.json ...@@ -326,7 +326,9 @@ pip-selfcheck.json
# Custom additions # Custom additions
.vscode .vscode
.DS_Store .DS_Store
snakemake/.*
runs/.* runs/.*
!runs/PUT_YOUR_WORKFLOW_RUN_CONFIGS_HERE !runs/PUT_YOUR_WORKFLOW_RUN_CONFIGS_HERE
._.DS_Store
.snakemake/ .snakemake/
logs/
results/
images/workflow_dag.svg
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View file @ d60fefdc
<?xml version="1.0" encoding="UTF-8" standalone="no"?> <?xml version="1.0" encoding="UTF-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" <!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
"http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd"> "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
<!-- Generated by graphviz version 2.42.3 (20191010.1750) <!-- Generated by graphviz version 2.38.0 (20140413.2041)
--> -->
<!-- Title: snakemake_dag Pages: 1 --> <!-- Title: snakemake_dag Pages: 1 -->
<svg width="699pt" height="188pt" <svg width="1229pt" height="337pt"
viewBox="0.00 0.00 699.00 188.00" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink"> viewBox="0.00 0.00 1228.50 337.00" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
<g id="graph0" class="graph" transform="scale(1 1) rotate(0) translate(4 184)"> <g id="graph0" class="graph" transform="scale(1 1) rotate(0) translate(4 333)">
<title>snakemake_dag</title> <title>snakemake_dag</title>
<polygon fill="white" stroke="transparent" points="-4,4 -4,-184 695,-184 695,4 -4,4"/> <polygon fill="white" stroke="none" points="-4,4 -4,-333 1224.5,-333 1224.5,4 -4,4"/>
<!-- 0 --> <!-- 0 -->
<g id="node1" class="node"> <g id="node1" class="node"><title>0</title>
<title>0</title> <path fill="none" stroke="#5692d8" stroke-width="2" d="M698.5,-36C698.5,-36 668.5,-36 668.5,-36 662.5,-36 656.5,-30 656.5,-24 656.5,-24 656.5,-12 656.5,-12 656.5,-6 662.5,-0 668.5,-0 668.5,-0 698.5,-0 698.5,-0 704.5,-0 710.5,-6 710.5,-12 710.5,-12 710.5,-24 710.5,-24 710.5,-30 704.5,-36 698.5,-36"/>
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<text text-anchor="middle" x="342.5" y="-15.5" font-family="sans" font-size="10.00">finish</text>
</g> </g>
<!-- 1 --> <!-- 1 -->
<g id="node2" class="node"> <g id="node2" class="node"><title>1</title>
<title>1</title> <path fill="none" stroke="#56d8c9" stroke-width="2" d="M145,-108C145,-108 12,-108 12,-108 6,-108 0,-102 0,-96 0,-96 0,-84 0,-84 0,-78 6,-72 12,-72 12,-72 145,-72 145,-72 151,-72 157,-78 157,-84 157,-84 157,-96 157,-96 157,-102 151,-108 145,-108"/>
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<text text-anchor="middle" x="83.5" y="-93" font-family="sans" font-size="10.00">pe_fastqc</text> <text text-anchor="middle" x="78.5" y="-82" font-family="sans" font-size="10.00">sample: HNRNPC_control_rep1</text>
<text text-anchor="middle" x="83.5" y="-82" font-family="sans" font-size="10.00">sample: HNRNPC_control_rep1</text>
</g> </g>
<!-- 1&#45;&gt;0 --> <!-- 1&#45;&gt;0 -->
<g id="edge1" class="edge"> <g id="edge1" class="edge"><title>1&#45;&gt;0</title>
<title>1&#45;&gt;0</title> <path fill="none" stroke="grey" stroke-width="2" d="M157.123,-73.4533C160.287,-72.9413 163.421,-72.4543 166.5,-72 345.404,-45.6025 561.075,-28.0522 646.281,-21.6765"/>
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<!-- 2 --> <!-- 2 -->
<g id="node3" class="node"> <g id="node3" class="node"><title>2</title>
<title>2</title> <path fill="none" stroke="#56d892" stroke-width="2" d="M305.5,-108C305.5,-108 187.5,-108 187.5,-108 181.5,-108 175.5,-102 175.5,-96 175.5,-96 175.5,-84 175.5,-84 175.5,-78 181.5,-72 187.5,-72 187.5,-72 305.5,-72 305.5,-72 311.5,-72 317.5,-78 317.5,-84 317.5,-84 317.5,-96 317.5,-96 317.5,-102 311.5,-108 305.5,-108"/>
<path fill="none" stroke="#56d873" stroke-width="2" d="M320,-108C320,-108 197,-108 197,-108 191,-108 185,-102 185,-96 185,-96 185,-84 185,-84 185,-78 191,-72 197,-72 197,-72 320,-72 320,-72 326,-72 332,-78 332,-84 332,-84 332,-96 332,-96 332,-102 326,-108 320,-108"/> <text text-anchor="middle" x="246.5" y="-93" font-family="sans" font-size="10.00">pe_fastqc</text>
<text text-anchor="middle" x="258.5" y="-93" font-family="sans" font-size="10.00">pe_fastqc</text> <text text-anchor="middle" x="246.5" y="-82" font-family="sans" font-size="10.00">sample: HNRNPC_KD_rep1</text>
<text text-anchor="middle" x="258.5" y="-82" font-family="sans" font-size="10.00">sample: HNRNPC_KD_rep1</text>
</g> </g>
<!-- 2&#45;&gt;0 --> <!-- 2&#45;&gt;0 -->
<g id="edge2" class="edge"> <g id="edge2" class="edge"><title>2&#45;&gt;0</title>
<title>2&#45;&gt;0</title> <path fill="none" stroke="grey" stroke-width="2" d="M317.555,-73.662C320.574,-73.0858 323.566,-72.5291 326.5,-72 442.449,-51.0944 580.667,-32.3061 645.887,-23.8032"/>
<path fill="none" stroke="grey" stroke-width="2" d="M279.26,-71.7C289.74,-62.97 302.61,-52.24 314,-42.75"/> <polygon fill="grey" stroke="grey" stroke-width="2" points="646.618,-27.2378 656.085,-22.4802 645.718,-20.296 646.618,-27.2378"/>
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<!-- 3 --> <!-- 3 -->
<g id="node4" class="node"> <g id="node4" class="node"><title>3</title>
<title>3</title> <path fill="none" stroke="#c6d856" stroke-width="2" d="M497.5,-108C497.5,-108 347.5,-108 347.5,-108 341.5,-108 335.5,-102 335.5,-96 335.5,-96 335.5,-84 335.5,-84 335.5,-78 341.5,-72 347.5,-72 347.5,-72 497.5,-72 497.5,-72 503.5,-72 509.5,-78 509.5,-84 509.5,-84 509.5,-96 509.5,-96 509.5,-102 503.5,-108 497.5,-108"/>
<path fill="none" stroke="#afd856" stroke-width="2" d="M490.5,-108C490.5,-108 362.5,-108 362.5,-108 356.5,-108 350.5,-102 350.5,-96 350.5,-96 350.5,-84 350.5,-84 350.5,-78 356.5,-72 362.5,-72 362.5,-72 490.5,-72 490.5,-72 496.5,-72 502.5,-78 502.5,-84 502.5,-84 502.5,-96 502.5,-96 502.5,-102 496.5,-108 490.5,-108"/> <text text-anchor="middle" x="422.5" y="-87.5" font-family="sans" font-size="10.00">index_genomic_alignment_samtools</text>
<text text-anchor="middle" x="426.5" y="-87.5" font-family="sans" font-size="10.00">pe_remove_polya_cutadapt</text>
</g> </g>
<!-- 3&#45;&gt;0 --> <!-- 3&#45;&gt;0 -->
<g id="edge3" class="edge"> <g id="edge3" class="edge"><title>3&#45;&gt;0</title>
<title>3&#45;&gt;0</title> <path fill="none" stroke="grey" stroke-width="2" d="M486.014,-71.9656C536.337,-58.4691 604.892,-40.0826 646.577,-28.9028"/>
<path fill="none" stroke="grey" stroke-width="2" d="M405.74,-71.7C395.26,-62.97 382.39,-52.24 371,-42.75"/> <polygon fill="grey" stroke="grey" stroke-width="2" points="647.562,-32.2623 656.314,-26.2912 645.749,-25.5012 647.562,-32.2623"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="372.95,-39.82 363.03,-36.1 368.47,-45.19 372.95,-39.82"/>
</g> </g>
<!-- 4 --> <!-- 4 -->
<g id="node5" class="node"> <g id="node5" class="node"><title>4</title>
<title>4</title> <path fill="none" stroke="#5673d8" stroke-width="2" d="M705.5,-108C705.5,-108 539.5,-108 539.5,-108 533.5,-108 527.5,-102 527.5,-96 527.5,-96 527.5,-84 527.5,-84 527.5,-78 533.5,-72 539.5,-72 539.5,-72 705.5,-72 705.5,-72 711.5,-72 717.5,-78 717.5,-84 717.5,-84 717.5,-96 717.5,-96 717.5,-102 711.5,-108 705.5,-108"/>
<path fill="none" stroke="#afd856" stroke-width="2" d="M667.5,-108C667.5,-108 539.5,-108 539.5,-108 533.5,-108 527.5,-102 527.5,-96 527.5,-96 527.5,-84 527.5,-84 527.5,-78 533.5,-72 539.5,-72 539.5,-72 667.5,-72 667.5,-72 673.5,-72 679.5,-78 679.5,-84 679.5,-84 679.5,-96 679.5,-96 679.5,-102 673.5,-108 667.5,-108"/> <text text-anchor="middle" x="622.5" y="-87.5" font-family="sans" font-size="10.00">pe_index_genomic_alignment_samtools</text>
<text text-anchor="middle" x="603.5" y="-87.5" font-family="sans" font-size="10.00">pe_remove_polya_cutadapt</text>
</g> </g>
<!-- 4&#45;&gt;0 --> <!-- 4&#45;&gt;0 -->
<g id="edge4" class="edge"> <g id="edge4" class="edge"><title>4&#45;&gt;0</title>
<title>4&#45;&gt;0</title> <path fill="none" stroke="grey" stroke-width="2" d="M637.579,-71.6966C644.892,-63.3046 653.81,-53.0705 661.835,-43.8613"/>
<path fill="none" stroke="grey" stroke-width="2" d="M539.99,-71.97C489.66,-58.47 421.11,-40.08 379.42,-28.9"/> <polygon fill="grey" stroke="grey" stroke-width="2" points="664.664,-45.9429 668.595,-36.1043 659.386,-41.344 664.664,-45.9429"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="380.25,-25.5 369.69,-26.29 378.44,-32.26 380.25,-25.5"/>
</g> </g>
<!-- 5 --> <!-- 5 -->
<g id="node6" class="node"> <g id="node6" class="node"><title>5</title>
<title>5</title> <path fill="none" stroke="#56a9d8" stroke-width="2" d="M711,-180C711,-180 624,-180 624,-180 618,-180 612,-174 612,-168 612,-168 612,-156 612,-156 612,-150 618,-144 624,-144 624,-144 711,-144 711,-144 717,-144 723,-150 723,-156 723,-156 723,-168 723,-168 723,-174 717,-180 711,-180"/>
<path fill="none" stroke="#5692d8" stroke-width="2" d="M494,-180C494,-180 351,-180 351,-180 345,-180 339,-174 339,-168 339,-168 339,-156 339,-156 339,-150 345,-144 351,-144 351,-144 494,-144 494,-144 500,-144 506,-150 506,-156 506,-156 506,-168 506,-168 506,-174 500,-180 494,-180"/> <text text-anchor="middle" x="667.5" y="-159.5" font-family="sans" font-size="10.00">quantification_salmon</text>
<text text-anchor="middle" x="422.5" y="-165" font-family="sans" font-size="10.00">pe_remove_adapters_cutadapt</text> </g>
<text text-anchor="middle" x="422.5" y="-154" font-family="sans" font-size="10.00">sample: HNRNPC_control_rep1</text> <!-- 5&#45;&gt;0 -->
</g> <g id="edge5" class="edge"><title>5&#45;&gt;0</title>
<!-- 5&#45;&gt;3 --> <path fill="none" stroke="grey" stroke-width="2" d="M695.3,-143.872C707.271,-134.837 719.995,-122.587 726.5,-108 733.016,-93.3871 731.848,-87.0798 726.5,-72 722.838,-61.6754 716.213,-51.8956 709.243,-43.6136"/>
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<title>5&#45;&gt;3</title>
<path fill="none" stroke="grey" stroke-width="2" d="M423.49,-143.7C423.93,-135.98 424.46,-126.71 424.95,-118.11"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="428.45,-118.29 425.52,-108.1 421.46,-117.89 428.45,-118.29"/>
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<!-- 6 --> <!-- 6 -->
<g id="node7" class="node"> <g id="node7" class="node"><title>6</title>
<title>6</title> <path fill="none" stroke="#d87556" stroke-width="2" d="M856,-180C856,-180 753,-180 753,-180 747,-180 741,-174 741,-168 741,-168 741,-156 741,-156 741,-150 747,-144 753,-144 753,-144 856,-144 856,-144 862,-144 868,-150 868,-156 868,-156 868,-168 868,-168 868,-174 862,-180 856,-180"/>
<path fill="none" stroke="#5692d8" stroke-width="2" d="M679,-180C679,-180 536,-180 536,-180 530,-180 524,-174 524,-168 524,-168 524,-156 524,-156 524,-150 530,-144 536,-144 536,-144 679,-144 679,-144 685,-144 691,-150 691,-156 691,-156 691,-168 691,-168 691,-174 685,-180 679,-180"/> <text text-anchor="middle" x="804.5" y="-159.5" font-family="sans" font-size="10.00">pe_quantification_salmon</text>
<text text-anchor="middle" x="607.5" y="-165" font-family="sans" font-size="10.00">pe_remove_adapters_cutadapt</text> </g>
<text text-anchor="middle" x="607.5" y="-154" font-family="sans" font-size="10.00">sample: HNRNPC_KD_rep1</text> <!-- 6&#45;&gt;0 -->
</g> <g id="edge6" class="edge"><title>6&#45;&gt;0</title>
<!-- 6&#45;&gt;4 --> <path fill="none" stroke="grey" stroke-width="2" d="M794.156,-143.745C782.643,-125.159 762.949,-95.1426 742.5,-72 733.436,-61.7416 722.513,-51.4573 712.542,-42.7145"/>
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<title>6&#45;&gt;4</title> </g>
<path fill="none" stroke="grey" stroke-width="2" d="M606.51,-143.7C606.07,-135.98 605.54,-126.71 605.05,-118.11"/> <!-- 7 -->
<polygon fill="grey" stroke="grey" stroke-width="2" points="608.54,-117.89 604.48,-108.1 601.55,-118.29 608.54,-117.89"/> <g id="node8" class="node"><title>7</title>
<path fill="none" stroke="#d8cb56" stroke-width="2" d="M1024.5,-180C1024.5,-180 898.5,-180 898.5,-180 892.5,-180 886.5,-174 886.5,-168 886.5,-168 886.5,-156 886.5,-156 886.5,-150 892.5,-144 898.5,-144 898.5,-144 1024.5,-144 1024.5,-144 1030.5,-144 1036.5,-150 1036.5,-156 1036.5,-156 1036.5,-168 1036.5,-168 1036.5,-174 1030.5,-180 1024.5,-180"/>
<text text-anchor="middle" x="961.5" y="-159.5" font-family="sans" font-size="10.00">genome_quantification_kallisto</text>
</g>
<!-- 7&#45;&gt;0 -->
<g id="edge7" class="edge"><title>7&#45;&gt;0</title>
<path fill="none" stroke="grey" stroke-width="2" d="M927.967,-143.871C875.381,-117.011 773.939,-65.1956 719.734,-37.5078"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="720.999,-34.2241 710.501,-32.7921 717.815,-40.4579 720.999,-34.2241"/>
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<!-- 8 -->
<g id="node9" class="node"><title>8</title>
<path fill="none" stroke="#d88d56" stroke-width="2" d="M1208.5,-180C1208.5,-180 1066.5,-180 1066.5,-180 1060.5,-180 1054.5,-174 1054.5,-168 1054.5,-168 1054.5,-156 1054.5,-156 1054.5,-150 1060.5,-144 1066.5,-144 1066.5,-144 1208.5,-144 1208.5,-144 1214.5,-144 1220.5,-150 1220.5,-156 1220.5,-156 1220.5,-168 1220.5,-168 1220.5,-174 1214.5,-180 1208.5,-180"/>
<text text-anchor="middle" x="1137.5" y="-159.5" font-family="sans" font-size="10.00">pe_genome_quantification_kallisto</text>
</g>
<!-- 8&#45;&gt;0 -->
<g id="edge8" class="edge"><title>8&#45;&gt;0</title>
<path fill="none" stroke="grey" stroke-width="2" d="M1082.74,-143.871C988.878,-114.515 799.714,-55.3489 720.116,-30.4527"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="721.109,-27.0961 710.52,-27.4513 719.02,-33.777 721.109,-27.0961"/>
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<!-- 9 -->
<g id="node10" class="node"><title>9</title>
<path fill="none" stroke="#56d873" stroke-width="2" d="M451,-180C451,-180 378,-180 378,-180 372,-180 366,-174 366,-168 366,-168 366,-156 366,-156 366,-150 372,-144 378,-144 378,-144 451,-144 451,-144 457,-144 463,-150 463,-156 463,-156 463,-168 463,-168 463,-174 457,-180 451,-180"/>
<text text-anchor="middle" x="414.5" y="-159.5" font-family="sans" font-size="10.00">map_genome_star</text>
</g>
<!-- 9&#45;&gt;3 -->
<g id="edge9" class="edge"><title>9&#45;&gt;3</title>
<path fill="none" stroke="grey" stroke-width="2" d="M416.478,-143.697C417.359,-135.983 418.419,-126.712 419.401,-118.112"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="422.887,-118.437 420.545,-108.104 415.932,-117.642 422.887,-118.437"/>
</g>
<!-- 10 -->
<g id="node11" class="node"><title>10</title>
<path fill="none" stroke="#56d8a9" stroke-width="2" d="M582,-180C582,-180 493,-180 493,-180 487,-180 481,-174 481,-168 481,-168 481,-156 481,-156 481,-150 487,-144 493,-144 493,-144 582,-144 582,-144 588,-144 594,-150 594,-156 594,-156 594,-168 594,-168 594,-174 588,-180 582,-180"/>
<text text-anchor="middle" x="537.5" y="-159.5" font-family="sans" font-size="10.00">pe_map_genome_star</text>
</g>
<!-- 10&#45;&gt;4 -->
<g id="edge10" class="edge"><title>10&#45;&gt;4</title>
<path fill="none" stroke="grey" stroke-width="2" d="M558.511,-143.697C569.216,-134.881 582.39,-124.032 593.996,-114.474"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="596.236,-117.163 601.73,-108.104 591.786,-111.76 596.236,-117.163"/>
</g>
<!-- 11 -->
<g id="node12" class="node"><title>11</title>
<path fill="none" stroke="#d8ac56" stroke-width="2" d="M657.5,-254.5C657.5,-254.5 561.5,-254.5 561.5,-254.5 555.5,-254.5 549.5,-248.5 549.5,-242.5 549.5,-242.5 549.5,-230.5 549.5,-230.5 549.5,-224.5 555.5,-218.5 561.5,-218.5 561.5,-218.5 657.5,-218.5 657.5,-218.5 663.5,-218.5 669.5,-224.5 669.5,-230.5 669.5,-230.5 669.5,-242.5 669.5,-242.5 669.5,-248.5 663.5,-254.5 657.5,-254.5"/>
<text text-anchor="middle" x="609.5" y="-234" font-family="sans" font-size="10.00">remove_polya_cutadapt</text>
</g>
<!-- 11&#45;&gt;5 -->
<g id="edge11" class="edge"><title>11&#45;&gt;5</title>
<path fill="none" stroke="grey" stroke-width="2" d="M623.245,-218.319C630.468,-209.29 639.457,-198.054 647.442,-188.072"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="650.34,-190.053 653.853,-180.058 644.873,-185.68 650.34,-190.053"/>
</g>
<!-- 11&#45;&gt;7 -->
<g id="edge15" class="edge"><title>11&#45;&gt;7</title>
<path fill="none" stroke="grey" stroke-width="2" d="M669.359,-218.435C672.782,-217.581 676.18,-216.762 679.5,-216 763.608,-196.682 787.967,-196.835 876.473,-180.165"/>
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<!-- 11&#45;&gt;9 -->
<g id="edge20" class="edge"><title>11&#45;&gt;9</title>
<path fill="none" stroke="grey" stroke-width="2" d="M563.288,-218.319C535.36,-207.935 499.584,-194.634 470.113,-183.677"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="470.973,-180.263 460.381,-180.058 468.534,-186.824 470.973,-180.263"/>
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<!-- 12 -->
<g id="node13" class="node"><title>12</title>
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<text text-anchor="middle" x="750.5" y="-245" font-family="sans" font-size="10.00">create_index_salmon</text>
<text text-anchor="middle" x="750.5" y="-234" font-family="sans" font-size="10.00">kmer: 31</text>
<text text-anchor="middle" x="750.5" y="-223" font-family="sans" font-size="10.00">organism: homo_sapiens</text>
</g>
<!-- 12&#45;&gt;5 -->
<g id="edge12" class="edge"><title>12&#45;&gt;5</title>
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<!-- 12&#45;&gt;6 -->
<g id="edge14" class="edge"><title>12&#45;&gt;6</title>
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</g>
<!-- 13 -->
<g id="node14" class="node"><title>13</title>
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<text text-anchor="middle" x="899.5" y="-234" font-family="sans" font-size="10.00">pe_remove_polya_cutadapt</text>
</g>
<!-- 13&#45;&gt;6 -->
<g id="edge13" class="edge"><title>13&#45;&gt;6</title>
<path fill="none" stroke="grey" stroke-width="2" d="M876.986,-218.319C864.445,-208.748 848.656,-196.698 835.018,-186.29"/>
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<!-- 13&#45;&gt;8 -->
<g id="edge17" class="edge"><title>13&#45;&gt;8</title>
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<!-- 13&#45;&gt;10 -->
<g id="edge22" class="edge"><title>13&#45;&gt;10</title>
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<!-- 14 -->
<g id="node15" class="node"><title>14</title>
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<text text-anchor="middle" x="1119.5" y="-239.5" font-family="sans" font-size="10.00">create_index_kallisto</text>
<text text-anchor="middle" x="1119.5" y="-228.5" font-family="sans" font-size="10.00">organism: homo_sapiens</text>
</g>
<!-- 14&#45;&gt;7 -->
<g id="edge16" class="edge"><title>14&#45;&gt;7</title>
<path fill="none" stroke="grey" stroke-width="2" d="M1082.06,-218.319C1059.82,-208.116 1031.45,-195.096 1007.81,-184.25"/>
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<!-- 14&#45;&gt;8 -->
<g id="edge18" class="edge"><title>14&#45;&gt;8</title>
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<!-- 15 -->
<g id="node16" class="node"><title>15</title>
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<text text-anchor="middle" x="432.5" y="-245" font-family="sans" font-size="10.00">create_index_star</text>
<text text-anchor="middle" x="432.5" y="-234" font-family="sans" font-size="10.00">index_size: 100</text>
<text text-anchor="middle" x="432.5" y="-223" font-family="sans" font-size="10.00">organism: homo_sapiens</text>
</g>
<!-- 15&#45;&gt;9 -->
<g id="edge19" class="edge"><title>15&#45;&gt;9</title>
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<!-- 15&#45;&gt;10 -->
<g id="edge21" class="edge"><title>15&#45;&gt;10</title>
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<!-- 16 -->
<g id="node17" class="node"><title>16</title>
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<text text-anchor="middle" x="609.5" y="-314" font-family="sans" font-size="10.00">remove_adapters_cutadapt</text>
<text text-anchor="middle" x="609.5" y="-303" font-family="sans" font-size="10.00">sample: HNRNPC_control_rep1</text>
</g>
<!-- 16&#45;&gt;11 -->
<g id="edge23" class="edge"><title>16&#45;&gt;11</title>
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<!-- 17 -->
<g id="node18" class="node"><title>17</title>
<path fill="none" stroke="#59d856" stroke-width="2" d="M962.5,-329C962.5,-329 836.5,-329 836.5,-329 830.5,-329 824.5,-323 824.5,-317 824.5,-317 824.5,-305 824.5,-305 824.5,-299 830.5,-293 836.5,-293 836.5,-293 962.5,-293 962.5,-293 968.5,-293 974.5,-299 974.5,-305 974.5,-305 974.5,-317 974.5,-317 974.5,-323 968.5,-329 962.5,-329"/>
<text text-anchor="middle" x="899.5" y="-314" font-family="sans" font-size="10.00">pe_remove_adapters_cutadapt</text>
<text text-anchor="middle" x="899.5" y="-303" font-family="sans" font-size="10.00">sample: HNRNPC_KD_rep1</text>
</g>
<!-- 17&#45;&gt;13 -->
<g id="edge24" class="edge"><title>17&#45;&gt;13</title>
<path fill="none" stroke="grey" stroke-width="2" d="M899.5,-292.819C899.5,-284.422 899.5,-274.116 899.5,-264.686"/>
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</g> </g>
</svg> </svg>
snakemake/Snakefile
+ 33
− 25
View file @ d60fefdc
...@@ -27,18 +27,29 @@ include: 'single_end.snakefile.smk' ...@@ -27,18 +27,29 @@ include: 'single_end.snakefile.smk'
rule finish: rule finish:
input: input:
outdir1 = expand(os.path.join(config["output_dir"], "paired_end", "{sample}", "mate1_fastqc"), sample=samples_table.index.values), outdir1 = expand(os.path.join(config["output_dir"], "{seqmode}", "{sample}", "mate1_fastqc"),
outdir2 = expand(os.path.join(config["output_dir"], "paired_end", "{sample}", "mate2_fastqc"), sample=samples_table.index.values), zip,
reads1 = expand(os.path.join(config["output_dir"], "paired_end", "{sample}", "{sample}.remove_polya_mate1.fastq.gz"), sample=samples_table.index.values) sample= [i for i in list(samples_table.index.values)],
seqmode= [samples_table.loc[i,"seqmode"] for i in list(samples_table.index.values)]),
bai_index_map = expand(os.path.join(config["output_dir"], "{seqmode}", "{sample}", "map_genome", "{sample}_Aligned.sortedByCoord.out.bam.bai"),
zip,
sample= [i for i in list(samples_table.index.values)],
seqmode= [samples_table.loc[i,"seqmode"] for i in list(samples_table.index.values)]),
salmon_gn_estimates = expand(os.path.join(config["output_dir"],"{seqmode}","{sample}","salmon_quant","quant.genes.sf"),
zip,
sample= [i for i in list(samples_table.index.values)],
seqmode= [samples_table.loc[i,"seqmode"] for i in list(samples_table.index.values)]),
pseudoalignment = expand(os.path.join(config["output_dir"],"{seqmode}","{sample}","quant_kallisto", "{sample}.kallisto.pseudo.sam"),
zip,
sample= [i for i in list(samples_table.index.values)],
seqmode= [samples_table.loc[i,"seqmode"] for i in list(samples_table.index.values)]),
rule create_index_star: rule create_index_star:
''' Create index using STAR''' ''' Create index using STAR'''
input: input:
genome = lambda wildcards: samples_table.loc[wildcards.sample, 'genome'], genome =lambda wildcards: samples_table["genome"][samples_table["organism"]==wildcards.organism][0],
gtf = lambda wildcards: samples_table.loc[wildcards.sample, 'gtf'] gtf =lambda wildcards: samples_table["gtf"][samples_table["organism"]==wildcards.organism][0]
output: output:
chromosome_info = os.path.join( chromosome_info = os.path.join(
config["star_indexes"], config["star_indexes"],
...@@ -63,8 +74,7 @@ rule create_index_star: ...@@ -63,8 +74,7 @@ rule create_index_star:
"{organism}", "{organism}",
"{index_size}", "{index_size}",
"STAR_index/STAR_"), "STAR_index/STAR_"),
sjdbOverhang = lambda wildcards: sjdbOverhang = "{index_size}"
samples_table[wildcards.sample, "index_size"],
singularity: singularity:
"docker://zavolab/star:2.6.0a" "docker://zavolab/star:2.6.0a"
threads: 12 threads: 12
...@@ -86,46 +96,44 @@ rule create_index_star: ...@@ -86,46 +96,44 @@ rule create_index_star:
rule create_index_salmon: rule create_index_salmon:
'''Create index for salmon quantification''' '''Create index for salmon quantification'''
input: input:
transcriptome = lambda wildcards: transcriptome = lambda wildcards: samples_table['tr_fasta_filtered'][samples_table["organism"]==wildcards.organism][0]
samples_table.loc[wildcards.sample, 'tr_fasta_filtered']
output: output:
index = os.path.join( index = directory(os.path.join(
config["salmon_indexes"], config["salmon_indexes"],
"{organism}", "{organism}",
"salmon.idx") "{kmer}",
"salmon.idx"))
params: params:
kmerLen = lambda wildcards: kmerLen = "{kmer}"
samples_table.loc[wildcards.sample, 'kmer']
singularity: singularity:
"docker://zavolab/salmon:0.11.0" "docker://zavolab/salmon:0.11.0"
log: log:
os.path.join(config["local_log"], "{organism}_create_index_salmon.log") os.path.join(config["local_log"], "{organism}_{kmer}_create_index_salmon.log")
threads: 8 threads: 8
shell: shell:
"(salmon index \ "(salmon index \
--t {input.transcriptome} \ --transcripts {input.transcriptome} \
--i {output.index} \ --index {output.index} \
--k {params.kmerLen} \ --kmerLen {params.kmerLen} \
--threads {threads}) &> {log}" --threads {threads}) &> {log}"
rule create_index_kallisto: rule create_index_kallisto:
'''Create index for running Kallisto''' '''Create index for running Kallisto'''
input: input:
transcriptome = lambda wildcards: transcriptome = lambda wildcards: samples_table['tr_fasta_filtered'][samples_table["organism"]==wildcards.organism][0]
samples_table.loc[wildcards.sample, 'tr_fasta_filtered']
output: output:
index = os.path.join( index = os.path.join(
config["kallisto_indexes"], config["kallisto_indexes"],
"{organism}", "{organism}",
"kallisto.idx") "kallisto.idx")
params: params:
output_dir = lambda wildcards: output_dir = os.path.join(
os.path.join(
config["kallisto_indexes"], config["kallisto_indexes"],
samples_table[wildcards.sample, 'organism']) "{organism}")
singularity: singularity:
"docker://zavolab/kallisto:0.9" "docker://zavolab/kallisto:0.46.1"
log: log:
os.path.join(config["local_log"], "{organism}_create_index_kallisto.log") os.path.join(config["local_log"], "{organism}_create_index_kallisto.log")
shell: shell:
......
snakemake/paired_end.snakefile.smk
+ 15
− 14
View file @ d60fefdc
...@@ -6,14 +6,14 @@ rule pe_fastqc: ...@@ -6,14 +6,14 @@ rule pe_fastqc:
reads1 = lambda wildcards: samples_table.loc[wildcards.sample, "fq1"], reads1 = lambda wildcards: samples_table.loc[wildcards.sample, "fq1"],
reads2 = lambda wildcards: samples_table.loc[wildcards.sample, "fq2"] reads2 = lambda wildcards: samples_table.loc[wildcards.sample, "fq2"]
output: output:
outdir1 = directory(os.path.join(config["output_dir"], "paired_end", "{sample}", "mate1_fastqc")), outdir1 = directory(os.path.join(config["output_dir"],"paired_end", "{sample}", "mate1_fastqc")),
outdir2 = directory(os.path.join(config["output_dir"], "paired_end", "{sample}", "mate2_fastqc")) outdir2 = directory(os.path.join(config["output_dir"],"paired_end", "{sample}", "mate2_fastqc"))
threads: threads:
2 2
singularity: singularity:
"docker://zavolab/fastqc:0.11.8" "docker://zavolab/fastqc:0.11.8"
log: log:
os.path.join(config["local_log"], "paired_end", "{sample}", "fastqc.log") os.path.join(config["local_log"],"paired_end", "{sample}", "fastqc.log")
shell: shell:
"(mkdir -p {output.outdir1}; \ "(mkdir -p {output.outdir1}; \
mkdir -p {output.outdir2}; \ mkdir -p {output.outdir2}; \
...@@ -127,8 +127,8 @@ rule pe_map_genome_star: ...@@ -127,8 +127,8 @@ rule pe_map_genome_star:
index = lambda wildcards: index = lambda wildcards:
os.path.join( os.path.join(
config["star_indexes"], config["star_indexes"],
samples_table.loc[wildcards.sample, "organism"], str(samples_table.loc[wildcards.sample, "organism"]),
samples_table.loc[wildcards.sample, "index_size"], str(samples_table.loc[wildcards.sample, "index_size"]),
"STAR_index", "STAR_index",
"chrNameLength.txt"), "chrNameLength.txt"),
reads1 = os.path.join( reads1 = os.path.join(
...@@ -159,7 +159,8 @@ rule pe_map_genome_star: ...@@ -159,7 +159,8 @@ rule pe_map_genome_star:
index = lambda wildcards: index = lambda wildcards:
os.path.join( os.path.join(
config["star_indexes"], config["star_indexes"],
samples_table.loc[wildcards.sample, "index_size"], str(samples_table.loc[wildcards.sample, "organism"]),
str(samples_table.loc[wildcards.sample, "index_size"]),
"STAR_index"), "STAR_index"),
outFileNamePrefix = os.path.join( outFileNamePrefix = os.path.join(
config["output_dir"], config["output_dir"],
...@@ -168,7 +169,7 @@ rule pe_map_genome_star: ...@@ -168,7 +169,7 @@ rule pe_map_genome_star:
"map_genome", "map_genome",
"{sample}_"), "{sample}_"),
multimappers = lambda wildcards: multimappers = lambda wildcards:
samples_table.loc[wildcards.sample, "mulitmappers"], str(samples_table.loc[wildcards.sample, "multimappers"]),
soft_clip = lambda wildcards: soft_clip = lambda wildcards:
samples_table.loc[wildcards.sample, "soft_clip"], samples_table.loc[wildcards.sample, "soft_clip"],
pass_mode = lambda wildcards: pass_mode = lambda wildcards:
...@@ -202,8 +203,8 @@ rule pe_map_genome_star: ...@@ -202,8 +203,8 @@ rule pe_map_genome_star:
--outFilterMatchNminOverLread 0.3 \ --outFilterMatchNminOverLread 0.3 \
--outFilterType BySJout \ --outFilterType BySJout \
--outReadsUnmapped None \ --outReadsUnmapped None \
--outSAMattrRGline ID:rnaseq_pipeline SM:{params.sample} \ --outSAMattrRGline ID:rnaseq_pipeline SM:{params.sample_id} \
--alignEndsType {params.soft_clip}} > {output.bam};) &> {log}" --alignEndsType {params.soft_clip} > {output.bam};) &> {log}"
rule pe_index_genomic_alignment_samtools: rule pe_index_genomic_alignment_samtools:
...@@ -249,7 +250,8 @@ rule pe_quantification_salmon: ...@@ -249,7 +250,8 @@ rule pe_quantification_salmon:
index = lambda wildcards: index = lambda wildcards:
os.path.join( os.path.join(
config["salmon_indexes"], config["salmon_indexes"],
samples_table.loc[wildcards.sample, 'organism'], str(samples_table.loc[wildcards.sample, "organism"]),
str(samples_table.loc[wildcards.sample, "kmer"]),
"salmon.idx") "salmon.idx")
output: output:
gn_estimates = os.path.join( gn_estimates = os.path.join(
...@@ -317,16 +319,15 @@ rule pe_genome_quantification_kallisto: ...@@ -317,16 +319,15 @@ rule pe_genome_quantification_kallisto:
"quant_kallisto", "quant_kallisto",
"{sample}.kallisto.pseudo.sam") "{sample}.kallisto.pseudo.sam")
params: params:
output_dir = lambda wildcards: output_dir = os.path.join(
os.path.join(
config["output_dir"], config["output_dir"],
"paired_end", "paired_end",
wildcards.sample, "{sample}",
"quant_kallisto"), "quant_kallisto"),
directionality = lambda wildcards: directionality = lambda wildcards:
samples_table.loc[wildcards.sample, "kallisto_directionality"] samples_table.loc[wildcards.sample, "kallisto_directionality"]
singularity: singularity:
"docker://zavolab/kallisto:0.9" "docker://zavolab/kallisto:0.46.1"
threads: 8 threads: 8
log: log:
os.path.join(config["local_log"], "paired_end", "{sample}", "genome_quantification_kallisto.log") os.path.join(config["local_log"], "paired_end", "{sample}", "genome_quantification_kallisto.log")
......
snakemake/preprocessing.snakefile.smk deleted 100644 → 0
+ 0
− 28
View file @ d5c96d88
rule index_genome_STAR:
'''
Create Star index
'''
input:
genome = os.path.join(config["output_dir"], "genome.fa"),
annotation = os.path.join(config["output_dir"], "annotation.gtf")
output:
output = os.path.join(config["database_path"], config['organism'], config['STAR_idx_folder], "STAR_index" + {sjdb})
params:
outputdir = os.path.join(config["output_dir"],"STAR_index"),
sjdb = lambda wildcards: samples.loc['sjdb']
threads: 8
singularity:
"docker://zavolab/star:2.6.0a"
log:
os.path.join(config["local_log"],"index_genome_STAR.log")
shell:
"mkdir -p {output.output}; \
chmod -R 777 {output.output}; \
(STAR --runMode genomeGenerate \
--sjdbOverhang {params.sjdbOverhang} \
--genomeDir {params.outputdir} \
--genomeFastaFiles {input.genome} \
--runThreadN {threads} \
--sjdbGTFfile {input.annotation}) &> {log}"
\ No newline at end of file
snakemake/single_end.snakefile.smk
+ 30
− 28
View file @ d60fefdc
...@@ -4,7 +4,9 @@ rule fastqc: ...@@ -4,7 +4,9 @@ rule fastqc:
input: input:
reads = lambda wildcards: samples_table.loc[wildcards.sample, "fq1"], reads = lambda wildcards: samples_table.loc[wildcards.sample, "fq1"],
output: output:
outdir = directory(os.path.join(config["output_dir"], "single_end", "{sample}", "fastqc")) outdir = directory(os.path.join(config["output_dir"], "single_end", "{sample}", "mate1_fastqc"))
params:
seqmode= lambda wildcards: samples_table.loc[wildcards.sample, "seqmode"]
singularity: singularity:
"docker://zavolab/fastqc:0.11.8" "docker://zavolab/fastqc:0.11.8"
log: log:
...@@ -21,7 +23,7 @@ rule remove_adapters_cutadapt: ...@@ -21,7 +23,7 @@ rule remove_adapters_cutadapt:
input: input:
reads = lambda wildcards: samples_table.loc[wildcards.sample, "fq1"] reads = lambda wildcards: samples_table.loc[wildcards.sample, "fq1"]
output: output:
reads = os.path.join(config["output_dir"], "single_end", "{sample}", "{sample}.remove_adapters.fastq.gz") reads = os.path.join(config["output_dir"], "single_end", "{sample}", "{sample}.remove_adapters_mate1.fastq.gz")
params: params:
adapters_3 = lambda wildcards: adapters_3 = lambda wildcards:
samples_table.loc[wildcards.sample, 'fq1_3p'], samples_table.loc[wildcards.sample, 'fq1_3p'],
...@@ -34,7 +36,7 @@ rule remove_adapters_cutadapt: ...@@ -34,7 +36,7 @@ rule remove_adapters_cutadapt:
log: log:
os.path.join(config["local_log"], "single_end", "{sample}", "remove_adapters_cutadapt.log") os.path.join(config["local_log"], "single_end", "{sample}", "remove_adapters_cutadapt.log")
shell: shell:
"cutadapt \ "(cutadapt \
-e 0.1 \ -e 0.1 \
-O 1 \ -O 1 \
-j {threads} \ -j {threads} \
...@@ -49,9 +51,9 @@ rule remove_adapters_cutadapt: ...@@ -49,9 +51,9 @@ rule remove_adapters_cutadapt:
rule remove_polya_cutadapt: rule remove_polya_cutadapt:
''' Remove ployA tails''' ''' Remove ployA tails'''
input: input:
reads = lambda wildcards: samples_table[wildcards.sample, "fq1"] reads = os.path.join(config["output_dir"], "single_end", "{sample}", "{sample}.remove_adapters_mate1.fastq.gz")
output: output:
reads = os.path.join(config["output_dir"], "single_end", "{sample}", "{sample}.remove_polya.fastq.gz") reads = os.path.join(config["output_dir"], "single_end", "{sample}", "{sample}.remove_polya_mate1.fastq.gz")
params: params:
polya_3 = lambda wildcards: polya_3 = lambda wildcards:
samples_table.loc[wildcards.sample, "fq1_polya"] samples_table.loc[wildcards.sample, "fq1_polya"]
...@@ -80,10 +82,10 @@ rule map_genome_star: ...@@ -80,10 +82,10 @@ rule map_genome_star:
index = lambda wildcards: index = lambda wildcards:
os.path.join( os.path.join(
config["star_indexes"], config["star_indexes"],
samples_table.loc[wildcards.sample, "organism"], str(samples_table.loc[wildcards.sample, "organism"]),
samples_table.loc[wildcards.sample, "index_size"], str(samples_table.loc[wildcards.sample, "index_size"]),
"STAR_index","chrNameLength.txt"), "STAR_index","chrNameLength.txt"),
reads = os.path.join(config["output_dir"], "single_end", "{sample}", "{sample}.remove_polya.fastq.gz") reads = os.path.join(config["output_dir"], "single_end", "{sample}", "{sample}.remove_polya_mate1.fastq.gz")
output: output:
bam = os.path.join(config["output_dir"], "single_end", bam = os.path.join(config["output_dir"], "single_end",
"{sample}", "{sample}",
...@@ -96,16 +98,15 @@ rule map_genome_star: ...@@ -96,16 +98,15 @@ rule map_genome_star:
params: params:
sample_id = "{sample}", sample_id = "{sample}",
index = lambda wildcards: index = lambda wildcards:
os.path.join( os.path.join(
config["star_indexes"], config["star_indexes"],
samples_table.loc["{sample}", "organism"], str(samples_table.loc[wildcards.sample, "organism"]),
samples_table.loc[wildcards.sample, "index_size"], str(samples_table.loc[wildcards.sample, "index_size"]),
"STAR_index"), "STAR_index"),
outFileNamePrefix = lambda wildcards: outFileNamePrefix = os.path.join(
os.path.join( config["output_dir"],
config["output_dir"], "single_end",
"single_end", "{sample}", "map_genome", "{sample}_"),
"{sample}", "map_genome", "{sample}_"),
multimappers = lambda wildcards: multimappers = lambda wildcards:
samples_table.loc[wildcards.sample, "multimappers"], samples_table.loc[wildcards.sample, "multimappers"],
soft_clip = lambda wildcards: soft_clip = lambda wildcards:
...@@ -138,7 +139,7 @@ rule map_genome_star: ...@@ -138,7 +139,7 @@ rule map_genome_star:
--outFilterType BySJout \ --outFilterType BySJout \
--outReadsUnmapped None \ --outReadsUnmapped None \
--outSAMattrRGline ID:rcrunch SM:{params.sample_id} \ --outSAMattrRGline ID:rcrunch SM:{params.sample_id} \
--alignEndsType {params.soft_clip}} > {output.bam};) &> {log}" --alignEndsType {params.soft_clip} > {output.bam};) &> {log}"
rule index_genomic_alignment_samtools: rule index_genomic_alignment_samtools:
...@@ -171,11 +172,12 @@ rule quantification_salmon: ...@@ -171,11 +172,12 @@ rule quantification_salmon:
config["output_dir"], config["output_dir"],
"single_end", "single_end",
"{sample}", "{sample}",
"{sample}.remove_polya.fastq.gz"), "{sample}.remove_polya_mate1.fastq.gz"),
index = lambda wildcards: index = lambda wildcards:
os.path.join( os.path.join(
config["salmon_indexes"], config["salmon_indexes"],
samples_table[wildcards.sample, 'organism'], str(samples_table.loc[wildcards.sample, "organism"]),
str(samples_table.loc[wildcards.sample, "kmer"]),
"salmon.idx"), "salmon.idx"),
gtf = lambda wildcards: samples_table.loc[wildcards.sample, "gtf_filtered"] gtf = lambda wildcards: samples_table.loc[wildcards.sample, "gtf_filtered"]
output: output:
...@@ -202,8 +204,8 @@ rule quantification_salmon: ...@@ -202,8 +204,8 @@ rule quantification_salmon:
log: log:
os.path.join(config["local_log"], "single_end", "{sample}", "quantification_salmon.log") os.path.join(config["local_log"], "single_end", "{sample}", "quantification_salmon.log")
threads: 12 threads: 12
conda: singularity:
"envs/salmon.yaml" "docker://zavolab/salmon:0.11.0"
shell: shell:
"(salmon quant \ "(salmon quant \
--libType {params.libType} \ --libType {params.libType} \
...@@ -224,7 +226,7 @@ rule genome_quantification_kallisto: ...@@ -224,7 +226,7 @@ rule genome_quantification_kallisto:
config["output_dir"], config["output_dir"],
"single_end", "single_end",
"{sample}", "{sample}",
"{sample}.remove_polya.fastq.gz"), "{sample}.remove_polya_mate1.fastq.gz"),
index = lambda wildcards: index = lambda wildcards:
os.path.join( os.path.join(
config["kallisto_indexes"], config["kallisto_indexes"],
...@@ -235,10 +237,10 @@ rule genome_quantification_kallisto: ...@@ -235,10 +237,10 @@ rule genome_quantification_kallisto:
config["output_dir"], config["output_dir"],
"single_end", "single_end",
"{sample}", "{sample}",
"quant_kallisto",
"{sample}.kallisto.pseudo.sam") "{sample}.kallisto.pseudo.sam")
params: params:
output_dir = lambda wildcards: output_dir = os.path.join(
os.path.join(
config["output_dir"], config["output_dir"],
"single_end", "single_end",
"{sample}", "{sample}",
...@@ -250,7 +252,7 @@ rule genome_quantification_kallisto: ...@@ -250,7 +252,7 @@ rule genome_quantification_kallisto:
log: log:
os.path.join(config["local_log"],"kallisto_align_{sample}.log") os.path.join(config["local_log"],"kallisto_align_{sample}.log")
singularity: singularity:
"docker://zavolab/kallisto:0.9" "docker://zavolab/kallisto:0.46.1"
shell: shell:
"(kallisto quant \ "(kallisto quant \
-i {input.index} \ -i {input.index} \
...@@ -262,4 +264,4 @@ rule genome_quantification_kallisto: ...@@ -262,4 +264,4 @@ rule genome_quantification_kallisto:
{params.directionality} \ {params.directionality} \
{input.reads} > {output.pseudoalignment}) &> {log}" {input.reads} > {output.pseudoalignment}) &> {log}"
\ No newline at end of file
tests/test_create_dag_chart/samples.tsv
+ 2
− 2
View file @ d60fefdc
sample fq1 fq2 fq1_3p fq1_5p fq2_3p fq2_5p fq1_polya fq2_polya organism index_size multimappers soft_clip pass_mode gtf_filtered libtype kallisto_directionality mean sd genome gtf tr_fasta_filtered kmer seqmode sample fq1 fq2 fq1_3p fq1_5p fq2_3p fq2_5p fq1_polya fq2_polya organism index_size multimappers soft_clip pass_mode gtf_filtered libtype kallisto_directionality mean sd genome gtf tr_fasta_filtered kmer seqmode
HNRNPC_control_rep1 input_files/GSM1502498_1.fastq.gz input_files/GSM1502498_2.fastq.gz AGATCGGAAGAGCACA XXXXXXXX AGATCGGAAGAGCGT XXXXXXXX AAAAAAAAAAAAAAAAAAAA TTTTTTTTTTTTTTTTTTT homo_sapiens 100 10 Local Basic input_files/Homo_sapiens.GRCh38.99.chr.chrom_22.gtf A kallisto_directionality 250 100 input_files/Homo_sapiens.GRCh38.dna_sm.primary_assembly.chrom_22.fa input_files/Homo_sapiens.GRCh38.99.chr.chrom_22.gtf input_files/transcripts_chrom_22.fa 31 fr HNRNPC_control_rep1 input_files/GSM1502498_1.fastq.gz input_files/GSM1502498_2.fastq.gz AGATCGGAAGAGCACA XXXXXXXX AGATCGGAAGAGCGT XXXXXXXX AAAAAAAAAAAAAAAAAAAA TTTTTTTTTTTTTTTTTTT homo_sapiens 100 10 Local Basic ../test_integration_workflow/input_files/Homo_sapiens.GRCh38.99.chr.chrom_22.gtf A kallisto_directionality 250 100 ../test_integration_workflow/input_files/Homo_sapiens.GRCh38.dna_sm.primary_assembly.chrom_22.fa ../test_integration_workflow/input_files/Homo_sapiens.GRCh38.99.chr.chrom_22.gtf ../test_integration_workflow/input_files/transcripts_chrom_22.fa 31 single_end
HNRNPC_KD_rep1 input_files/GSM1502500_1.fastq.gz input_files/GSM1502500_2.fastq.gz AGATCGGAAGAGCACA XXXXXXXX AGATCGGAAGAGCGT XXXXXXXX AAAAAAAAAAAAAAAAAAAA TTTTTTTTTTTTTTTTTTT homo_sapiens 100 10 Local Basic input_files/Homo_sapiens.GRCh38.99.chr.filterd.chrom_22.gtf A kallisto_directionality 250 100 input_files/Homo_sapiens.GRCh38.dna_sm.primary_assembly.chrom_22.fa input_files/Homo_sapiens.GRCh38.99.chr.chrom_22.gtf input_files/transcripts_chrom_22.fa 31 fr HNRNPC_KD_rep1 input_files/GSM1502500_1.fastq.gz input_files/GSM1502500_2.fastq.gz AGATCGGAAGAGCACA XXXXXXXX AGATCGGAAGAGCGT XXXXXXXX AAAAAAAAAAAAAAAAAAAA TTTTTTTTTTTTTTTTTTT homo_sapiens 100 10 Local Basic ../test_integration_workflow/input_files/Homo_sapiens.GRCh38.99.chr.chrom_22.gtf A kallisto_directionality 250 100 ../test_integration_workflow/input_files/Homo_sapiens.GRCh38.dna_sm.primary_assembly.chrom_22.fa ../test_integration_workflow/input_files/Homo_sapiens.GRCh38.99.chr.chrom_22.gtf ../test_integration_workflow/input_files/transcripts_chrom_22.fa 31 paired_end
\ No newline at end of file
tests/test_integration_workflow/expected_output.md5
+ 8
− 4
View file @ d60fefdc
c45be0333e4d84285d530855342763e0 results/paired_end/HNRNPC_control_rep1/HNRNPC_control_rep1.remove_adapters_mate1.fastq 7be61b24952edd765a151a82fa8ad8bb results/single_end/HNRNPC_control_rep1/HNRNPC_control_rep1.remove_adapters_mate1.fastq
e1e0d16add8db1a314c780d497e863c9 results/paired_end/HNRNPC_control_rep1/HNRNPC_control_rep1.remove_polya_mate2.fastq d41d8cd98f00b204e9800998ecf8427e results/single_end/HNRNPC_control_rep1/quant_kallisto/HNRNPC_control_rep1.kallisto.pseudo.sam
a46359f784d3eca4268c788a74789bf2 results/paired_end/HNRNPC_control_rep1/HNRNPC_control_rep1.remove_polya_mate1.fastq efec14c44f708c23a99c5653fc020966 results/single_end/HNRNPC_control_rep1/quant_kallisto/pseudoalignments.bam
58ef63f61c82e050f05b871eea8d4b25 results/paired_end/HNRNPC_control_rep1/HNRNPC_control_rep1.remove_adapters_mate2.fastq adf0922672c7088138f564d418e2c055 results/single_end/HNRNPC_control_rep1/HNRNPC_control_rep1.remove_polya_mate1.fastq
6a62e57dc1765f8881bd114a64c69563 results/single_end/HNRNPC_control_rep1/map_genome/HNRNPC_control_rep1_Aligned.sortedByCoord.out.bam
d3898e6e03d98db65b61172f8275f319 results/paired_end/HNRNPC_KD_rep1/HNRNPC_KD_rep1.remove_adapters_mate2.fastq d3898e6e03d98db65b61172f8275f319 results/paired_end/HNRNPC_KD_rep1/HNRNPC_KD_rep1.remove_adapters_mate2.fastq
d41d8cd98f00b204e9800998ecf8427e results/paired_end/HNRNPC_KD_rep1/quant_kallisto/HNRNPC_KD_rep1.kallisto.pseudo.sam
67fd10e98d6b1b9041c0171b1cea4eb0 results/paired_end/HNRNPC_KD_rep1/quant_kallisto/pseudoalignments.bam
489e5a5bd92fafe9a79e164fb334e036 results/paired_end/HNRNPC_KD_rep1/HNRNPC_KD_rep1.remove_polya_mate2.fastq 489e5a5bd92fafe9a79e164fb334e036 results/paired_end/HNRNPC_KD_rep1/HNRNPC_KD_rep1.remove_polya_mate2.fastq
8a01f7aa476992c2bc32d3457f703865 results/paired_end/HNRNPC_KD_rep1/HNRNPC_KD_rep1.remove_adapters_mate1.fastq 8a01f7aa476992c2bc32d3457f703865 results/paired_end/HNRNPC_KD_rep1/HNRNPC_KD_rep1.remove_adapters_mate1.fastq
5c415fd62934c389dfd76abb7e9875c2 results/paired_end/HNRNPC_KD_rep1/map_genome/HNRNPC_KD_rep1_Aligned.sortedByCoord.out.bam
f048f50b6695c80e2c9d4ecf10c0d0a9 results/paired_end/HNRNPC_KD_rep1/HNRNPC_KD_rep1.remove_polya_mate1.fastq f048f50b6695c80e2c9d4ecf10c0d0a9 results/paired_end/HNRNPC_KD_rep1/HNRNPC_KD_rep1.remove_polya_mate1.fastq
tests/test_integration_workflow/samples.tsv
+ 2
− 2
View file @ d60fefdc
sample fq1 fq2 fq1_3p fq1_5p fq2_3p fq2_5p fq1_polya fq2_polya organism index_size multimappers soft_clip pass_mode gtf_filtered libtype kallisto_directionality mean sd genome gtf tr_fasta_filtered kmer seqmode sample fq1 fq2 fq1_3p fq1_5p fq2_3p fq2_5p fq1_polya fq2_polya organism index_size multimappers soft_clip pass_mode gtf_filtered libtype kallisto_directionality mean sd genome gtf tr_fasta_filtered kmer seqmode
HNRNPC_control_rep1 input_files/GSM1502498_1.fastq.gz input_files/GSM1502498_2.fastq.gz AGATCGGAAGAGCACA XXXXXXXX AGATCGGAAGAGCGT XXXXXXXX AAAAAAAAAAAAAAAAAAAA TTTTTTTTTTTTTTTTTTT homo_sapiens 100 10 Local Basic input_files/Homo_sapiens.GRCh38.99.chr.chrom_22.gtf A kallisto_directionality 250 100 input_files/Homo_sapiens.GRCh38.dna_sm.primary_assembly.chrom_22.fa input_files/Homo_sapiens.GRCh38.99.chr.chrom_22.gtf input_files/transcripts_chrom_22.fa 31 fr HNRNPC_control_rep1 input_files/GSM1502498_1.fastq.gz input_files/GSM1502498_2.fastq.gz AGATCGGAAGAGCACA XXXXXXXX AGATCGGAAGAGCGT XXXXXXXX AAAAAAAAAAAAAAAAAAAA TTTTTTTTTTTTTTTTTTT homo_sapiens 100 10 Local Basic input_files/Homo_sapiens.GRCh38.99.chr.chrom_22.gtf A --fr 250 100 input_files/Homo_sapiens.GRCh38.dna_sm.primary_assembly.chrom_22.fa input_files/Homo_sapiens.GRCh38.99.chr.chrom_22.gtf input_files/transcripts_chrom_22.fa 31 single_end
HNRNPC_KD_rep1 input_files/GSM1502500_1.fastq.gz input_files/GSM1502500_2.fastq.gz AGATCGGAAGAGCACA XXXXXXXX AGATCGGAAGAGCGT XXXXXXXX AAAAAAAAAAAAAAAAAAAA TTTTTTTTTTTTTTTTTTT homo_sapiens 100 10 Local Basic input_files/Homo_sapiens.GRCh38.99.chr.filterd.chrom_22.gtf A kallisto_directionality 250 100 input_files/Homo_sapiens.GRCh38.dna_sm.primary_assembly.chrom_22.fa input_files/Homo_sapiens.GRCh38.99.chr.chrom_22.gtf input_files/transcripts_chrom_22.fa 31 fr HNRNPC_KD_rep1 input_files/GSM1502500_1.fastq.gz input_files/GSM1502500_2.fastq.gz AGATCGGAAGAGCACA XXXXXXXX AGATCGGAAGAGCGT XXXXXXXX AAAAAAAAAAAAAAAAAAAA TTTTTTTTTTTTTTTTTTT homo_sapiens 100 10 Local Basic input_files/Homo_sapiens.GRCh38.99.chr.chrom_22.gtf A --fr 250 100 input_files/Homo_sapiens.GRCh38.dna_sm.primary_assembly.chrom_22.fa input_files/Homo_sapiens.GRCh38.99.chr.chrom_22.gtf input_files/transcripts_chrom_22.fa 31 paired_end
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