diff --git a/Snakefile b/Snakefile
index 963b69111a69a8a6a31ed3a200ca635f39d7c3c5..695d72f563aa363e773650bdb20107fa0cbfbdf8 100644
--- a/Snakefile
+++ b/Snakefile
@@ -102,10 +102,8 @@ rule finish:
for i in list(samples_table.index.values)
]
),
- salmon_merge_genes = os.path.join(config["output_dir"], "summary_salmon", "quantmerge", "genes_tpm.tsv"),
- salmon_merge_tr = os.path.join(config["output_dir"], "summary_salmon", "quantmerge", "tr_tpm.tsv"),
-
-
+ salmon_merge_genes = expand(os.path.join(config["output_dir"], "summary_salmon", "quantmerge", "genes_{salmon_merge_on}.tsv"), salmon_merge_on=["tpm", "numreads"]),
+ salmon_merge_transcripts = expand(os.path.join(config["output_dir"], "summary_salmon", "quantmerge", "transcripts_{salmon_merge_on}.tsv"), salmon_merge_on=["tpm", "numreads"])
rule create_index_star:
"""Create index for STAR alignments"""
@@ -311,32 +309,33 @@ rule calculate_TIN_scores:
2> {log}"
-rule salmon_quantmerge_genes_tpm:
+rule salmon_quantmerge_genes:
''' Merge gene quantifications into a single file. '''
input:
salmon_in = expand(os.path.join(
- config["output_dir"],
- "{seqmode}",
- "{sample}",
+ config["output_dir"],
+ "{seqmode}",
+ "{sample}",
"salmon_quant",
- "quant.genes.sf"),
+ "quant.genes.sf"),
zip,
- sample= list(samples_table.index.values),
+ sample= list(samples_table.index.values),
seqmode= list(samples_table["seqmode"])),
output:
- salmon_out = os.path.join(config["output_dir"], "summary_salmon", "quantmerge", "genes_tpm.tsv")
+ salmon_out = os.path.join(config["output_dir"], "summary_salmon", "quantmerge", "genes_{salmon_merge_on}.tsv")
params:
salmon_dir = expand(os.path.join(
- config["output_dir"],
- "{seqmode}",
- "{sample}",
- "salmon_quant"),
+ config["output_dir"],
+ "{seqmode}",
+ "{sample}",
+ "salmon_quant"),
zip,
- sample= list(samples_table.index.values),
+ sample= list(samples_table.index.values),
seqmode= list(samples_table["seqmode"])),
- sample_name_list = expand("{sample}", sample= list(samples_table.index.values))
+ sample_name_list = expand("{sample}", sample= list(samples_table.index.values)),
+ salmon_merge_on = "{salmon_merge_on}"
log:
- os.path.join(config["log_dir"], "salmon_quantmerge_genes_tpm.log")
+ os.path.join(config["log_dir"], "salmon_quantmerge_genes_{salmon_merge_on}.log")
threads: 1
singularity:
"docker://zavolab/salmon:1.1.0-slim"
@@ -345,41 +344,42 @@ rule salmon_quantmerge_genes_tpm:
--quants {params.salmon_dir} \
--genes \
--names {params.sample_name_list} \
- --column tpm \
+ --column {params.salmon_merge_on} \
--output {output.salmon_out}) &> {log}"
-rule salmon_quantmerge_tr_tpm:
+rule salmon_quantmerge_transcripts:
''' Merge gene quantifications into a single file. '''
input:
salmon_in = expand(os.path.join(
- config["output_dir"],
- "{seqmode}",
- "{sample}",
+ config["output_dir"],
+ "{seqmode}",
+ "{sample}",
"salmon_quant",
- "quant.sf"),
+ "quant.sf"),
zip,
- sample= list(samples_table.index.values),
+ sample= list(samples_table.index.values),
seqmode= list(samples_table["seqmode"])),
output:
- salmon_out = os.path.join(config["output_dir"], "summary_salmon", "quantmerge", "tr_tpm.tsv")
+ salmon_out = os.path.join(config["output_dir"], "summary_salmon", "quantmerge", "transcripts_{salmon_merge_on}.tsv")
params:
salmon_dir = expand(os.path.join(
- config["output_dir"],
- "{seqmode}",
- "{sample}",
- "salmon_quant"),
+ config["output_dir"],
+ "{seqmode}",
+ "{sample}",
+ "salmon_quant"),
zip,
- sample= list(samples_table.index.values),
+ sample= list(samples_table.index.values),
seqmode= list(samples_table["seqmode"])),
- sample_name_list = expand("{sample}", sample= list(samples_table.index.values))
+ sample_name_list = expand("{sample}", sample= list(samples_table.index.values)),
+ salmon_merge_on = "{salmon_merge_on}"
log:
- os.path.join(config["log_dir"], "salmon_quantmerge_tr_tpm.log")
+ os.path.join(config["log_dir"], "salmon_quantmerge_transcripts_{salmon_merge_on}.log")
threads: 1
singularity:
- "docker://zavolab/salmon:1.1.0-slim"
+ "docker://zavolab/salmon:1.1.0-slim"
shell:
"(salmon quantmerge \
--quants {params.salmon_dir} \
--names {params.sample_name_list} \
- --column tpm \
+ --column {params.salmon_merge_on} \
--output {output.salmon_out}) &> {log}"
diff --git a/images/dag_test_workflow.svg b/images/dag_test_workflow.svg
index 7427f6c36460bb53053c9a18d6b0ce9376dde1cd..3327b03a863b8443c752d6fe32fa07c21ca8bc79 100644
--- a/images/dag_test_workflow.svg
+++ b/images/dag_test_workflow.svg
@@ -1,366 +1,353 @@
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
"http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
-<!-- Generated by graphviz version 2.40.1 (20161225.0304)
+<!-- Generated by graphviz version 2.38.0 (20140413.2041)
-->
<!-- Title: snakemake_dag Pages: 1 -->
-<svg width="1833pt" height="414pt"
- viewBox="0.00 0.00 1832.50 414.00" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
+<svg width="1962pt" height="414pt"
+ viewBox="0.00 0.00 1962.00 414.00" 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(4 410)">
<title>snakemake_dag</title>
-<polygon fill="#ffffff" stroke="transparent" points="-4,4 -4,-410 1828.5,-410 1828.5,4 -4,4"/>
+<polygon fill="white" stroke="none" points="-4,4 -4,-410 1958,-410 1958,4 -4,4"/>
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-<g id="node1" class="node">
-<title>0</title>
-<path fill="none" stroke="#566bd8" stroke-width="2" d="M959.5,-36C959.5,-36 929.5,-36 929.5,-36 923.5,-36 917.5,-30 917.5,-24 917.5,-24 917.5,-12 917.5,-12 917.5,-6 923.5,0 929.5,0 929.5,0 959.5,0 959.5,0 965.5,0 971.5,-6 971.5,-12 971.5,-12 971.5,-24 971.5,-24 971.5,-30 965.5,-36 959.5,-36"/>
-<text text-anchor="middle" x="944.5" y="-15.5" font-family="sans" font-size="10.00" fill="#000000">finish</text>
+<g id="node1" class="node"><title>0</title>
+<path fill="none" stroke="#d88556" stroke-width="2" d="M1050,-36C1050,-36 1020,-36 1020,-36 1014,-36 1008,-30 1008,-24 1008,-24 1008,-12 1008,-12 1008,-6 1014,-0 1020,-0 1020,-0 1050,-0 1050,-0 1056,-0 1062,-6 1062,-12 1062,-12 1062,-24 1062,-24 1062,-30 1056,-36 1050,-36"/>
+<text text-anchor="middle" x="1035" y="-15.5" font-family="sans" font-size="10.00">finish</text>
</g>
<!-- 1 -->
-<g id="node2" class="node">
-<title>1</title>
-<path fill="none" stroke="#56c9d8" stroke-width="2" d="M313,-108C313,-108 12,-108 12,-108 6,-108 0,-102 0,-96 0,-96 0,-84 0,-84 0,-78 6,-72 12,-72 12,-72 313,-72 313,-72 319,-72 325,-78 325,-84 325,-84 325,-96 325,-96 325,-102 319,-108 313,-108"/>
-<text text-anchor="middle" x="162.5" y="-93" font-family="sans" font-size="10.00" fill="#000000">pe_fastqc</text>
-<text text-anchor="middle" x="162.5" y="-82" font-family="sans" font-size="10.00" fill="#000000">sample: synthetic_10_reads_paired_synthetic_10_reads_paired</text>
+<g id="node2" class="node"><title>1</title>
+<path fill="none" stroke="#569ad8" stroke-width="2" d="M280,-108C280,-108 12,-108 12,-108 6,-108 0,-102 0,-96 0,-96 0,-84 0,-84 0,-78 6,-72 12,-72 12,-72 280,-72 280,-72 286,-72 292,-78 292,-84 292,-84 292,-96 292,-96 292,-102 286,-108 280,-108"/>
+<text text-anchor="middle" x="146" y="-93" font-family="sans" font-size="10.00">pe_fastqc</text>
+<text text-anchor="middle" x="146" y="-82" font-family="sans" font-size="10.00">sample: synthetic_10_reads_paired_synthetic_10_reads_paired</text>
</g>
<!-- 1->0 -->
-<g id="edge1" class="edge">
-<title>1->0</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M325.4126,-72.7882C328.1284,-72.5218 330.8259,-72.2589 333.5,-72 550.8548,-50.9569 812.0397,-28.9772 907.3724,-21.0636"/>
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+<g id="edge1" class="edge"><title>1->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M292.017,-72.8323C295.037,-72.5474 298.034,-72.2696 301,-72 567.9,-47.736 890.22,-27.651 997.94,-21.1875"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="998.204,-24.6781 1007.98,-20.5875 997.786,-17.6906 998.204,-24.6781"/>
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-<g id="node3" class="node">
-<title>2</title>
-<path fill="none" stroke="#56d86b" stroke-width="2" d="M668,-108C668,-108 355,-108 355,-108 349,-108 343,-102 343,-96 343,-96 343,-84 343,-84 343,-78 349,-72 355,-72 355,-72 668,-72 668,-72 674,-72 680,-78 680,-84 680,-84 680,-96 680,-96 680,-102 674,-108 668,-108"/>
-<text text-anchor="middle" x="511.5" y="-93" font-family="sans" font-size="10.00" fill="#000000">fastqc</text>
-<text text-anchor="middle" x="511.5" y="-82" font-family="sans" font-size="10.00" fill="#000000">sample: synthetic_10_reads_mate_1_synthetic_10_reads_mate_1</text>
+<g id="node3" class="node"><title>2</title>
+<path fill="none" stroke="#56d89a" stroke-width="2" d="M602,-108C602,-108 322,-108 322,-108 316,-108 310,-102 310,-96 310,-96 310,-84 310,-84 310,-78 316,-72 322,-72 322,-72 602,-72 602,-72 608,-72 614,-78 614,-84 614,-84 614,-96 614,-96 614,-102 608,-108 602,-108"/>
+<text text-anchor="middle" x="462" y="-93" font-family="sans" font-size="10.00">fastqc</text>
+<text text-anchor="middle" x="462" y="-82" font-family="sans" font-size="10.00">sample: synthetic_10_reads_mate_1_synthetic_10_reads_mate_1</text>
</g>
<!-- 2->0 -->
-<g id="edge2" class="edge">
-<title>2->0</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M619.9262,-71.9707C713.8941,-56.3456 844.3945,-34.6457 907.4564,-24.1597"/>
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+<g id="edge2" class="edge"><title>2->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M601.439,-71.9656C732.107,-56.0027 918.769,-33.1992 997.595,-23.5696"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="998.483,-26.9872 1007.98,-22.3003 997.634,-20.0389 998.483,-26.9872"/>
</g>
<!-- 3 -->
-<g id="node4" class="node">
-<title>3</title>
-<path fill="none" stroke="#d89c56" stroke-width="2" d="M916.5,-180C916.5,-180 798.5,-180 798.5,-180 792.5,-180 786.5,-174 786.5,-168 786.5,-168 786.5,-156 786.5,-156 786.5,-150 792.5,-144 798.5,-144 798.5,-144 916.5,-144 916.5,-144 922.5,-144 928.5,-150 928.5,-156 928.5,-156 928.5,-168 928.5,-168 928.5,-174 922.5,-180 916.5,-180"/>
-<text text-anchor="middle" x="857.5" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">pe_quantification_salmon</text>
+<g id="node4" class="node"><title>3</title>
+<path fill="none" stroke="#56d882" stroke-width="2" d="M1039.5,-180C1039.5,-180 936.5,-180 936.5,-180 930.5,-180 924.5,-174 924.5,-168 924.5,-168 924.5,-156 924.5,-156 924.5,-150 930.5,-144 936.5,-144 936.5,-144 1039.5,-144 1039.5,-144 1045.5,-144 1051.5,-150 1051.5,-156 1051.5,-156 1051.5,-168 1051.5,-168 1051.5,-174 1045.5,-180 1039.5,-180"/>
+<text text-anchor="middle" x="988" y="-159.5" font-family="sans" font-size="10.00">pe_quantification_salmon</text>
</g>
<!-- 3->0 -->
-<g id="edge3" class="edge">
-<title>3->0</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M806.4145,-143.9348C790.4334,-135.5922 774.6105,-123.9115 765.5,-108 757.5498,-94.115 755.959,-84.844 765.5,-72 782.451,-49.1807 859.9959,-32.3091 907.2865,-23.9282"/>
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+<g id="edge3" class="edge"><title>3->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M924.308,-161.332C821.372,-159.74 636.097,-146.808 700,-72 737.975,-27.5452 918.617,-20.167 997.736,-19.0937"/>
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-<g id="node10" class="node">
-<title>9</title>
-<path fill="none" stroke="#88d856" stroke-width="2" d="M1112.5,-108C1112.5,-108 960.5,-108 960.5,-108 954.5,-108 948.5,-102 948.5,-96 948.5,-96 948.5,-84 948.5,-84 948.5,-78 954.5,-72 960.5,-72 960.5,-72 1112.5,-72 1112.5,-72 1118.5,-72 1124.5,-78 1124.5,-84 1124.5,-84 1124.5,-96 1124.5,-96 1124.5,-102 1118.5,-108 1112.5,-108"/>
-<text text-anchor="middle" x="1036.5" y="-87.5" font-family="sans" font-size="10.00" fill="#000000">salmon_quantmerge_genes_tpm</text>
+<g id="node10" class="node"><title>9</title>
+<path fill="none" stroke="#b6d856" stroke-width="2" d="M1342,-108C1342,-108 1230,-108 1230,-108 1224,-108 1218,-102 1218,-96 1218,-96 1218,-84 1218,-84 1218,-78 1224,-72 1230,-72 1230,-72 1342,-72 1342,-72 1348,-72 1354,-78 1354,-84 1354,-84 1354,-96 1354,-96 1354,-102 1348,-108 1342,-108"/>
+<text text-anchor="middle" x="1286" y="-93" font-family="sans" font-size="10.00">salmon_quantmerge_genes</text>
+<text text-anchor="middle" x="1286" y="-82" font-family="sans" font-size="10.00">salmon_merge_on: tpm</text>
</g>
<!-- 3->9 -->
-<g id="edge23" class="edge">
-<title>3->9</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M902.6693,-143.8314C926.8223,-134.1162 956.7378,-122.0831 982.1556,-111.8592"/>
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+<g id="edge25" class="edge"><title>3->9</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1051.56,-146.069C1097.3,-135.326 1159.26,-120.772 1207.99,-109.324"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1208.93,-112.698 1217.87,-107.004 1207.33,-105.884 1208.93,-112.698"/>
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<!-- 10 -->
-<g id="node11" class="node">
-<title>10</title>
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-<text text-anchor="middle" x="852.5" y="-87.5" font-family="sans" font-size="10.00" fill="#000000">salmon_quantmerge_tr_tpm</text>
+<g id="node11" class="node"><title>10</title>
+<path fill="none" stroke="#b6d856" stroke-width="2" d="M841.5,-108C841.5,-108 720.5,-108 720.5,-108 714.5,-108 708.5,-102 708.5,-96 708.5,-96 708.5,-84 708.5,-84 708.5,-78 714.5,-72 720.5,-72 720.5,-72 841.5,-72 841.5,-72 847.5,-72 853.5,-78 853.5,-84 853.5,-84 853.5,-96 853.5,-96 853.5,-102 847.5,-108 841.5,-108"/>
+<text text-anchor="middle" x="781" y="-93" font-family="sans" font-size="10.00">salmon_quantmerge_genes</text>
+<text text-anchor="middle" x="781" y="-82" font-family="sans" font-size="10.00">salmon_merge_on: numreads</text>
</g>
<!-- 3->10 -->
-<g id="edge25" class="edge">
-<title>3->10</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M856.2383,-143.8314C855.7035,-136.131 855.0677,-126.9743 854.4734,-118.4166"/>
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+<g id="edge27" class="edge"><title>3->10</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M937.627,-143.966C908.579,-134.142 871.87,-121.729 841.294,-111.389"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="842.193,-107.999 831.599,-108.111 839.951,-114.63 842.193,-107.999"/>
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+<!-- 11 -->
+<g id="node12" class="node"><title>11</title>
+<path fill="none" stroke="#d85656" stroke-width="2" d="M1014.5,-108C1014.5,-108 883.5,-108 883.5,-108 877.5,-108 871.5,-102 871.5,-96 871.5,-96 871.5,-84 871.5,-84 871.5,-78 877.5,-72 883.5,-72 883.5,-72 1014.5,-72 1014.5,-72 1020.5,-72 1026.5,-78 1026.5,-84 1026.5,-84 1026.5,-96 1026.5,-96 1026.5,-102 1020.5,-108 1014.5,-108"/>
+<text text-anchor="middle" x="949" y="-93" font-family="sans" font-size="10.00">salmon_quantmerge_transcripts</text>
+<text text-anchor="middle" x="949" y="-82" font-family="sans" font-size="10.00">salmon_merge_on: tpm</text>
+</g>
+<!-- 3->11 -->
+<g id="edge29" class="edge"><title>3->11</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M978.36,-143.697C973.873,-135.644 968.441,-125.894 963.476,-116.982"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="966.454,-115.137 958.53,-108.104 960.339,-118.544 966.454,-115.137"/>
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+<!-- 12 -->
+<g id="node13" class="node"><title>12</title>
+<path fill="none" stroke="#d85656" stroke-width="2" d="M1187.5,-108C1187.5,-108 1056.5,-108 1056.5,-108 1050.5,-108 1044.5,-102 1044.5,-96 1044.5,-96 1044.5,-84 1044.5,-84 1044.5,-78 1050.5,-72 1056.5,-72 1056.5,-72 1187.5,-72 1187.5,-72 1193.5,-72 1199.5,-78 1199.5,-84 1199.5,-84 1199.5,-96 1199.5,-96 1199.5,-102 1193.5,-108 1187.5,-108"/>
+<text text-anchor="middle" x="1122" y="-93" font-family="sans" font-size="10.00">salmon_quantmerge_transcripts</text>
+<text text-anchor="middle" x="1122" y="-82" font-family="sans" font-size="10.00">salmon_merge_on: numreads</text>
+</g>
+<!-- 3->12 -->
+<g id="edge31" class="edge"><title>3->12</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1020.78,-143.876C1038.63,-134.554 1060.9,-122.919 1080,-112.939"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1081.85,-115.922 1089.09,-108.19 1078.61,-109.718 1081.85,-115.922"/>
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-<text text-anchor="middle" x="1036.5" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">quantification_salmon</text>
+<g id="node5" class="node"><title>4</title>
+<path fill="none" stroke="#88d856" stroke-width="2" d="M1168.5,-180C1168.5,-180 1081.5,-180 1081.5,-180 1075.5,-180 1069.5,-174 1069.5,-168 1069.5,-168 1069.5,-156 1069.5,-156 1069.5,-150 1075.5,-144 1081.5,-144 1081.5,-144 1168.5,-144 1168.5,-144 1174.5,-144 1180.5,-150 1180.5,-156 1180.5,-156 1180.5,-168 1180.5,-168 1180.5,-174 1174.5,-180 1168.5,-180"/>
+<text text-anchor="middle" x="1125" y="-159.5" font-family="sans" font-size="10.00">quantification_salmon</text>
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<!-- 4->0 -->
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-<title>4->0</title>
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+<g id="edge4" class="edge"><title>4->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1180.58,-158.69C1266.45,-153.149 1416.19,-134.476 1363,-72 1326.04,-28.5839 1150.54,-20.6164 1072.53,-19.2392"/>
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-<title>4->9</title>
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-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1040.0001,-118.4132 1036.5,-108.4133 1033.0001,-118.4133 1040.0001,-118.4132"/>
+<g id="edge26" class="edge"><title>4->9</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1164.39,-143.876C1186.39,-134.307 1214.01,-122.3 1237.36,-112.148"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1238.97,-115.265 1246.74,-108.068 1236.18,-108.846 1238.97,-115.265"/>
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-<title>4->10</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M990.069,-143.8314C965.132,-134.0734 934.2191,-121.977 908.0174,-111.7242"/>
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+<g id="edge28" class="edge"><title>4->10</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1069.22,-145.902C1066.44,-145.24 1063.69,-144.601 1061,-144 976.777,-125.189 952.487,-125.064 863.814,-108.122"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="864.341,-104.659 853.859,-106.202 863.015,-111.533 864.341,-104.659"/>
+</g>
+<!-- 4->11 -->
+<g id="edge30" class="edge"><title>4->11</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1081.95,-143.876C1057.67,-134.222 1027.16,-122.087 1001.49,-111.878"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1002.5,-108.512 991.915,-108.068 999.913,-115.016 1002.5,-108.512"/>
+</g>
+<!-- 4->12 -->
+<g id="edge32" class="edge"><title>4->12</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1124.26,-143.697C1123.93,-135.983 1123.53,-126.712 1123.16,-118.112"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1126.66,-117.945 1122.73,-108.104 1119.66,-118.245 1126.66,-117.945"/>
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-<title>5</title>
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-<text text-anchor="middle" x="708.5" y="-234" font-family="sans" font-size="10.00" fill="#000000">pe_genome_quantification_kallisto</text>
+<g id="node6" class="node"><title>5</title>
+<path fill="none" stroke="#d8cb56" stroke-width="2" d="M925,-254.5C925,-254.5 783,-254.5 783,-254.5 777,-254.5 771,-248.5 771,-242.5 771,-242.5 771,-230.5 771,-230.5 771,-224.5 777,-218.5 783,-218.5 783,-218.5 925,-218.5 925,-218.5 931,-218.5 937,-224.5 937,-230.5 937,-230.5 937,-242.5 937,-242.5 937,-248.5 931,-254.5 925,-254.5"/>
+<text text-anchor="middle" x="854" y="-234" font-family="sans" font-size="10.00">pe_genome_quantification_kallisto</text>
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<!-- 5->0 -->
-<g id="edge5" class="edge">
-<title>5->0</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M708.2829,-218.3577C708.9002,-184.6935 715.1754,-112.3246 755.5,-72 776.8453,-50.6547 858.9524,-33.0222 907.6447,-24.165"/>
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+<g id="edge5" class="edge"><title>5->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M810.971,-218.422C745.148,-189.906 632.065,-129.992 682,-72 722.482,-24.9863 915.576,-19.0926 997.796,-18.7562"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="997.952,-22.2561 1007.95,-18.741 997.941,-15.2561 997.952,-22.2561"/>
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-<g id="node7" class="node">
-<title>6</title>
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-<text text-anchor="middle" x="1166.5" y="-234" font-family="sans" font-size="10.00" fill="#000000">genome_quantification_kallisto</text>
+<g id="node7" class="node"><title>6</title>
+<path fill="none" stroke="#d89c56" stroke-width="2" d="M1383,-254.5C1383,-254.5 1257,-254.5 1257,-254.5 1251,-254.5 1245,-248.5 1245,-242.5 1245,-242.5 1245,-230.5 1245,-230.5 1245,-224.5 1251,-218.5 1257,-218.5 1257,-218.5 1383,-218.5 1383,-218.5 1389,-218.5 1395,-224.5 1395,-230.5 1395,-230.5 1395,-242.5 1395,-242.5 1395,-248.5 1389,-254.5 1383,-254.5"/>
+<text text-anchor="middle" x="1320" y="-234" font-family="sans" font-size="10.00">genome_quantification_kallisto</text>
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<!-- 6->0 -->
-<g id="edge6" class="edge">
-<title>6->0</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1170.7516,-218.3996C1177.4112,-185.1257 1186.1376,-113.8248 1150.5,-72 1128.8067,-46.5404 1034.8716,-30.0943 981.6507,-22.6387"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="981.9637,-19.1491 971.5828,-21.2674 981.019,-26.085 981.9637,-19.1491"/>
+<g id="edge6" class="edge"><title>6->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1336.81,-218.244C1366.11,-186.077 1419.98,-116.217 1382,-72 1342.39,-25.8749 1153.71,-19.4546 1072.41,-18.8661"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1072.15,-15.365 1062.13,-18.8191 1072.11,-22.3649 1072.15,-15.365"/>
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<!-- 7 -->
-<g id="node8" class="node">
-<title>7</title>
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-<text text-anchor="middle" x="1325.5" y="-93" font-family="sans" font-size="10.00" fill="#000000">calculate_TIN_scores</text>
-<text text-anchor="middle" x="1325.5" y="-82" font-family="sans" font-size="10.00" fill="#000000">seqmode: paired_end</text>
+<g id="node8" class="node"><title>7</title>
+<path fill="none" stroke="#56d8b1" stroke-width="2" d="M1548,-108C1548,-108 1460,-108 1460,-108 1454,-108 1448,-102 1448,-96 1448,-96 1448,-84 1448,-84 1448,-78 1454,-72 1460,-72 1460,-72 1548,-72 1548,-72 1554,-72 1560,-78 1560,-84 1560,-84 1560,-96 1560,-96 1560,-102 1554,-108 1548,-108"/>
+<text text-anchor="middle" x="1504" y="-93" font-family="sans" font-size="10.00">calculate_TIN_scores</text>
+<text text-anchor="middle" x="1504" y="-82" font-family="sans" font-size="10.00">seqmode: paired_end</text>
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<!-- 7->0 -->
-<g id="edge7" class="edge">
-<title>7->0</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1264.2858,-78.432C1184.418,-63.3388 1047.1445,-37.3974 981.5291,-24.9976"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="982.1093,-21.5454 971.6332,-23.1275 980.8094,-28.4237 982.1093,-21.5454"/>
+<g id="edge7" class="edge"><title>7->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1447.95,-74.8329C1443.24,-73.8126 1438.55,-72.8519 1434,-72 1302.03,-47.2826 1143.4,-29.8127 1072.47,-22.6347"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1072.55,-19.1257 1062.25,-21.611 1071.85,-26.0908 1072.55,-19.1257"/>
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<!-- 8 -->
-<g id="node9" class="node">
-<title>8</title>
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-<text text-anchor="middle" x="1530.5" y="-93" font-family="sans" font-size="10.00" fill="#000000">calculate_TIN_scores</text>
-<text text-anchor="middle" x="1530.5" y="-82" font-family="sans" font-size="10.00" fill="#000000">seqmode: single_end</text>
+<g id="node9" class="node"><title>8</title>
+<path fill="none" stroke="#56d8b1" stroke-width="2" d="M1733,-108C1733,-108 1645,-108 1645,-108 1639,-108 1633,-102 1633,-96 1633,-96 1633,-84 1633,-84 1633,-78 1639,-72 1645,-72 1645,-72 1733,-72 1733,-72 1739,-72 1745,-78 1745,-84 1745,-84 1745,-96 1745,-96 1745,-102 1739,-108 1733,-108"/>
+<text text-anchor="middle" x="1689" y="-93" font-family="sans" font-size="10.00">calculate_TIN_scores</text>
+<text text-anchor="middle" x="1689" y="-82" font-family="sans" font-size="10.00">seqmode: single_end</text>
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<!-- 8->0 -->
-<g id="edge8" class="edge">
-<title>8->0</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1470.3756,-81.8081C1447.009,-78.6704 1420.0135,-75.1016 1395.5,-72 1242.1378,-52.5954 1059.1989,-31.2452 981.9049,-22.3071"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="982.0492,-18.8006 971.7136,-21.1298 981.2459,-25.7543 982.0492,-18.8006"/>
+<g id="edge8" class="edge"><title>8->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1632.9,-80.5575C1612.77,-77.6595 1589.89,-74.5153 1569,-72 1382.98,-49.6022 1159.67,-29.6862 1072.46,-22.1756"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1072.54,-18.6691 1062.27,-21.3013 1071.94,-25.6435 1072.54,-18.6691"/>
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<!-- 9->0 -->
-<g id="edge9" class="edge">
-<title>9->0</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1013.2845,-71.8314C1001.953,-62.9632 988.1536,-52.1637 975.8973,-42.5718"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="977.7402,-39.5697 967.7081,-36.1628 973.426,-45.0822 977.7402,-39.5697"/>
+<g id="edge9" class="edge"><title>9->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1224.92,-71.9656C1177.03,-58.6095 1111.97,-40.4647 1071.77,-29.2542"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1072.68,-25.8757 1062.11,-26.5606 1070.8,-32.6184 1072.68,-25.8757"/>
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<!-- 10->0 -->
-<g id="edge10" class="edge">
-<title>10->0</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M875.7155,-71.8314C887.047,-62.9632 900.8464,-52.1637 913.1027,-42.5718"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="915.574,-45.0822 921.2919,-36.1628 911.2598,-39.5697 915.574,-45.0822"/>
+<g id="edge10" class="edge"><title>10->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M842.811,-71.9656C891.409,-58.5722 957.482,-40.3633 998.132,-29.1604"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="999.183,-32.5015 1007.89,-26.4704 997.323,-25.7531 999.183,-32.5015"/>
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-<g id="node12" class="node">
-<title>11</title>
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-<text text-anchor="middle" x="862.5" y="-311" font-family="sans" font-size="10.00" fill="#000000">pe_remove_polya_cutadapt</text>
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-<!-- 11->3 -->
-<g id="edge11" class="edge">
-<title>11->3</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M861.8969,-295.2256C861.0372,-269.1777 859.4516,-221.1339 858.4379,-190.4171"/>
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-<!-- 11->5 -->
-<g id="edge15" class="edge">
-<title>11->5</title>
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+<!-- 11->0 -->
+<g id="edge11" class="edge"><title>11->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M970.258,-71.6966C981.089,-62.8807 994.418,-52.0321 1006.16,-42.4742"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1008.44,-45.1316 1013.99,-36.1043 1004.02,-39.7026 1008.44,-45.1316"/>
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-<g id="node21" class="node">
-<title>20</title>
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-<text text-anchor="middle" x="1332.5" y="-234" font-family="sans" font-size="10.00" fill="#000000">pe_map_genome_star</text>
+<!-- 12->0 -->
+<g id="edge12" class="edge"><title>12->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1100.49,-71.6966C1089.54,-62.8807 1076.05,-52.0321 1064.18,-42.4742"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1066.24,-39.6462 1056.26,-36.1043 1061.86,-45.1001 1066.24,-39.6462"/>
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-<g id="edge32" class="edge">
-<title>11->20</title>
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+<!-- 13 -->
+<g id="node14" class="node"><title>13</title>
+<path fill="none" stroke="#70d856" stroke-width="2" d="M1059,-331.5C1059,-331.5 947,-331.5 947,-331.5 941,-331.5 935,-325.5 935,-319.5 935,-319.5 935,-307.5 935,-307.5 935,-301.5 941,-295.5 947,-295.5 947,-295.5 1059,-295.5 1059,-295.5 1065,-295.5 1071,-301.5 1071,-307.5 1071,-307.5 1071,-319.5 1071,-319.5 1071,-325.5 1065,-331.5 1059,-331.5"/>
+<text text-anchor="middle" x="1003" y="-311" font-family="sans" font-size="10.00">pe_remove_polya_cutadapt</text>
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-<g id="node13" class="node">
-<title>12</title>
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-<g id="edge12" class="edge">
-<title>12->3</title>
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-<g id="edge14" class="edge">
-<title>12->4</title>
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+<!-- 13->3 -->
+<g id="edge13" class="edge"><title>13->3</title>
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-<g id="node14" class="node">
-<title>13</title>
-<path fill="none" stroke="#ced856" stroke-width="2" d="M1226.5,-331.5C1226.5,-331.5 1116.5,-331.5 1116.5,-331.5 1110.5,-331.5 1104.5,-325.5 1104.5,-319.5 1104.5,-319.5 1104.5,-307.5 1104.5,-307.5 1104.5,-301.5 1110.5,-295.5 1116.5,-295.5 1116.5,-295.5 1226.5,-295.5 1226.5,-295.5 1232.5,-295.5 1238.5,-301.5 1238.5,-307.5 1238.5,-307.5 1238.5,-319.5 1238.5,-319.5 1238.5,-325.5 1232.5,-331.5 1226.5,-331.5"/>
-<text text-anchor="middle" x="1171.5" y="-311" font-family="sans" font-size="10.00" fill="#000000">remove_polya_cutadapt</text>
-</g>
-<!-- 13->4 -->
-<g id="edge13" class="edge">
-<title>13->4</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1125.4281,-295.4773C1106.9108,-286.3067 1086.6434,-273.5479 1072.5,-257 1056.2035,-237.9328 1046.9034,-210.7334 1041.8556,-190.3208"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1045.2175,-189.3201 1039.589,-180.344 1038.3914,-190.8709 1045.2175,-189.3201"/>
-</g>
-<!-- 13->6 -->
-<g id="edge17" class="edge">
-<title>13->6</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1170.3151,-295.2521C1169.7235,-286.1422 1168.9946,-274.9174 1168.333,-264.7282"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1171.8171,-264.3691 1167.6764,-254.6169 1164.8319,-264.8228 1171.8171,-264.3691"/>
+<!-- 13->5 -->
+<g id="edge17" class="edge"><title>13->5</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M969.19,-295.481C947.833,-284.731 920.042,-270.742 897.107,-259.198"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="898.44,-255.951 887.934,-254.581 895.293,-262.203 898.44,-255.951"/>
</g>
-<!-- 21 -->
-<g id="node22" class="node">
-<title>21</title>
-<path fill="none" stroke="#56d8b1" stroke-width="2" d="M1508,-254.5C1508,-254.5 1425,-254.5 1425,-254.5 1419,-254.5 1413,-248.5 1413,-242.5 1413,-242.5 1413,-230.5 1413,-230.5 1413,-224.5 1419,-218.5 1425,-218.5 1425,-218.5 1508,-218.5 1508,-218.5 1514,-218.5 1520,-224.5 1520,-230.5 1520,-230.5 1520,-242.5 1520,-242.5 1520,-248.5 1514,-254.5 1508,-254.5"/>
-<text text-anchor="middle" x="1466.5" y="-234" font-family="sans" font-size="10.00" fill="#000000">map_genome_star</text>
+<!-- 22 -->
+<g id="node23" class="node"><title>22</title>
+<path fill="none" stroke="#56c9d8" stroke-width="2" d="M1540.5,-254.5C1540.5,-254.5 1451.5,-254.5 1451.5,-254.5 1445.5,-254.5 1439.5,-248.5 1439.5,-242.5 1439.5,-242.5 1439.5,-230.5 1439.5,-230.5 1439.5,-224.5 1445.5,-218.5 1451.5,-218.5 1451.5,-218.5 1540.5,-218.5 1540.5,-218.5 1546.5,-218.5 1552.5,-224.5 1552.5,-230.5 1552.5,-230.5 1552.5,-242.5 1552.5,-242.5 1552.5,-248.5 1546.5,-254.5 1540.5,-254.5"/>
+<text text-anchor="middle" x="1496" y="-234" font-family="sans" font-size="10.00">pe_map_genome_star</text>
</g>
-<!-- 13->21 -->
-<g id="edge34" class="edge">
-<title>13->21</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1238.6681,-298.7385C1283.048,-288.6322 1342.6532,-274.3904 1403.107,-257.3127"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1404.1559,-260.6532 1412.8145,-254.5476 1402.2382,-253.921 1404.1559,-260.6532"/>
+<!-- 13->22 -->
+<g id="edge38" class="edge"><title>13->22</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1071.35,-304.548C1151.34,-294.891 1287.69,-277.348 1404,-257 1412.21,-255.564 1420.8,-253.926 1429.29,-252.223"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1430.1,-255.631 1439.19,-250.202 1428.7,-248.773 1430.1,-255.631"/>
</g>
<!-- 14 -->
-<g id="node15" class="node">
-<title>14</title>
-<path fill="none" stroke="#59d856" stroke-width="2" d="M756,-331.5C756,-331.5 641,-331.5 641,-331.5 635,-331.5 629,-325.5 629,-319.5 629,-319.5 629,-307.5 629,-307.5 629,-301.5 635,-295.5 641,-295.5 641,-295.5 756,-295.5 756,-295.5 762,-295.5 768,-301.5 768,-307.5 768,-307.5 768,-319.5 768,-319.5 768,-325.5 762,-331.5 756,-331.5"/>
-<text text-anchor="middle" x="698.5" y="-316.5" font-family="sans" font-size="10.00" fill="#000000">create_index_kallisto</text>
-<text text-anchor="middle" x="698.5" y="-305.5" font-family="sans" font-size="10.00" fill="#000000">organism: homo_sapiens</text>
-</g>
-<!-- 14->5 -->
-<g id="edge16" class="edge">
-<title>14->5</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M700.8699,-295.2521C702.053,-286.1422 703.5107,-274.9174 704.834,-264.7282"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="708.33,-264.9845 706.1472,-254.6169 701.3883,-264.0829 708.33,-264.9845"/>
-</g>
-<!-- 14->6 -->
-<g id="edge18" class="edge">
-<title>14->6</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M766.0419,-295.4294C769.9084,-294.5646 773.7479,-293.7471 777.5,-293 890.6171,-270.478 920.4001,-273.8505 1034.5,-257 1046.448,-255.2355 1058.9976,-253.3405 1071.4094,-251.4412"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1071.9669,-254.8967 1081.3198,-249.9194 1070.9044,-247.9778 1071.9669,-254.8967"/>
+<g id="node15" class="node"><title>14</title>
+<path fill="none" stroke="#ced856" stroke-width="2" d="M1153.5,-257C1153.5,-257 1052.5,-257 1052.5,-257 1046.5,-257 1040.5,-251 1040.5,-245 1040.5,-245 1040.5,-228 1040.5,-228 1040.5,-222 1046.5,-216 1052.5,-216 1052.5,-216 1153.5,-216 1153.5,-216 1159.5,-216 1165.5,-222 1165.5,-228 1165.5,-228 1165.5,-245 1165.5,-245 1165.5,-251 1159.5,-257 1153.5,-257"/>
+<text text-anchor="middle" x="1103" y="-245" font-family="sans" font-size="10.00">create_index_salmon</text>
+<text text-anchor="middle" x="1103" y="-234" font-family="sans" font-size="10.00">kmer: 31</text>
+<text text-anchor="middle" x="1103" y="-223" font-family="sans" font-size="10.00">organism: homo_sapiens</text>
+</g>
+<!-- 14->3 -->
+<g id="edge14" class="edge"><title>14->3</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1071.88,-215.88C1057.09,-206.556 1039.32,-195.356 1023.96,-185.669"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1025.56,-182.539 1015.23,-180.166 1021.82,-188.46 1025.56,-182.539"/>
+</g>
+<!-- 14->4 -->
+<g id="edge16" class="edge"><title>14->4</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1109.01,-215.689C1111.4,-207.82 1114.19,-198.64 1116.76,-190.168"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1120.19,-190.905 1119.74,-180.319 1113.49,-188.872 1120.19,-190.905"/>
</g>
<!-- 15 -->
-<g id="node16" class="node">
-<title>15</title>
-<path fill="none" stroke="#d86e56" stroke-width="2" d="M1420,-180C1420,-180 1231,-180 1231,-180 1225,-180 1219,-174 1219,-168 1219,-168 1219,-156 1219,-156 1219,-150 1225,-144 1231,-144 1231,-144 1420,-144 1420,-144 1426,-144 1432,-150 1432,-156 1432,-156 1432,-168 1432,-168 1432,-174 1426,-180 1420,-180"/>
-<text text-anchor="middle" x="1325.5" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">pe_index_genomic_alignment_samtools</text>
-</g>
-<!-- 15->7 -->
-<g id="edge19" class="edge">
-<title>15->7</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1325.5,-143.8314C1325.5,-136.131 1325.5,-126.9743 1325.5,-118.4166"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1329.0001,-118.4132 1325.5,-108.4133 1322.0001,-118.4133 1329.0001,-118.4132"/>
+<g id="node16" class="node"><title>15</title>
+<path fill="none" stroke="#59d856" stroke-width="2" d="M1368,-331.5C1368,-331.5 1272,-331.5 1272,-331.5 1266,-331.5 1260,-325.5 1260,-319.5 1260,-319.5 1260,-307.5 1260,-307.5 1260,-301.5 1266,-295.5 1272,-295.5 1272,-295.5 1368,-295.5 1368,-295.5 1374,-295.5 1380,-301.5 1380,-307.5 1380,-307.5 1380,-319.5 1380,-319.5 1380,-325.5 1374,-331.5 1368,-331.5"/>
+<text text-anchor="middle" x="1320" y="-311" font-family="sans" font-size="10.00">remove_polya_cutadapt</text>
+</g>
+<!-- 15->4 -->
+<g id="edge15" class="edge"><title>15->4</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1292.2,-295.305C1275.56,-284.728 1254.18,-270.629 1236,-257 1205.95,-234.472 1173.35,-206.391 1151.3,-186.814"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1153.48,-184.061 1143.68,-180.012 1148.81,-189.283 1153.48,-184.061"/>
+</g>
+<!-- 15->6 -->
+<g id="edge19" class="edge"><title>15->6</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1320,-295.481C1320,-286.436 1320,-275.097 1320,-264.851"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1323.5,-264.711 1320,-254.711 1316.5,-264.711 1323.5,-264.711"/>
+</g>
+<!-- 23 -->
+<g id="node24" class="node"><title>23</title>
+<path fill="none" stroke="#d86e56" stroke-width="2" d="M1655.5,-254.5C1655.5,-254.5 1582.5,-254.5 1582.5,-254.5 1576.5,-254.5 1570.5,-248.5 1570.5,-242.5 1570.5,-242.5 1570.5,-230.5 1570.5,-230.5 1570.5,-224.5 1576.5,-218.5 1582.5,-218.5 1582.5,-218.5 1655.5,-218.5 1655.5,-218.5 1661.5,-218.5 1667.5,-224.5 1667.5,-230.5 1667.5,-230.5 1667.5,-242.5 1667.5,-242.5 1667.5,-248.5 1661.5,-254.5 1655.5,-254.5"/>
+<text text-anchor="middle" x="1619" y="-234" font-family="sans" font-size="10.00">map_genome_star</text>
+</g>
+<!-- 15->23 -->
+<g id="edge40" class="edge"><title>15->23</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1380.11,-300.533C1427.04,-290.777 1494.01,-275.949 1560.49,-257.315"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1561.62,-260.631 1570.29,-254.538 1559.71,-253.896 1561.62,-260.631"/>
</g>
<!-- 16 -->
-<g id="node17" class="node">
-<title>16</title>
-<path fill="none" stroke="#569ad8" stroke-width="2" d="M1598.5,-180C1598.5,-180 1462.5,-180 1462.5,-180 1456.5,-180 1450.5,-174 1450.5,-168 1450.5,-168 1450.5,-156 1450.5,-156 1450.5,-150 1456.5,-144 1462.5,-144 1462.5,-144 1598.5,-144 1598.5,-144 1604.5,-144 1610.5,-150 1610.5,-156 1610.5,-156 1610.5,-168 1610.5,-168 1610.5,-174 1604.5,-180 1598.5,-180"/>
-<text text-anchor="middle" x="1530.5" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">extract_transcripts_as_bed12</text>
-</g>
-<!-- 16->7 -->
-<g id="edge20" class="edge">
-<title>16->7</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1479.0345,-143.9243C1451.0098,-134.0815 1416.1516,-121.8386 1386.736,-111.5073"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1387.5816,-108.0947 1376.9867,-108.0831 1385.2619,-114.6992 1387.5816,-108.0947"/>
-</g>
-<!-- 16->8 -->
-<g id="edge22" class="edge">
-<title>16->8</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1530.5,-143.8314C1530.5,-136.131 1530.5,-126.9743 1530.5,-118.4166"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1534.0001,-118.4132 1530.5,-108.4133 1527.0001,-118.4133 1534.0001,-118.4132"/>
+<g id="node17" class="node"><title>16</title>
+<path fill="none" stroke="#d8b456" stroke-width="2" d="M904.5,-331.5C904.5,-331.5 803.5,-331.5 803.5,-331.5 797.5,-331.5 791.5,-325.5 791.5,-319.5 791.5,-319.5 791.5,-307.5 791.5,-307.5 791.5,-301.5 797.5,-295.5 803.5,-295.5 803.5,-295.5 904.5,-295.5 904.5,-295.5 910.5,-295.5 916.5,-301.5 916.5,-307.5 916.5,-307.5 916.5,-319.5 916.5,-319.5 916.5,-325.5 910.5,-331.5 904.5,-331.5"/>
+<text text-anchor="middle" x="854" y="-316.5" font-family="sans" font-size="10.00">create_index_kallisto</text>
+<text text-anchor="middle" x="854" y="-305.5" font-family="sans" font-size="10.00">organism: homo_sapiens</text>
+</g>
+<!-- 16->5 -->
+<g id="edge18" class="edge"><title>16->5</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M854,-295.481C854,-286.436 854,-275.097 854,-264.851"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="857.5,-264.711 854,-254.711 850.5,-264.711 857.5,-264.711"/>
+</g>
+<!-- 16->6 -->
+<g id="edge20" class="edge"><title>16->6</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M914.759,-295.473C918.551,-294.588 922.321,-293.754 926,-293 955.541,-286.944 1128.09,-263.327 1234.82,-248.924"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1235.49,-252.365 1244.93,-247.56 1234.56,-245.428 1235.49,-252.365"/>
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<!-- 17 -->
-<g id="node18" class="node">
-<title>17</title>
-<path fill="none" stroke="#56d8c9" stroke-width="2" d="M1812.5,-180C1812.5,-180 1640.5,-180 1640.5,-180 1634.5,-180 1628.5,-174 1628.5,-168 1628.5,-168 1628.5,-156 1628.5,-156 1628.5,-150 1634.5,-144 1640.5,-144 1640.5,-144 1812.5,-144 1812.5,-144 1818.5,-144 1824.5,-150 1824.5,-156 1824.5,-156 1824.5,-168 1824.5,-168 1824.5,-174 1818.5,-180 1812.5,-180"/>
-<text text-anchor="middle" x="1726.5" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">index_genomic_alignment_samtools</text>
+<g id="node18" class="node"><title>17</title>
+<path fill="none" stroke="#56d86b" stroke-width="2" d="M1586,-180C1586,-180 1420,-180 1420,-180 1414,-180 1408,-174 1408,-168 1408,-168 1408,-156 1408,-156 1408,-150 1414,-144 1420,-144 1420,-144 1586,-144 1586,-144 1592,-144 1598,-150 1598,-156 1598,-156 1598,-168 1598,-168 1598,-174 1592,-180 1586,-180"/>
+<text text-anchor="middle" x="1503" y="-159.5" font-family="sans" font-size="10.00">pe_index_genomic_alignment_samtools</text>
</g>
-<!-- 17->8 -->
-<g id="edge21" class="edge">
-<title>17->8</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1677.2939,-143.9243C1650.6161,-134.1243 1617.4614,-121.945 1589.4148,-111.6422"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1590.3199,-108.246 1579.7263,-108.0831 1587.9062,-114.8167 1590.3199,-108.246"/>
+<!-- 17->7 -->
+<g id="edge21" class="edge"><title>17->7</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1503.25,-143.697C1503.36,-135.983 1503.49,-126.712 1503.61,-118.112"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1507.11,-118.153 1503.76,-108.104 1500.11,-118.053 1507.11,-118.153"/>
</g>
<!-- 18 -->
-<g id="node19" class="node">
-<title>18</title>
-<path fill="none" stroke="#d8b456" stroke-width="2" d="M993,-406C993,-406 692,-406 692,-406 686,-406 680,-400 680,-394 680,-394 680,-382 680,-382 680,-376 686,-370 692,-370 692,-370 993,-370 993,-370 999,-370 1005,-376 1005,-382 1005,-382 1005,-394 1005,-394 1005,-400 999,-406 993,-406"/>
-<text text-anchor="middle" x="842.5" y="-391" font-family="sans" font-size="10.00" fill="#000000">pe_remove_adapters_cutadapt</text>
-<text text-anchor="middle" x="842.5" y="-380" font-family="sans" font-size="10.00" fill="#000000">sample: synthetic_10_reads_paired_synthetic_10_reads_paired</text>
-</g>
-<!-- 18->11 -->
-<g id="edge27" class="edge">
-<title>18->11</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M847.3414,-369.9656C849.6337,-361.427 852.424,-351.0333 854.9827,-341.502"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="858.4213,-342.192 857.6338,-331.6265 851.6607,-340.3771 858.4213,-342.192"/>
+<g id="node19" class="node"><title>18</title>
+<path fill="none" stroke="#56b1d8" stroke-width="2" d="M1749.5,-180C1749.5,-180 1628.5,-180 1628.5,-180 1622.5,-180 1616.5,-174 1616.5,-168 1616.5,-168 1616.5,-156 1616.5,-156 1616.5,-150 1622.5,-144 1628.5,-144 1628.5,-144 1749.5,-144 1749.5,-144 1755.5,-144 1761.5,-150 1761.5,-156 1761.5,-156 1761.5,-168 1761.5,-168 1761.5,-174 1755.5,-180 1749.5,-180"/>
+<text text-anchor="middle" x="1689" y="-159.5" font-family="sans" font-size="10.00">extract_transcripts_as_bed12</text>
+</g>
+<!-- 18->7 -->
+<g id="edge22" class="edge"><title>18->7</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1643.74,-143.876C1618,-134.137 1585.59,-121.872 1558.46,-111.608"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1559.7,-108.334 1549.11,-108.068 1557.22,-114.881 1559.7,-108.334"/>
+</g>
+<!-- 18->8 -->
+<g id="edge24" class="edge"><title>18->8</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1689,-143.697C1689,-135.983 1689,-126.712 1689,-118.112"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1692.5,-118.104 1689,-108.104 1685.5,-118.104 1692.5,-118.104"/>
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<!-- 19 -->
-<g id="node20" class="node">
-<title>19</title>
-<path fill="none" stroke="#70d856" stroke-width="2" d="M1348,-406C1348,-406 1035,-406 1035,-406 1029,-406 1023,-400 1023,-394 1023,-394 1023,-382 1023,-382 1023,-376 1029,-370 1035,-370 1035,-370 1348,-370 1348,-370 1354,-370 1360,-376 1360,-382 1360,-382 1360,-394 1360,-394 1360,-400 1354,-406 1348,-406"/>
-<text text-anchor="middle" x="1191.5" y="-391" font-family="sans" font-size="10.00" fill="#000000">remove_adapters_cutadapt</text>
-<text text-anchor="middle" x="1191.5" y="-380" font-family="sans" font-size="10.00" fill="#000000">sample: synthetic_10_reads_mate_1_synthetic_10_reads_mate_1</text>
-</g>
-<!-- 19->13 -->
-<g id="edge28" class="edge">
-<title>19->13</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1186.6586,-369.9656C1184.3663,-361.427 1181.576,-351.0333 1179.0173,-341.502"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1182.3393,-340.3771 1176.3662,-331.6265 1175.5787,-342.192 1182.3393,-340.3771"/>
-</g>
-<!-- 20->15 -->
-<g id="edge29" class="edge">
-<title>20->15</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1330.8055,-218.4656C1330.0117,-210.0178 1329.0474,-199.7542 1328.1597,-190.3064"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1331.6234,-189.7552 1327.2032,-180.1265 1324.6541,-190.4101 1331.6234,-189.7552"/>
-</g>
-<!-- 21->17 -->
-<g id="edge30" class="edge">
-<title>21->17</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1520.0569,-221.1539C1558.6725,-210.089 1611.2447,-195.0251 1653.6717,-182.8681"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1654.7411,-186.2026 1663.3902,-180.0834 1652.8129,-179.4734 1654.7411,-186.2026"/>
+<g id="node20" class="node"><title>19</title>
+<path fill="none" stroke="#566bd8" stroke-width="2" d="M1942,-180C1942,-180 1792,-180 1792,-180 1786,-180 1780,-174 1780,-168 1780,-168 1780,-156 1780,-156 1780,-150 1786,-144 1792,-144 1792,-144 1942,-144 1942,-144 1948,-144 1954,-150 1954,-156 1954,-156 1954,-168 1954,-168 1954,-174 1948,-180 1942,-180"/>
+<text text-anchor="middle" x="1867" y="-159.5" font-family="sans" font-size="10.00">index_genomic_alignment_samtools</text>
</g>
-<!-- 22 -->
-<g id="node23" class="node">
-<title>22</title>
-<path fill="none" stroke="#5682d8" stroke-width="2" d="M1457,-334C1457,-334 1342,-334 1342,-334 1336,-334 1330,-328 1330,-322 1330,-322 1330,-305 1330,-305 1330,-299 1336,-293 1342,-293 1342,-293 1457,-293 1457,-293 1463,-293 1469,-299 1469,-305 1469,-305 1469,-322 1469,-322 1469,-328 1463,-334 1457,-334"/>
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-<text text-anchor="middle" x="1399.5" y="-311" font-family="sans" font-size="10.00" fill="#000000">index_size: 75</text>
-<text text-anchor="middle" x="1399.5" y="-300" font-family="sans" font-size="10.00" fill="#000000">organism: homo_sapiens</text>
-</g>
-<!-- 22->20 -->
-<g id="edge31" class="edge">
-<title>22->20</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1381.5452,-292.8654C1373.3483,-283.445 1363.5558,-272.191 1354.8841,-262.225"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1357.4264,-259.8148 1348.2217,-254.5683 1352.1456,-264.4097 1357.4264,-259.8148"/>
-</g>
-<!-- 22->21 -->
-<g id="edge33" class="edge">
-<title>22->21</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1417.4548,-292.8654C1425.6517,-283.445 1435.4442,-272.191 1444.1159,-262.225"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1446.8544,-264.4097 1450.7783,-254.5683 1441.5736,-259.8148 1446.8544,-264.4097"/>
+<!-- 19->8 -->
+<g id="edge23" class="edge"><title>19->8</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1823.46,-143.876C1798.8,-134.179 1767.78,-121.98 1741.75,-111.743"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1742.99,-108.471 1732.4,-108.068 1740.43,-114.985 1742.99,-108.471"/>
+</g>
+<!-- 20 -->
+<g id="node21" class="node"><title>20</title>
+<path fill="none" stroke="#5682d8" stroke-width="2" d="M1137,-406C1137,-406 869,-406 869,-406 863,-406 857,-400 857,-394 857,-394 857,-382 857,-382 857,-376 863,-370 869,-370 869,-370 1137,-370 1137,-370 1143,-370 1149,-376 1149,-382 1149,-382 1149,-394 1149,-394 1149,-400 1143,-406 1137,-406"/>
+<text text-anchor="middle" x="1003" y="-391" font-family="sans" font-size="10.00">pe_remove_adapters_cutadapt</text>
+<text text-anchor="middle" x="1003" y="-380" font-family="sans" font-size="10.00">sample: synthetic_10_reads_paired_synthetic_10_reads_paired</text>
+</g>
+<!-- 20->13 -->
+<g id="edge33" class="edge"><title>20->13</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1003,-369.819C1003,-361.422 1003,-351.116 1003,-341.686"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1006.5,-341.558 1003,-331.558 999.5,-341.558 1006.5,-341.558"/>
+</g>
+<!-- 21 -->
+<g id="node22" class="node"><title>21</title>
+<path fill="none" stroke="#56d8c9" stroke-width="2" d="M1460,-406C1460,-406 1180,-406 1180,-406 1174,-406 1168,-400 1168,-394 1168,-394 1168,-382 1168,-382 1168,-376 1174,-370 1180,-370 1180,-370 1460,-370 1460,-370 1466,-370 1472,-376 1472,-382 1472,-382 1472,-394 1472,-394 1472,-400 1466,-406 1460,-406"/>
+<text text-anchor="middle" x="1320" y="-391" font-family="sans" font-size="10.00">remove_adapters_cutadapt</text>
+<text text-anchor="middle" x="1320" y="-380" font-family="sans" font-size="10.00">sample: synthetic_10_reads_mate_1_synthetic_10_reads_mate_1</text>
+</g>
+<!-- 21->15 -->
+<g id="edge34" class="edge"><title>21->15</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1320,-369.819C1320,-361.422 1320,-351.116 1320,-341.686"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1323.5,-341.558 1320,-331.558 1316.5,-341.558 1323.5,-341.558"/>
+</g>
+<!-- 22->17 -->
+<g id="edge35" class="edge"><title>22->17</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1497.66,-218.319C1498.47,-209.922 1499.46,-199.616 1500.38,-190.186"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1503.88,-190.348 1501.35,-180.058 1496.91,-189.675 1503.88,-190.348"/>
+</g>
+<!-- 23->19 -->
+<g id="edge36" class="edge"><title>23->19</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1667.7,-221.263C1705.18,-210.306 1757.43,-195.031 1799.03,-182.87"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1800.2,-186.174 1808.82,-180.009 1798.24,-179.456 1800.2,-186.174"/>
+</g>
+<!-- 24 -->
+<g id="node25" class="node"><title>24</title>
+<path fill="none" stroke="#9fd856" stroke-width="2" d="M1607.5,-334C1607.5,-334 1506.5,-334 1506.5,-334 1500.5,-334 1494.5,-328 1494.5,-322 1494.5,-322 1494.5,-305 1494.5,-305 1494.5,-299 1500.5,-293 1506.5,-293 1506.5,-293 1607.5,-293 1607.5,-293 1613.5,-293 1619.5,-299 1619.5,-305 1619.5,-305 1619.5,-322 1619.5,-322 1619.5,-328 1613.5,-334 1607.5,-334"/>
+<text text-anchor="middle" x="1557" y="-322" font-family="sans" font-size="10.00">create_index_star</text>
+<text text-anchor="middle" x="1557" y="-311" font-family="sans" font-size="10.00">index_size: 75</text>
+<text text-anchor="middle" x="1557" y="-300" font-family="sans" font-size="10.00">organism: homo_sapiens</text>
+</g>
+<!-- 24->22 -->
+<g id="edge37" class="edge"><title>24->22</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1540.97,-292.795C1533.47,-283.572 1524.45,-272.48 1516.46,-262.659"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1519.08,-260.327 1510.05,-254.777 1513.65,-264.744 1519.08,-260.327"/>
+</g>
+<!-- 24->23 -->
+<g id="edge39" class="edge"><title>24->23</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1573.29,-292.795C1580.91,-283.572 1590.08,-272.48 1598.2,-262.659"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1601.04,-264.715 1604.72,-254.777 1595.65,-260.255 1601.04,-264.715"/>
</g>
</g>
</svg>
diff --git a/images/rule_graph.svg b/images/rule_graph.svg
index 9756a86350c383b6c395873d280835c5995c9248..0bf578e1cb28665282e74d7c6d12769b8ec53c23 100644
--- a/images/rule_graph.svg
+++ b/images/rule_graph.svg
@@ -1,337 +1,283 @@
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<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
"http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
-<!-- Generated by graphviz version 2.40.1 (20161225.0304)
+<!-- Generated by graphviz version 2.38.0 (20140413.2041)
-->
<!-- Title: snakemake_dag Pages: 1 -->
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- viewBox="0.00 0.00 1215.50 404.00" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
+<svg width="1107pt" height="404pt"
+ viewBox="0.00 0.00 1106.50 404.00" 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(4 400)">
<title>snakemake_dag</title>
-<polygon fill="#ffffff" stroke="transparent" points="-4,4 -4,-400 1211.5,-400 1211.5,4 -4,4"/>
+<polygon fill="white" stroke="none" points="-4,4 -4,-400 1102.5,-400 1102.5,4 -4,4"/>
<!-- 0 -->
-<g id="node1" class="node">
-<title>0</title>
-<path fill="none" stroke="#d89c56" stroke-width="2" d="M278.5,-36C278.5,-36 248.5,-36 248.5,-36 242.5,-36 236.5,-30 236.5,-24 236.5,-24 236.5,-12 236.5,-12 236.5,-6 242.5,0 248.5,0 248.5,0 278.5,0 278.5,0 284.5,0 290.5,-6 290.5,-12 290.5,-12 290.5,-24 290.5,-24 290.5,-30 284.5,-36 278.5,-36"/>
-<text text-anchor="middle" x="263.5" y="-15.5" font-family="sans" font-size="10.00" fill="#000000">finish</text>
+<g id="node1" class="node"><title>0</title>
+<path fill="none" stroke="#9fd856" stroke-width="2" d="M250.5,-36C250.5,-36 220.5,-36 220.5,-36 214.5,-36 208.5,-30 208.5,-24 208.5,-24 208.5,-12 208.5,-12 208.5,-6 214.5,-0 220.5,-0 220.5,-0 250.5,-0 250.5,-0 256.5,-0 262.5,-6 262.5,-12 262.5,-12 262.5,-24 262.5,-24 262.5,-30 256.5,-36 250.5,-36"/>
+<text text-anchor="middle" x="235.5" y="-15.5" font-family="sans" font-size="10.00">finish</text>
</g>
<!-- 1 -->
-<g id="node2" class="node">
-<title>1</title>
-<path fill="none" stroke="#d85656" stroke-width="2" d="M75.5,-108C75.5,-108 35.5,-108 35.5,-108 29.5,-108 23.5,-102 23.5,-96 23.5,-96 23.5,-84 23.5,-84 23.5,-78 29.5,-72 35.5,-72 35.5,-72 75.5,-72 75.5,-72 81.5,-72 87.5,-78 87.5,-84 87.5,-84 87.5,-96 87.5,-96 87.5,-102 81.5,-108 75.5,-108"/>
-<text text-anchor="middle" x="55.5" y="-87.5" font-family="sans" font-size="10.00" fill="#000000">pe_fastqc</text>
+<g id="node2" class="node"><title>1</title>
+<path fill="none" stroke="#56d882" stroke-width="2" d="M47,-108C47,-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 47,-72 47,-72 53,-72 59,-78 59,-84 59,-84 59,-96 59,-96 59,-102 53,-108 47,-108"/>
+<text text-anchor="middle" x="29.5" y="-87.5" font-family="sans" font-size="10.00">pe_fastqc</text>
</g>
<!-- 1->0 -->
-<g id="edge1" class="edge">
-<title>1->0</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M87.602,-75.5405C90.594,-74.3037 93.5933,-73.1048 96.5,-72 140.5109,-55.2724 192.2328,-39.0651 226.324,-28.844"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="227.7248,-32.0788 236.3099,-25.8702 225.7269,-25.37 227.7248,-32.0788"/>
+<g id="edge9" class="edge"><title>1->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M59.1802,-75.6843C62.3088,-74.3943 65.4575,-73.1424 68.5,-72 112.501,-55.4786 164.225,-39.5929 198.319,-29.5943"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="199.684,-32.8425 208.306,-26.6862 197.727,-26.1217 199.684,-32.8425"/>
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-<g id="node3" class="node">
-<title>2</title>
-<path fill="none" stroke="#59d856" stroke-width="2" d="M147.5,-108C147.5,-108 117.5,-108 117.5,-108 111.5,-108 105.5,-102 105.5,-96 105.5,-96 105.5,-84 105.5,-84 105.5,-78 111.5,-72 117.5,-72 117.5,-72 147.5,-72 147.5,-72 153.5,-72 159.5,-78 159.5,-84 159.5,-84 159.5,-96 159.5,-96 159.5,-102 153.5,-108 147.5,-108"/>
-<text text-anchor="middle" x="132.5" y="-87.5" font-family="sans" font-size="10.00" fill="#000000">fastqc</text>
+<g id="node3" class="node"><title>2</title>
+<path fill="none" stroke="#ced856" stroke-width="2" d="M119.5,-108C119.5,-108 89.5,-108 89.5,-108 83.5,-108 77.5,-102 77.5,-96 77.5,-96 77.5,-84 77.5,-84 77.5,-78 83.5,-72 89.5,-72 89.5,-72 119.5,-72 119.5,-72 125.5,-72 131.5,-78 131.5,-84 131.5,-84 131.5,-96 131.5,-96 131.5,-102 125.5,-108 119.5,-108"/>
+<text text-anchor="middle" x="104.5" y="-87.5" font-family="sans" font-size="10.00">fastqc</text>
</g>
<!-- 2->0 -->
-<g id="edge7" class="edge">
-<title>2->0</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M159.6433,-75.0816C179.3158,-64.2692 206.1157,-49.5395 227.5636,-37.7513"/>
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+<g id="edge1" class="edge"><title>2->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M131.643,-74.496C151.316,-63.9839 178.116,-49.6634 199.564,-38.2027"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="201.221,-41.2853 208.391,-33.4855 197.922,-35.1115 201.221,-41.2853"/>
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-<g id="node4" class="node">
-<title>3</title>
-<path fill="none" stroke="#d86e56" stroke-width="2" d="M428.5,-180C428.5,-180 310.5,-180 310.5,-180 304.5,-180 298.5,-174 298.5,-168 298.5,-168 298.5,-156 298.5,-156 298.5,-150 304.5,-144 310.5,-144 310.5,-144 428.5,-144 428.5,-144 434.5,-144 440.5,-150 440.5,-156 440.5,-156 440.5,-168 440.5,-168 440.5,-174 434.5,-180 428.5,-180"/>
-<text text-anchor="middle" x="369.5" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">pe_quantification_salmon</text>
+<g id="node4" class="node"><title>3</title>
+<path fill="none" stroke="#56d89a" stroke-width="2" d="M393,-180C393,-180 290,-180 290,-180 284,-180 278,-174 278,-168 278,-168 278,-156 278,-156 278,-150 284,-144 290,-144 290,-144 393,-144 393,-144 399,-144 405,-150 405,-156 405,-156 405,-168 405,-168 405,-174 399,-180 393,-180"/>
+<text text-anchor="middle" x="341.5" y="-159.5" font-family="sans" font-size="10.00">pe_quantification_salmon</text>
</g>
<!-- 3->0 -->
-<g id="edge2" class="edge">
-<title>3->0</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M326.0408,-143.997C310.0967,-135.3368 293.3209,-123.4271 282.5,-108 269.8693,-89.9927 265.3299,-65.3098 263.8314,-46.3472"/>
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+<g id="edge3" class="edge"><title>3->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M298.969,-143.961C282.762,-135.446 265.551,-123.579 254.5,-108 241.756,-90.0343 237.257,-65.2413 235.803,-46.3852"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="239.295,-46.1334 235.267,-36.334 232.305,-46.5062 239.295,-46.1334"/>
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-<g id="node9" class="node">
-<title>8</title>
-<path fill="none" stroke="#b6d856" stroke-width="2" d="M629.5,-108C629.5,-108 477.5,-108 477.5,-108 471.5,-108 465.5,-102 465.5,-96 465.5,-96 465.5,-84 465.5,-84 465.5,-78 471.5,-72 477.5,-72 477.5,-72 629.5,-72 629.5,-72 635.5,-72 641.5,-78 641.5,-84 641.5,-84 641.5,-96 641.5,-96 641.5,-102 635.5,-108 629.5,-108"/>
-<text text-anchor="middle" x="553.5" y="-87.5" font-family="sans" font-size="10.00" fill="#000000">salmon_quantmerge_genes_tpm</text>
+<g id="node9" class="node"><title>8</title>
+<path fill="none" stroke="#56c9d8" stroke-width="2" d="M561.5,-108C561.5,-108 449.5,-108 449.5,-108 443.5,-108 437.5,-102 437.5,-96 437.5,-96 437.5,-84 437.5,-84 437.5,-78 443.5,-72 449.5,-72 449.5,-72 561.5,-72 561.5,-72 567.5,-72 573.5,-78 573.5,-84 573.5,-84 573.5,-96 573.5,-96 573.5,-102 567.5,-108 561.5,-108"/>
+<text text-anchor="middle" x="505.5" y="-87.5" font-family="sans" font-size="10.00">salmon_quantmerge_genes</text>
</g>
<!-- 3->8 -->
-<g id="edge22" class="edge">
-<title>3->8</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M415.931,-143.8314C440.868,-134.0734 471.7809,-121.977 497.9826,-111.7242"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="499.3659,-114.9414 507.4029,-108.038 496.8151,-108.4227 499.3659,-114.9414"/>
+<g id="edge22" class="edge"><title>3->8</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M381.619,-143.876C404.138,-134.264 432.418,-122.193 456.271,-112.013"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="457.688,-115.213 465.511,-108.068 454.94,-108.775 457.688,-115.213"/>
</g>
<!-- 9 -->
-<g id="node10" class="node">
-<title>9</title>
-<path fill="none" stroke="#56d882" stroke-width="2" d="M435,-108C435,-108 304,-108 304,-108 298,-108 292,-102 292,-96 292,-96 292,-84 292,-84 292,-78 298,-72 304,-72 304,-72 435,-72 435,-72 441,-72 447,-78 447,-84 447,-84 447,-96 447,-96 447,-102 441,-108 435,-108"/>
-<text text-anchor="middle" x="369.5" y="-87.5" font-family="sans" font-size="10.00" fill="#000000">salmon_quantmerge_tr_tpm</text>
+<g id="node10" class="node"><title>9</title>
+<path fill="none" stroke="#5682d8" stroke-width="2" d="M407,-108C407,-108 276,-108 276,-108 270,-108 264,-102 264,-96 264,-96 264,-84 264,-84 264,-78 270,-72 276,-72 276,-72 407,-72 407,-72 413,-72 419,-78 419,-84 419,-84 419,-96 419,-96 419,-102 413,-108 407,-108"/>
+<text text-anchor="middle" x="341.5" y="-87.5" font-family="sans" font-size="10.00">salmon_quantmerge_transcripts</text>
</g>
<!-- 3->9 -->
-<g id="edge24" class="edge">
-<title>3->9</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M369.5,-143.8314C369.5,-136.131 369.5,-126.9743 369.5,-118.4166"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="373.0001,-118.4132 369.5,-108.4133 366.0001,-118.4133 373.0001,-118.4132"/>
+<g id="edge24" class="edge"><title>3->9</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M341.5,-143.697C341.5,-135.983 341.5,-126.712 341.5,-118.112"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="345,-118.104 341.5,-108.104 338,-118.104 345,-118.104"/>
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-<g id="node5" class="node">
-<title>4</title>
-<path fill="none" stroke="#9fd856" stroke-width="2" d="M572,-180C572,-180 471,-180 471,-180 465,-180 459,-174 459,-168 459,-168 459,-156 459,-156 459,-150 465,-144 471,-144 471,-144 572,-144 572,-144 578,-144 584,-150 584,-156 584,-156 584,-168 584,-168 584,-174 578,-180 572,-180"/>
-<text text-anchor="middle" x="521.5" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">quantification_salmon</text>
+<g id="node5" class="node"><title>4</title>
+<path fill="none" stroke="#566bd8" stroke-width="2" d="M522,-180C522,-180 435,-180 435,-180 429,-180 423,-174 423,-168 423,-168 423,-156 423,-156 423,-150 429,-144 435,-144 435,-144 522,-144 522,-144 528,-144 534,-150 534,-156 534,-156 534,-168 534,-168 534,-174 528,-180 522,-180"/>
+<text text-anchor="middle" x="478.5" y="-159.5" font-family="sans" font-size="10.00">quantification_salmon</text>
</g>
<!-- 4->0 -->
-<g id="edge6" class="edge">
-<title>4->0</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M581.6631,-143.9748C611.1402,-133.8034 642.0932,-120.6327 650.5,-108 659.3642,-94.6799 661.0029,-84.0702 650.5,-72 627.6671,-45.7599 393.0238,-26.9047 300.6114,-20.4437"/>
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+<g id="edge8" class="edge"><title>4->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M534.128,-145.789C552.813,-137.736 571.648,-125.711 582.5,-108 590.859,-94.3575 592.925,-84.1378 582.5,-72 542.885,-25.8749 354.205,-19.4546 272.908,-18.8661"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="272.647,-15.365 262.631,-18.8191 272.615,-22.3649 272.647,-15.365"/>
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<!-- 4->8 -->
-<g id="edge21" class="edge">
-<title>4->8</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M529.575,-143.8314C533.1102,-135.8771 537.336,-126.369 541.2456,-117.5723"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="544.4532,-118.9729 545.3163,-108.4133 538.0565,-116.1299 544.4532,-118.9729"/>
+<g id="edge21" class="edge"><title>4->8</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M485.174,-143.697C488.215,-135.813 491.883,-126.304 495.261,-117.546"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="498.569,-118.694 498.903,-108.104 492.038,-116.175 498.569,-118.694"/>
</g>
<!-- 4->9 -->
-<g id="edge23" class="edge">
-<title>4->9</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M483.144,-143.8314C462.9956,-134.2874 438.1248,-122.5065 416.7917,-112.4013"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="418.1159,-109.1558 407.5802,-108.038 415.1193,-115.482 418.1159,-109.1558"/>
+<g id="edge23" class="edge"><title>4->9</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M444.986,-143.876C426.659,-134.512 403.764,-122.814 384.172,-112.803"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="385.64,-109.623 375.143,-108.19 382.455,-115.857 385.64,-109.623"/>
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<!-- 5 -->
-<g id="node6" class="node">
-<title>5</title>
-<path fill="none" stroke="#d8cb56" stroke-width="2" d="M175,-252C175,-252 12,-252 12,-252 6,-252 0,-246 0,-240 0,-240 0,-228 0,-228 0,-222 6,-216 12,-216 12,-216 175,-216 175,-216 181,-216 187,-222 187,-228 187,-228 187,-240 187,-240 187,-246 181,-252 175,-252"/>
-<text text-anchor="middle" x="93.5" y="-231.5" font-family="sans" font-size="10.00" fill="#000000">pe_genome_quantification_kallisto</text>
+<g id="node6" class="node"><title>5</title>
+<path fill="none" stroke="#70d856" stroke-width="2" d="M160.5,-252C160.5,-252 18.5,-252 18.5,-252 12.5,-252 6.5,-246 6.5,-240 6.5,-240 6.5,-228 6.5,-228 6.5,-222 12.5,-216 18.5,-216 18.5,-216 160.5,-216 160.5,-216 166.5,-216 172.5,-222 172.5,-228 172.5,-228 172.5,-240 172.5,-240 172.5,-246 166.5,-252 160.5,-252"/>
+<text text-anchor="middle" x="89.5" y="-231.5" font-family="sans" font-size="10.00">pe_genome_quantification_kallisto</text>
</g>
<!-- 5->0 -->
-<g id="edge3" class="edge">
-<title>5->0</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M107.7017,-215.9555C137.7641,-177.7585 207.9332,-88.6025 242.9143,-44.1559"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="245.7848,-46.1679 249.2192,-36.1451 240.2841,-41.8386 245.7848,-46.1679"/>
+<g id="edge5" class="edge"><title>5->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M101.201,-215.849C126.776,-178.362 187.778,-88.9491 217.965,-44.7025"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="220.999,-46.4656 223.743,-36.2325 215.216,-42.5206 220.999,-46.4656"/>
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<!-- 6 -->
-<g id="node7" class="node">
-<title>6</title>
-<path fill="none" stroke="#566bd8" stroke-width="2" d="M363.5,-252C363.5,-252 217.5,-252 217.5,-252 211.5,-252 205.5,-246 205.5,-240 205.5,-240 205.5,-228 205.5,-228 205.5,-222 211.5,-216 217.5,-216 217.5,-216 363.5,-216 363.5,-216 369.5,-216 375.5,-222 375.5,-228 375.5,-228 375.5,-240 375.5,-240 375.5,-246 369.5,-252 363.5,-252"/>
-<text text-anchor="middle" x="290.5" y="-231.5" font-family="sans" font-size="10.00" fill="#000000">genome_quantification_kallisto</text>
+<g id="node7" class="node"><title>6</title>
+<path fill="none" stroke="#d86e56" stroke-width="2" d="M328.5,-252C328.5,-252 202.5,-252 202.5,-252 196.5,-252 190.5,-246 190.5,-240 190.5,-240 190.5,-228 190.5,-228 190.5,-222 196.5,-216 202.5,-216 202.5,-216 328.5,-216 328.5,-216 334.5,-216 340.5,-222 340.5,-228 340.5,-228 340.5,-240 340.5,-240 340.5,-246 334.5,-252 328.5,-252"/>
+<text text-anchor="middle" x="265.5" y="-231.5" font-family="sans" font-size="10.00">genome_quantification_kallisto</text>
</g>
<!-- 6->0 -->
-<g id="edge4" class="edge">
-<title>6->0</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M285.5956,-215.8118C279.2989,-191.4728 268.6861,-146.863 264.5,-108 262.2861,-87.4468 262.0933,-64.1016 262.4239,-46.3388"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="265.923,-46.4174 262.6759,-36.3324 258.9252,-46.2411 265.923,-46.4174"/>
+<g id="edge6" class="edge"><title>6->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M260.264,-215.82C253.267,-191.918 241.205,-147.15 236.5,-108 234.027,-87.4178 233.871,-63.966 234.283,-46.3046"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="237.787,-46.237 234.597,-36.1336 230.79,-46.0207 237.787,-46.237"/>
</g>
<!-- 7 -->
-<g id="node8" class="node">
-<title>7</title>
-<path fill="none" stroke="#56d89a" stroke-width="2" d="M883,-108C883,-108 788,-108 788,-108 782,-108 776,-102 776,-96 776,-96 776,-84 776,-84 776,-78 782,-72 788,-72 788,-72 883,-72 883,-72 889,-72 895,-78 895,-84 895,-84 895,-96 895,-96 895,-102 889,-108 883,-108"/>
-<text text-anchor="middle" x="835.5" y="-87.5" font-family="sans" font-size="10.00" fill="#000000">calculate_TIN_scores</text>
+<g id="node8" class="node"><title>7</title>
+<path fill="none" stroke="#88d856" stroke-width="2" d="M803.5,-108C803.5,-108 715.5,-108 715.5,-108 709.5,-108 703.5,-102 703.5,-96 703.5,-96 703.5,-84 703.5,-84 703.5,-78 709.5,-72 715.5,-72 715.5,-72 803.5,-72 803.5,-72 809.5,-72 815.5,-78 815.5,-84 815.5,-84 815.5,-96 815.5,-96 815.5,-102 809.5,-108 803.5,-108"/>
+<text text-anchor="middle" x="759.5" y="-87.5" font-family="sans" font-size="10.00">calculate_TIN_scores</text>
</g>
<!-- 7->0 -->
-<g id="edge9" class="edge">
-<title>7->0</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M775.9047,-82.4985C658,-67.6573 397.9937,-34.9293 300.9757,-22.7172"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="301.1269,-19.2087 290.768,-21.4323 300.2526,-26.1539 301.1269,-19.2087"/>
+<g id="edge4" class="edge"><title>7->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M703.423,-81.5088C595.869,-67.1409 363.245,-36.0652 272.661,-23.9643"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="272.962,-20.4734 262.586,-22.6184 272.035,-27.4118 272.962,-20.4734"/>
</g>
<!-- 8->0 -->
-<g id="edge5" class="edge">
-<title>8->0</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M480.6951,-71.9243C423.4138,-57.7027 345.9515,-38.4707 300.6911,-27.2337"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="301.2742,-23.7722 290.7254,-24.7594 299.5874,-30.566 301.2742,-23.7722"/>
+<g id="edge7" class="edge"><title>8->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M439.796,-71.9656C387.194,-58.3281 315.335,-39.698 272.355,-28.555"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="273.158,-25.1475 262.6,-26.0258 271.401,-31.9235 273.158,-25.1475"/>
</g>
<!-- 9->0 -->
-<g id="edge8" class="edge">
-<title>9->0</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M342.7517,-71.8314C329.4447,-62.7927 313.184,-51.7476 298.8625,-42.0198"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="300.4785,-38.8864 290.2397,-36.1628 296.5453,-44.677 300.4785,-38.8864"/>
+<g id="edge2" class="edge"><title>9->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M315.569,-71.8761C301.838,-62.8083 284.794,-51.5523 269.964,-41.7592"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="271.804,-38.7798 261.53,-36.1898 267.946,-44.621 271.804,-38.7798"/>
</g>
<!-- 10 -->
-<g id="node11" class="node">
-<title>10</title>
-<path fill="none" stroke="#56c9d8" stroke-width="2" d="M467.5,-324C467.5,-324 339.5,-324 339.5,-324 333.5,-324 327.5,-318 327.5,-312 327.5,-312 327.5,-300 327.5,-300 327.5,-294 333.5,-288 339.5,-288 339.5,-288 467.5,-288 467.5,-288 473.5,-288 479.5,-294 479.5,-300 479.5,-300 479.5,-312 479.5,-312 479.5,-318 473.5,-324 467.5,-324"/>
-<text text-anchor="middle" x="403.5" y="-303.5" font-family="sans" font-size="10.00" fill="#000000">pe_remove_polya_cutadapt</text>
+<g id="node11" class="node"><title>10</title>
+<path fill="none" stroke="#d88556" stroke-width="2" d="M424.5,-324C424.5,-324 312.5,-324 312.5,-324 306.5,-324 300.5,-318 300.5,-312 300.5,-312 300.5,-300 300.5,-300 300.5,-294 306.5,-288 312.5,-288 312.5,-288 424.5,-288 424.5,-288 430.5,-288 436.5,-294 436.5,-300 436.5,-300 436.5,-312 436.5,-312 436.5,-318 430.5,-324 424.5,-324"/>
+<text text-anchor="middle" x="368.5" y="-303.5" font-family="sans" font-size="10.00">pe_remove_polya_cutadapt</text>
</g>
<!-- 10->3 -->
-<g id="edge11" class="edge">
-<title>10->3</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M400.0453,-287.9951C396.4678,-269.7725 390.5612,-240.8217 384.5,-216 382.4324,-207.5329 379.9752,-198.3795 377.6542,-190.0569"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="381.0174,-189.0876 374.9259,-180.4191 374.2821,-190.9943 381.0174,-189.0876"/>
+<g id="edge11" class="edge"><title>10->3</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M365.243,-287.871C360.642,-263.67 352.188,-219.211 346.709,-190.393"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="350.075,-189.359 344.768,-180.189 343.198,-190.667 350.075,-189.359"/>
</g>
<!-- 10->5 -->
-<g id="edge15" class="edge">
-<title>10->5</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M327.2684,-288.2946C283.0085,-278.0149 227.0782,-265.0246 181.0234,-254.328"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="181.5861,-250.8656 171.0536,-252.0124 180.0024,-257.6841 181.5861,-250.8656"/>
+<g id="edge14" class="edge"><title>10->5</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M300.606,-287.966C260.437,-277.887 209.4,-265.082 167.571,-254.588"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="168.25,-251.15 157.699,-252.111 166.546,-257.939 168.25,-251.15"/>
</g>
<!-- 19 -->
-<g id="node20" class="node">
-<title>19</title>
-<path fill="none" stroke="#d8b456" stroke-width="2" d="M753,-252C753,-252 652,-252 652,-252 646,-252 640,-246 640,-240 640,-240 640,-228 640,-228 640,-222 646,-216 652,-216 652,-216 753,-216 753,-216 759,-216 765,-222 765,-228 765,-228 765,-240 765,-240 765,-246 759,-252 753,-252"/>
-<text text-anchor="middle" x="702.5" y="-231.5" font-family="sans" font-size="10.00" fill="#000000">pe_map_genome_star</text>
+<g id="node20" class="node"><title>19</title>
+<path fill="none" stroke="#d85656" stroke-width="2" d="M692,-252C692,-252 603,-252 603,-252 597,-252 591,-246 591,-240 591,-240 591,-228 591,-228 591,-222 597,-216 603,-216 603,-216 692,-216 692,-216 698,-216 704,-222 704,-228 704,-228 704,-240 704,-240 704,-246 698,-252 692,-252"/>
+<text text-anchor="middle" x="647.5" y="-231.5" font-family="sans" font-size="10.00">pe_map_genome_star</text>
</g>
<!-- 10->19 -->
-<g id="edge29" class="edge">
-<title>10->19</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M478.5644,-287.9243C524.8179,-276.7863 583.8339,-262.5751 629.6681,-251.5381"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="630.6316,-254.9062 639.5343,-249.1623 628.9927,-248.1008 630.6316,-254.9062"/>
+<g id="edge29" class="edge"><title>10->19</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M436.394,-287.966C480.239,-276.965 537.032,-262.716 580.666,-251.768"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="581.764,-255.102 590.611,-249.273 580.06,-248.312 581.764,-255.102"/>
</g>
<!-- 11 -->
-<g id="node12" class="node">
-<title>11</title>
-<path fill="none" stroke="#70d856" stroke-width="2" d="M541,-252C541,-252 444,-252 444,-252 438,-252 432,-246 432,-240 432,-240 432,-228 432,-228 432,-222 438,-216 444,-216 444,-216 541,-216 541,-216 547,-216 553,-222 553,-228 553,-228 553,-240 553,-240 553,-246 547,-252 541,-252"/>
-<text text-anchor="middle" x="492.5" y="-231.5" font-family="sans" font-size="10.00" fill="#000000">create_index_salmon</text>
+<g id="node12" class="node"><title>11</title>
+<path fill="none" stroke="#56d86b" stroke-width="2" d="M494,-252C494,-252 409,-252 409,-252 403,-252 397,-246 397,-240 397,-240 397,-228 397,-228 397,-222 403,-216 409,-216 409,-216 494,-216 494,-216 500,-216 506,-222 506,-228 506,-228 506,-240 506,-240 506,-246 500,-252 494,-252"/>
+<text text-anchor="middle" x="451.5" y="-231.5" font-family="sans" font-size="10.00">create_index_salmon</text>
</g>
<!-- 11->3 -->
-<g id="edge10" class="edge">
-<title>11->3</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M461.4619,-215.8314C445.7295,-206.6221 426.4389,-195.3301 409.5956,-185.4706"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="410.9265,-182.1941 400.5282,-180.1628 407.3902,-188.2352 410.9265,-182.1941"/>
+<g id="edge10" class="edge"><title>11->3</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M424.591,-215.876C410.342,-206.808 392.654,-195.552 377.264,-185.759"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="378.828,-182.606 368.512,-180.19 375.07,-188.511 378.828,-182.606"/>
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<!-- 11->4 -->
-<g id="edge12" class="edge">
-<title>11->4</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M499.8179,-215.8314C502.9876,-207.9617 506.77,-198.5712 510.2813,-189.8533"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="513.5939,-190.9968 514.0835,-180.4133 507.1008,-188.3815 513.5939,-190.9968"/>
+<g id="edge12" class="edge"><title>11->4</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M458.174,-215.697C461.215,-207.813 464.883,-198.304 468.261,-189.546"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="471.569,-190.694 471.903,-180.104 465.038,-188.175 471.569,-190.694"/>
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<!-- 12 -->
-<g id="node13" class="node">
-<title>12</title>
-<path fill="none" stroke="#d88556" stroke-width="2" d="M636.5,-324C636.5,-324 526.5,-324 526.5,-324 520.5,-324 514.5,-318 514.5,-312 514.5,-312 514.5,-300 514.5,-300 514.5,-294 520.5,-288 526.5,-288 526.5,-288 636.5,-288 636.5,-288 642.5,-288 648.5,-294 648.5,-300 648.5,-300 648.5,-312 648.5,-312 648.5,-318 642.5,-324 636.5,-324"/>
-<text text-anchor="middle" x="581.5" y="-303.5" font-family="sans" font-size="10.00" fill="#000000">remove_polya_cutadapt</text>
+<g id="node13" class="node"><title>12</title>
+<path fill="none" stroke="#569ad8" stroke-width="2" d="M582.5,-324C582.5,-324 486.5,-324 486.5,-324 480.5,-324 474.5,-318 474.5,-312 474.5,-312 474.5,-300 474.5,-300 474.5,-294 480.5,-288 486.5,-288 486.5,-288 582.5,-288 582.5,-288 588.5,-288 594.5,-294 594.5,-300 594.5,-300 594.5,-312 594.5,-312 594.5,-318 588.5,-324 582.5,-324"/>
+<text text-anchor="middle" x="534.5" y="-303.5" font-family="sans" font-size="10.00">remove_polya_cutadapt</text>
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<!-- 12->4 -->
-<g id="edge13" class="edge">
-<title>12->4</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M580.0081,-287.6774C577.9477,-268.9522 573.1883,-239.3838 562.5,-216 558.0225,-206.2043 551.508,-196.5125 544.9846,-188.1017"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="547.5556,-185.7156 538.5333,-180.1615 542.1228,-190.1297 547.5556,-185.7156"/>
+<g id="edge13" class="edge"><title>12->4</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M532.903,-287.986C530.719,-269.607 525.826,-239.765 515.5,-216 511.318,-206.375 505.254,-196.71 499.241,-188.318"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="501.872,-185.992 493.074,-180.089 496.27,-190.19 501.872,-185.992"/>
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-<g id="edge16" class="edge">
-<title>12->6</title>
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+<g id="edge16" class="edge"><title>12->6</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M474.466,-289.378C434.961,-279.098 382.94,-265.561 340.686,-254.565"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="341.56,-251.176 331,-252.045 339.797,-257.95 341.56,-251.176"/>
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-<g id="node21" class="node">
-<title>20</title>
-<path fill="none" stroke="#56d8b1" stroke-width="2" d="M878,-252C878,-252 795,-252 795,-252 789,-252 783,-246 783,-240 783,-240 783,-228 783,-228 783,-222 789,-216 795,-216 795,-216 878,-216 878,-216 884,-216 890,-222 890,-228 890,-228 890,-240 890,-240 890,-246 884,-252 878,-252"/>
-<text text-anchor="middle" x="836.5" y="-231.5" font-family="sans" font-size="10.00" fill="#000000">map_genome_star</text>
+<g id="node21" class="node"><title>20</title>
+<path fill="none" stroke="#56d8b1" stroke-width="2" d="M807,-252C807,-252 734,-252 734,-252 728,-252 722,-246 722,-240 722,-240 722,-228 722,-228 722,-222 728,-216 734,-216 734,-216 807,-216 807,-216 813,-216 819,-222 819,-228 819,-228 819,-240 819,-240 819,-246 813,-252 807,-252"/>
+<text text-anchor="middle" x="770.5" y="-231.5" font-family="sans" font-size="10.00">map_genome_star</text>
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-<g id="edge31" class="edge">
-<title>12->20</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M646.7594,-287.9111C681.7622,-278.169 725.8822,-265.8263 772.9686,-252.4263"/>
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+<g id="edge31" class="edge"><title>12->20</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M592.147,-287.963C624.904,-278.274 666.932,-265.832 712.269,-252.363"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="713.403,-255.678 721.992,-249.474 711.409,-248.968 713.403,-255.678"/>
</g>
<!-- 13 -->
-<g id="node14" class="node">
-<title>13</title>
-<path fill="none" stroke="#56d8c9" stroke-width="2" d="M220,-324C220,-324 123,-324 123,-324 117,-324 111,-318 111,-312 111,-312 111,-300 111,-300 111,-294 117,-288 123,-288 123,-288 220,-288 220,-288 226,-288 232,-294 232,-300 232,-300 232,-312 232,-312 232,-318 226,-324 220,-324"/>
-<text text-anchor="middle" x="171.5" y="-303.5" font-family="sans" font-size="10.00" fill="#000000">create_index_kallisto</text>
+<g id="node14" class="node"><title>13</title>
+<path fill="none" stroke="#56b1d8" stroke-width="2" d="M200.5,-324C200.5,-324 116.5,-324 116.5,-324 110.5,-324 104.5,-318 104.5,-312 104.5,-312 104.5,-300 104.5,-300 104.5,-294 110.5,-288 116.5,-288 116.5,-288 200.5,-288 200.5,-288 206.5,-288 212.5,-294 212.5,-300 212.5,-300 212.5,-312 212.5,-312 212.5,-318 206.5,-324 200.5,-324"/>
+<text text-anchor="middle" x="158.5" y="-303.5" font-family="sans" font-size="10.00">create_index_kallisto</text>
</g>
<!-- 13->5 -->
-<g id="edge14" class="edge">
-<title>13->5</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M151.8173,-287.8314C142.3949,-279.1337 130.9599,-268.5783 120.7204,-259.1265"/>
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+<g id="edge15" class="edge"><title>13->5</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M141.444,-287.697C133.005,-279.135 122.675,-268.656 113.457,-259.304"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="115.873,-256.769 106.36,-252.104 110.887,-261.683 115.873,-256.769"/>
</g>
<!-- 13->6 -->
-<g id="edge17" class="edge">
-<title>13->6</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M201.5287,-287.8314C216.7496,-278.6221 235.4128,-267.3301 251.7083,-257.4706"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="253.7369,-260.3341 260.4809,-252.1628 250.1132,-254.345 253.7369,-260.3341"/>
+<g id="edge17" class="edge"><title>13->6</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M184.675,-287.876C198.536,-278.808 215.741,-267.552 230.711,-257.759"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="232.772,-260.593 239.224,-252.19 228.94,-254.735 232.772,-260.593"/>
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<!-- 14 -->
-<g id="node15" class="node">
-<title>14</title>
-<path fill="none" stroke="#56b1d8" stroke-width="2" d="M803,-180C803,-180 614,-180 614,-180 608,-180 602,-174 602,-168 602,-168 602,-156 602,-156 602,-150 608,-144 614,-144 614,-144 803,-144 803,-144 809,-144 815,-150 815,-156 815,-156 815,-168 815,-168 815,-174 809,-180 803,-180"/>
-<text text-anchor="middle" x="708.5" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">pe_index_genomic_alignment_samtools</text>
+<g id="node15" class="node"><title>14</title>
+<path fill="none" stroke="#d8cb56" stroke-width="2" d="M730.5,-180C730.5,-180 564.5,-180 564.5,-180 558.5,-180 552.5,-174 552.5,-168 552.5,-168 552.5,-156 552.5,-156 552.5,-150 558.5,-144 564.5,-144 564.5,-144 730.5,-144 730.5,-144 736.5,-144 742.5,-150 742.5,-156 742.5,-156 742.5,-168 742.5,-168 742.5,-174 736.5,-180 730.5,-180"/>
+<text text-anchor="middle" x="647.5" y="-159.5" font-family="sans" font-size="10.00">pe_index_genomic_alignment_samtools</text>
</g>
<!-- 14->7 -->
-<g id="edge19" class="edge">
-<title>14->7</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M740.5475,-143.8314C756.942,-134.5368 777.0786,-123.1208 794.5829,-113.1971"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="796.4897,-116.1395 803.4628,-108.1628 793.0374,-110.05 796.4897,-116.1395"/>
+<g id="edge20" class="edge"><title>14->7</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M674.898,-143.876C689.407,-134.808 707.416,-123.552 723.085,-113.759"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="725.371,-116.458 731.996,-108.19 721.661,-110.522 725.371,-116.458"/>
</g>
<!-- 15 -->
-<g id="node16" class="node">
-<title>15</title>
-<path fill="none" stroke="#569ad8" stroke-width="2" d="M981.5,-180C981.5,-180 845.5,-180 845.5,-180 839.5,-180 833.5,-174 833.5,-168 833.5,-168 833.5,-156 833.5,-156 833.5,-150 839.5,-144 845.5,-144 845.5,-144 981.5,-144 981.5,-144 987.5,-144 993.5,-150 993.5,-156 993.5,-156 993.5,-168 993.5,-168 993.5,-174 987.5,-180 981.5,-180"/>
-<text text-anchor="middle" x="913.5" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">extract_transcripts_as_bed12</text>
+<g id="node16" class="node"><title>15</title>
+<path fill="none" stroke="#56d8c9" stroke-width="2" d="M894,-180C894,-180 773,-180 773,-180 767,-180 761,-174 761,-168 761,-168 761,-156 761,-156 761,-150 767,-144 773,-144 773,-144 894,-144 894,-144 900,-144 906,-150 906,-156 906,-156 906,-168 906,-168 906,-174 900,-180 894,-180"/>
+<text text-anchor="middle" x="833.5" y="-159.5" font-family="sans" font-size="10.00">extract_transcripts_as_bed12</text>
</g>
<!-- 15->7 -->
-<g id="edge18" class="edge">
-<title>15->7</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M893.8173,-143.8314C884.3949,-135.1337 872.9599,-124.5783 862.7204,-115.1265"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="864.8984,-112.3738 855.1764,-108.1628 860.1505,-117.5175 864.8984,-112.3738"/>
+<g id="edge18" class="edge"><title>15->7</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M815.208,-143.697C806.067,-135.05 794.86,-124.449 784.9,-115.027"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="787.252,-112.434 777.582,-108.104 782.441,-117.519 787.252,-112.434"/>
</g>
<!-- 16 -->
-<g id="node17" class="node">
-<title>16</title>
-<path fill="none" stroke="#56d86b" stroke-width="2" d="M1195.5,-180C1195.5,-180 1023.5,-180 1023.5,-180 1017.5,-180 1011.5,-174 1011.5,-168 1011.5,-168 1011.5,-156 1011.5,-156 1011.5,-150 1017.5,-144 1023.5,-144 1023.5,-144 1195.5,-144 1195.5,-144 1201.5,-144 1207.5,-150 1207.5,-156 1207.5,-156 1207.5,-168 1207.5,-168 1207.5,-174 1201.5,-180 1195.5,-180"/>
-<text text-anchor="middle" x="1109.5" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">index_genomic_alignment_samtools</text>
+<g id="node17" class="node"><title>16</title>
+<path fill="none" stroke="#59d856" stroke-width="2" d="M1086.5,-180C1086.5,-180 936.5,-180 936.5,-180 930.5,-180 924.5,-174 924.5,-168 924.5,-168 924.5,-156 924.5,-156 924.5,-150 930.5,-144 936.5,-144 936.5,-144 1086.5,-144 1086.5,-144 1092.5,-144 1098.5,-150 1098.5,-156 1098.5,-156 1098.5,-168 1098.5,-168 1098.5,-174 1092.5,-180 1086.5,-180"/>
+<text text-anchor="middle" x="1011.5" y="-159.5" font-family="sans" font-size="10.00">index_genomic_alignment_samtools</text>
</g>
<!-- 16->7 -->
-<g id="edge20" class="edge">
-<title>16->7</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1040.7119,-143.9243C999.1793,-133.0106 946.4177,-119.1463 904.7944,-108.2087"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="905.5712,-104.7941 895.01,-105.6377 903.7921,-111.5643 905.5712,-104.7941"/>
+<g id="edge19" class="edge"><title>16->7</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M950.176,-143.966C912.596,-133.527 864.484,-120.162 825.992,-109.47"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="826.489,-105.976 815.917,-106.671 824.615,-112.72 826.489,-105.976"/>
</g>
<!-- 17 -->
-<g id="node18" class="node">
-<title>17</title>
-<path fill="none" stroke="#5682d8" stroke-width="2" d="M475,-396C475,-396 332,-396 332,-396 326,-396 320,-390 320,-384 320,-384 320,-372 320,-372 320,-366 326,-360 332,-360 332,-360 475,-360 475,-360 481,-360 487,-366 487,-372 487,-372 487,-384 487,-384 487,-390 481,-396 475,-396"/>
-<text text-anchor="middle" x="403.5" y="-375.5" font-family="sans" font-size="10.00" fill="#000000">pe_remove_adapters_cutadapt</text>
+<g id="node18" class="node"><title>17</title>
+<path fill="none" stroke="#d8b456" stroke-width="2" d="M431.5,-396C431.5,-396 305.5,-396 305.5,-396 299.5,-396 293.5,-390 293.5,-384 293.5,-384 293.5,-372 293.5,-372 293.5,-366 299.5,-360 305.5,-360 305.5,-360 431.5,-360 431.5,-360 437.5,-360 443.5,-366 443.5,-372 443.5,-372 443.5,-384 443.5,-384 443.5,-390 437.5,-396 431.5,-396"/>
+<text text-anchor="middle" x="368.5" y="-375.5" font-family="sans" font-size="10.00">pe_remove_adapters_cutadapt</text>
</g>
<!-- 17->10 -->
-<g id="edge25" class="edge">
-<title>17->10</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M403.5,-359.8314C403.5,-352.131 403.5,-342.9743 403.5,-334.4166"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="407.0001,-334.4132 403.5,-324.4133 400.0001,-334.4133 407.0001,-334.4132"/>
+<g id="edge25" class="edge"><title>17->10</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M368.5,-359.697C368.5,-351.983 368.5,-342.712 368.5,-334.112"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="372,-334.104 368.5,-324.104 365,-334.104 372,-334.104"/>
</g>
<!-- 18 -->
-<g id="node19" class="node">
-<title>18</title>
-<path fill="none" stroke="#ced856" stroke-width="2" d="M644.5,-396C644.5,-396 518.5,-396 518.5,-396 512.5,-396 506.5,-390 506.5,-384 506.5,-384 506.5,-372 506.5,-372 506.5,-366 512.5,-360 518.5,-360 518.5,-360 644.5,-360 644.5,-360 650.5,-360 656.5,-366 656.5,-372 656.5,-372 656.5,-384 656.5,-384 656.5,-390 650.5,-396 644.5,-396"/>
-<text text-anchor="middle" x="581.5" y="-375.5" font-family="sans" font-size="10.00" fill="#000000">remove_adapters_cutadapt</text>
+<g id="node19" class="node"><title>18</title>
+<path fill="none" stroke="#b6d856" stroke-width="2" d="M589.5,-396C589.5,-396 479.5,-396 479.5,-396 473.5,-396 467.5,-390 467.5,-384 467.5,-384 467.5,-372 467.5,-372 467.5,-366 473.5,-360 479.5,-360 479.5,-360 589.5,-360 589.5,-360 595.5,-360 601.5,-366 601.5,-372 601.5,-372 601.5,-384 601.5,-384 601.5,-390 595.5,-396 589.5,-396"/>
+<text text-anchor="middle" x="534.5" y="-375.5" font-family="sans" font-size="10.00">remove_adapters_cutadapt</text>
</g>
<!-- 18->12 -->
-<g id="edge26" class="edge">
-<title>18->12</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M581.5,-359.8314C581.5,-352.131 581.5,-342.9743 581.5,-334.4166"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="585.0001,-334.4132 581.5,-324.4133 578.0001,-334.4133 585.0001,-334.4132"/>
+<g id="edge26" class="edge"><title>18->12</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M534.5,-359.697C534.5,-351.983 534.5,-342.712 534.5,-334.112"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="538,-334.104 534.5,-324.104 531,-334.104 538,-334.104"/>
</g>
<!-- 19->14 -->
-<g id="edge27" class="edge">
-<title>19->14</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M704.0141,-215.8314C704.6558,-208.131 705.4188,-198.9743 706.1319,-190.4166"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="709.6229,-190.6694 706.9656,-180.4133 702.6471,-190.088 709.6229,-190.6694"/>
+<g id="edge27" class="edge"><title>19->14</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M647.5,-215.697C647.5,-207.983 647.5,-198.712 647.5,-190.112"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="651,-190.104 647.5,-180.104 644,-190.104 651,-190.104"/>
</g>
<!-- 20->16 -->
-<g id="edge28" class="edge">
-<title>20->16</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M890.1103,-219.861C930.4003,-209.2351 986.1963,-194.5197 1031.4359,-182.5883"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1032.4367,-185.9441 1041.2135,-180.0096 1030.6515,-179.1756 1032.4367,-185.9441"/>
+<g id="edge28" class="edge"><title>20->16</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M819.27,-218.834C854.773,-208.522 903.337,-194.417 942.769,-182.963"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="943.956,-186.263 952.583,-180.113 942.004,-179.541 943.956,-186.263"/>
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<!-- 21 -->
-<g id="node22" class="node">
-<title>21</title>
-<path fill="none" stroke="#88d856" stroke-width="2" d="M770.5,-324C770.5,-324 690.5,-324 690.5,-324 684.5,-324 678.5,-318 678.5,-312 678.5,-312 678.5,-300 678.5,-300 678.5,-294 684.5,-288 690.5,-288 690.5,-288 770.5,-288 770.5,-288 776.5,-288 782.5,-294 782.5,-300 782.5,-300 782.5,-312 782.5,-312 782.5,-318 776.5,-324 770.5,-324"/>
-<text text-anchor="middle" x="730.5" y="-303.5" font-family="sans" font-size="10.00" fill="#000000">create_index_star</text>
+<g id="node22" class="node"><title>21</title>
+<path fill="none" stroke="#d89c56" stroke-width="2" d="M736.5,-324C736.5,-324 666.5,-324 666.5,-324 660.5,-324 654.5,-318 654.5,-312 654.5,-312 654.5,-300 654.5,-300 654.5,-294 660.5,-288 666.5,-288 666.5,-288 736.5,-288 736.5,-288 742.5,-288 748.5,-294 748.5,-300 748.5,-300 748.5,-312 748.5,-312 748.5,-318 742.5,-324 736.5,-324"/>
+<text text-anchor="middle" x="701.5" y="-303.5" font-family="sans" font-size="10.00">create_index_star</text>
</g>
<!-- 21->19 -->
-<g id="edge30" class="edge">
-<title>21->19</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M723.4344,-287.8314C720.374,-279.9617 716.7221,-270.5712 713.3318,-261.8533"/>
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+<g id="edge30" class="edge"><title>21->19</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M688.152,-287.697C681.743,-279.389 673.942,-269.277 666.894,-260.141"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="669.574,-257.884 660.695,-252.104 664.032,-262.16 669.574,-257.884"/>
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<!-- 21->20 -->
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-<title>21->20</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M757.2483,-287.8314C770.5553,-278.7927 786.816,-267.7476 801.1375,-258.0198"/>
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+<g id="edge32" class="edge"><title>21->20</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M718.556,-287.697C726.995,-279.135 737.325,-268.656 746.543,-259.304"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="749.113,-261.683 753.64,-252.104 744.127,-256.769 749.113,-261.683"/>
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</g>
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diff --git a/install/environment.dev.yml b/install/environment.dev.yml
index 54f012ec84b04ff7a9546e778c38e4bddf44e9fa..ea44dfbcfb7f02409682d231014e528c2845cb83 100644
--- a/install/environment.dev.yml
+++ b/install/environment.dev.yml
@@ -8,6 +8,7 @@ dependencies:
- unzip=6.0
- pip=20.0.2
- pip:
+ - pandas==1.0.1
- biopython==1.76
- labkey==1.2.0