diff --git a/Snakefile b/Snakefile
index ae56321599dbb0283c27afefc0359345aef8ae5a..275397284f5aa858c69186113ecf0496f29b3e8f 100644
--- a/Snakefile
+++ b/Snakefile
@@ -57,7 +57,6 @@ rule finish:
sample=pd.unique(samples_table.index.values),
strand=["plus", "minus"],
unique_type=["Unique", "UniqueMultiple"]),
-
salmon_merge_genes = expand(
os.path.join(
config["output_dir"],
@@ -65,7 +64,6 @@ rule finish:
"quantmerge",
"genes_{salmon_merge_on}.tsv"),
salmon_merge_on=["tpm", "numreads"]),
-
salmon_merge_transcripts = expand(
os.path.join(
config["output_dir"],
@@ -73,6 +71,14 @@ rule finish:
"quantmerge",
"transcripts_{salmon_merge_on}.tsv"),
salmon_merge_on=["tpm", "numreads"]),
+ kallisto_merge_transcripts = os.path.join(
+ config["output_dir"],
+ "summary_kallisto",
+ "transcripts_tpm.tsv"),
+ kallisto_merge_genes = os.path.join(
+ config["output_dir"],
+ "summary_kallisto",
+ "genes_tpm.tsv")
rule start:
@@ -707,7 +713,7 @@ rule salmon_quantmerge_genes:
rule salmon_quantmerge_transcripts:
'''
- Merge gene quantifications into a single file
+ Merge transcript quantifications into a single file
'''
input:
salmon_in = expand(
@@ -774,6 +780,137 @@ rule salmon_quantmerge_transcripts:
1> {log.stdout} 2> {log.stderr}"
+rule kallisto_merge_genes:
+ '''
+ Merge gene quantifications into single file
+ '''
+ input:
+ pseudoalignment = expand(
+ os.path.join(
+ config["output_dir"],
+ "samples",
+ "{sample}",
+ "quant_kallisto",
+ "{sample}.{seqmode}.kallisto.pseudo.sam"),
+ zip,
+ sample=[i for i in pd.unique(samples_table.index.values)],
+ seqmode=[get_sample(
+ 'seqmode',
+ search_id='index',
+ search_value=i)
+ for i in pd.unique(samples_table.index.values)]),
+ gtf = get_sample('gtf')
+
+ output:
+ gn_out = os.path.join(
+ config["output_dir"],
+ "summary_kallisto",
+ "genes_tpm.tsv")
+
+ params:
+ dir_out = os.path.join(
+ config["output_dir"],
+ "summary_kallisto"),
+ tables = ','.join(expand(
+ os.path.join(
+ config["output_dir"],
+ "samples",
+ "{sample}",
+ "quant_kallisto",
+ "abundance.h5"),
+ sample=[i for i in pd.unique(samples_table.index.values)])),
+ sample_name_list = ','.join(expand(
+ "{sample}",
+ sample=pd.unique(samples_table.index.values))),
+
+ log:
+ stderr = os.path.join(
+ config["log_dir"],
+ "kallisto_merge_genes.stderr.log"),
+ stdout = os.path.join(
+ config["log_dir"],
+ "kallisto_merge_genes.stdout.log")
+
+ threads: 1
+
+ singularity:
+ "docker://zavolab/merge_kallisto:0.6"
+
+ shell:
+ "(merge_kallisto.R \
+ --input {params.tables} \
+ --names {params.sample_name_list} \
+ --txOut FALSE \
+ --anno {input.gtf} \
+ --output {params.dir_out} \
+ --verbose) \
+ 1> {log.stdout} 2> {log.stderr}"
+
+
+rule kallisto_merge_transcripts:
+ '''
+ Merge transcript quantifications into a single files
+ '''
+ input:
+ pseudoalignment = expand(
+ os.path.join(
+ config["output_dir"],
+ "samples",
+ "{sample}",
+ "quant_kallisto",
+ "{sample}.{seqmode}.kallisto.pseudo.sam"),
+ zip,
+ sample=[i for i in pd.unique(samples_table.index.values)],
+ seqmode=[get_sample(
+ 'seqmode',
+ search_id='index',
+ search_value=i)
+ for i in pd.unique(samples_table.index.values)]),
+
+ output:
+ tx_out = os.path.join(
+ config["output_dir"],
+ "summary_kallisto",
+ "transcripts_tpm.tsv")
+
+ params:
+ dir_out = os.path.join(
+ config["output_dir"],
+ "summary_kallisto"),
+ tables = ','.join(expand(
+ os.path.join(
+ config["output_dir"],
+ "samples",
+ "{sample}",
+ "quant_kallisto",
+ "abundance.h5"),
+ sample=[i for i in pd.unique(samples_table.index.values)])),
+ sample_name_list = ','.join(expand(
+ "{sample}",
+ sample=pd.unique(samples_table.index.values))),
+
+ log:
+ stderr = os.path.join(
+ config["log_dir"],
+ "kallisto_merge_transcripts.stderr.log"),
+ stdout = os.path.join(
+ config["log_dir"],
+ "kallisto_merge_transcripts.stdout.log")
+
+ threads: 1
+
+ singularity:
+ "docker://zavolab/merge_kallisto:0.6"
+
+ shell:
+ "(merge_kallisto.R \
+ --input {params.tables} \
+ --names {params.sample_name_list} \
+ --output {params.dir_out} \
+ --verbose) \
+ 1> {log.stdout} 2> {log.stderr}"
+
+
rule star_rpm:
'''
Create stranded bedgraph coverage with STARs RPM normalisation
diff --git a/images/rule_graph.svg b/images/rule_graph.svg
index 79aa7491895e5db0636051a228a40e58c7a6d062..3cb5d62265295574e6b130bf12683c9e82cdd434 100644
--- a/images/rule_graph.svg
+++ b/images/rule_graph.svg
@@ -4,550 +4,598 @@
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+<g id="edge8" class="edge">
<title>8->1</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M229.8968,-215.9479C222.6638,-205.8743 214.2869,-192.8047 209,-180 200.7977,-160.1341 195.9684,-136.2814 193.2325,-118.1244"/>
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+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M611.6646,-143.8314C635.6385,-134.0792 665.354,-121.9916 690.5493,-111.7427"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="692.0187,-114.9235 699.9629,-107.9134 689.3811,-108.4394 692.0187,-114.9235"/>
+</g>
+<!-- 8->5 -->
+<g id="edge19" class="edge">
+<title>8->5</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M561.4485,-143.8314C559.0697,-136.0463 556.2362,-126.7729 553.5967,-118.1347"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="556.8958,-116.954 550.6263,-108.4133 550.2013,-118.9996 556.8958,-116.954"/>
+</g>
+<!-- 8->6 -->
+<g id="edge21" class="edge">
+<title>8->6</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M522.8401,-143.8314C499.2268,-134.1162 469.9798,-122.0831 445.13,-111.8592"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="446.4219,-108.6061 435.8423,-108.038 443.7585,-115.0797 446.4219,-108.6061"/>
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<!-- 9 -->
<g id="node10" class="node">
<title>9</title>
-<path fill="none" stroke="#56a2d8" stroke-width="2" d="M317.5,-180C317.5,-180 230.5,-180 230.5,-180 224.5,-180 218.5,-174 218.5,-168 218.5,-168 218.5,-156 218.5,-156 218.5,-150 224.5,-144 230.5,-144 230.5,-144 317.5,-144 317.5,-144 323.5,-144 329.5,-150 329.5,-156 329.5,-156 329.5,-168 329.5,-168 329.5,-174 323.5,-180 317.5,-180"/>
-<text text-anchor="middle" x="274" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">alfa_concat_results</text>
+<path fill="none" stroke="#5682d8" stroke-width="2" d="M443,-180C443,-180 297,-180 297,-180 291,-180 285,-174 285,-168 285,-168 285,-156 285,-156 285,-150 291,-144 297,-144 297,-144 443,-144 443,-144 449,-144 455,-150 455,-156 455,-156 455,-168 455,-168 455,-174 449,-180 443,-180"/>
+<text text-anchor="middle" x="370" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">genome_quantification_kallisto</text>
</g>
<!-- 9->1 -->
-<g id="edge7" class="edge">
+<g id="edge12" class="edge">
<title>9->1</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M252.8033,-143.8314C242.5566,-135.0485 230.0997,-124.3712 218.9903,-114.8489"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="221.0603,-112.0134 211.19,-108.1628 216.5048,-117.3282 221.0603,-112.0134"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M455.3344,-145.572C527.4246,-131.6937 628.4768,-112.2398 689.9122,-100.4126"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="690.6344,-103.838 699.7924,-98.5106 689.311,-96.9642 690.6344,-103.838"/>
+</g>
+<!-- 9->5 -->
+<g id="edge20" class="edge">
+<title>9->5</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M414.1599,-143.8314C437.7732,-134.1162 467.0202,-122.0831 491.87,-111.8592"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="493.2415,-115.0797 501.1577,-108.038 490.5781,-108.6061 493.2415,-115.0797"/>
+</g>
+<!-- 9->6 -->
+<g id="edge22" class="edge">
+<title>9->6</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M375.5515,-143.8314C377.9303,-136.0463 380.7638,-126.7729 383.4033,-118.1347"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="386.7987,-118.9996 386.3737,-108.4133 380.1042,-116.954 386.7987,-118.9996"/>
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<!-- 10 -->
<g id="node11" class="node">
<title>10</title>
-<path fill="none" stroke="#5682d8" stroke-width="2" d="M466.5,-180C466.5,-180 359.5,-180 359.5,-180 353.5,-180 347.5,-174 347.5,-168 347.5,-168 347.5,-156 347.5,-156 347.5,-150 353.5,-144 359.5,-144 359.5,-144 466.5,-144 466.5,-144 472.5,-144 478.5,-150 478.5,-156 478.5,-156 478.5,-168 478.5,-168 478.5,-174 472.5,-180 466.5,-180"/>
-<text text-anchor="middle" x="413" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">prepare_multiqc_config</text>
+<path fill="none" stroke="#88d856" stroke-width="2" d="M835,-324C835,-324 765,-324 765,-324 759,-324 753,-318 753,-312 753,-312 753,-300 753,-300 753,-294 759,-288 765,-288 765,-288 835,-288 835,-288 841,-288 847,-294 847,-300 847,-300 847,-312 847,-312 847,-318 841,-324 835,-324"/>
+<text text-anchor="middle" x="800" y="-303.5" font-family="sans" font-size="10.00" fill="#000000">plot_TIN_scores</text>
</g>
<!-- 10->1 -->
-<g id="edge8" class="edge">
+<g id="edge11" class="edge">
<title>10->1</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M357.0155,-143.9243C322.3749,-132.7399 278.1361,-118.4565 243.8922,-107.4002"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="244.654,-103.9683 234.0623,-104.2264 242.5032,-110.6297 244.654,-103.9683"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M808.447,-287.8113C821.6472,-256.5398 843.2711,-191.3829 819,-144 812.763,-131.8238 802.3605,-121.7682 791.2593,-113.7713"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="792.9527,-110.6937 782.6914,-108.0563 789.0684,-116.5171 792.9527,-110.6937"/>
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<!-- 11 -->
<g id="node12" class="node">
<title>11</title>
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-<text text-anchor="middle" x="656" y="-303.5" font-family="sans" font-size="10.00" fill="#000000">sort_bed_4_big</text>
+<path fill="none" stroke="#d87556" stroke-width="2" d="M966.5,-180C966.5,-180 879.5,-180 879.5,-180 873.5,-180 867.5,-174 867.5,-168 867.5,-168 867.5,-156 867.5,-156 867.5,-150 873.5,-144 879.5,-144 879.5,-144 966.5,-144 966.5,-144 972.5,-144 978.5,-150 978.5,-156 978.5,-156 978.5,-168 978.5,-168 978.5,-174 972.5,-180 966.5,-180"/>
+<text text-anchor="middle" x="923" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">alfa_concat_results</text>
</g>
-<!-- 11->2 -->
-<g id="edge12" class="edge">
-<title>11->2</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M683.5053,-287.8314C697.318,-278.7074 714.2256,-267.539 729.0529,-257.7449"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="731.0886,-260.5949 737.5035,-252.1628 727.2304,-254.7541 731.0886,-260.5949"/>
+<!-- 11->1 -->
+<g id="edge7" class="edge">
+<title>11->1</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M877.8307,-143.8314C853.4941,-134.0423 823.3069,-121.9 797.7653,-111.6263"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="798.8094,-108.2738 788.2257,-107.7891 796.1971,-114.7681 798.8094,-108.2738"/>
</g>
<!-- 12 -->
<g id="node13" class="node">
<title>12</title>
-<path fill="none" stroke="#56d8c9" stroke-width="2" d="M791,-684C791,-684 711,-684 711,-684 705,-684 699,-678 699,-672 699,-672 699,-660 699,-660 699,-654 705,-648 711,-648 711,-648 791,-648 791,-648 797,-648 803,-654 803,-660 803,-660 803,-672 803,-672 803,-678 797,-684 791,-684"/>
-<text text-anchor="middle" x="751" y="-663.5" font-family="sans" font-size="10.00" fill="#000000">create_index_star</text>
-</g>
-<!-- 12->2 -->
-<g id="edge11" class="edge">
-<title>12->2</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M753.9008,-647.8696C758.0015,-620.6233 765,-567.4634 765,-522 765,-522 765,-522 765,-378 765,-337.876 765,-291.4631 765,-262.4177"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="768.5001,-262.1853 765,-252.1854 761.5001,-262.1854 768.5001,-262.1853"/>
-</g>
-<!-- 22 -->
-<g id="node23" class="node">
-<title>22</title>
-<path fill="none" stroke="#56d85b" stroke-width="2" d="M978.5,-612C978.5,-612 881.5,-612 881.5,-612 875.5,-612 869.5,-606 869.5,-600 869.5,-600 869.5,-588 869.5,-588 869.5,-582 875.5,-576 881.5,-576 881.5,-576 978.5,-576 978.5,-576 984.5,-576 990.5,-582 990.5,-588 990.5,-588 990.5,-600 990.5,-600 990.5,-606 984.5,-612 978.5,-612"/>
-<text text-anchor="middle" x="930" y="-591.5" font-family="sans" font-size="10.00" fill="#000000">create_index_salmon</text>
-</g>
-<!-- 12->22 -->
-<g id="edge35" class="edge">
-<title>12->22</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M796.1693,-647.8314C820.3223,-638.1162 850.2378,-626.0831 875.6556,-615.8592"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="877.1841,-619.017 885.1556,-612.038 874.5718,-612.5227 877.1841,-619.017"/>
-</g>
-<!-- 30 -->
-<g id="node31" class="node">
-<title>30</title>
-<path fill="none" stroke="#88d856" stroke-width="2" d="M549.5,-612C549.5,-612 448.5,-612 448.5,-612 442.5,-612 436.5,-606 436.5,-600 436.5,-600 436.5,-588 436.5,-588 436.5,-582 442.5,-576 448.5,-576 448.5,-576 549.5,-576 549.5,-576 555.5,-576 561.5,-582 561.5,-588 561.5,-588 561.5,-600 561.5,-600 561.5,-606 555.5,-612 549.5,-612"/>
-<text text-anchor="middle" x="499" y="-591.5" font-family="sans" font-size="10.00" fill="#000000">pe_map_genome_star</text>
-</g>
-<!-- 12->30 -->
-<g id="edge50" class="edge">
-<title>12->30</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M698.768,-650.5447C695.8027,-649.6805 692.8641,-648.8274 690,-648 650.9637,-636.7227 607.3664,-624.3778 571.6913,-614.3413"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="572.4237,-610.9115 561.8496,-611.5745 570.5292,-617.6503 572.4237,-610.9115"/>
-</g>
-<!-- 33 -->
-<g id="node34" class="node">
-<title>33</title>
-<path fill="none" stroke="#56c1d8" stroke-width="2" d="M674.5,-612C674.5,-612 591.5,-612 591.5,-612 585.5,-612 579.5,-606 579.5,-600 579.5,-600 579.5,-588 579.5,-588 579.5,-582 585.5,-576 591.5,-576 591.5,-576 674.5,-576 674.5,-576 680.5,-576 686.5,-582 686.5,-588 686.5,-588 686.5,-600 686.5,-600 686.5,-606 680.5,-612 674.5,-612"/>
-<text text-anchor="middle" x="633" y="-591.5" font-family="sans" font-size="10.00" fill="#000000">map_genome_star</text>
-</g>
-<!-- 12->33 -->
-<g id="edge53" class="edge">
-<title>12->33</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M721.2236,-647.8314C706.1307,-638.6221 687.6243,-627.3301 671.4657,-617.4706"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="673.1263,-614.3838 662.7669,-612.1628 669.4802,-620.3593 673.1263,-614.3838"/>
-</g>
-<!-- 34 -->
-<g id="node35" class="node">
-<title>34</title>
-<path fill="none" stroke="#d89556" stroke-width="2" d="M725,-396C725,-396 633,-396 633,-396 627,-396 621,-390 621,-384 621,-384 621,-372 621,-372 621,-366 627,-360 633,-360 633,-360 725,-360 725,-360 731,-360 737,-366 737,-372 737,-372 737,-384 737,-384 737,-390 731,-396 725,-396"/>
-<text text-anchor="middle" x="679" y="-375.5" font-family="sans" font-size="10.00" fill="#000000">generate_alfa_index</text>
+<path fill="none" stroke="#56d86b" stroke-width="2" d="M797.5,-180C797.5,-180 690.5,-180 690.5,-180 684.5,-180 678.5,-174 678.5,-168 678.5,-168 678.5,-156 678.5,-156 678.5,-150 684.5,-144 690.5,-144 690.5,-144 797.5,-144 797.5,-144 803.5,-144 809.5,-150 809.5,-156 809.5,-156 809.5,-168 809.5,-168 809.5,-174 803.5,-180 797.5,-180"/>
+<text text-anchor="middle" x="744" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">prepare_multiqc_config</text>
</g>
-<!-- 12->34 -->
-<g id="edge55" class="edge">
-<title>12->34</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M746.4961,-647.9843C734.3235,-599.2939 700.699,-464.7961 686.0143,-406.0573"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="689.3231,-404.8614 683.5022,-396.0089 682.5321,-406.5592 689.3231,-404.8614"/>
+<!-- 12->1 -->
+<g id="edge9" class="edge">
+<title>12->1</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M744,-143.8314C744,-136.131 744,-126.9743 744,-118.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="747.5001,-118.4132 744,-108.4133 740.5001,-118.4133 747.5001,-118.4132"/>
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<!-- 13 -->
<g id="node14" class="node">
<title>13</title>
-<path fill="none" stroke="#56d0d8" stroke-width="2" d="M926,-540C926,-540 808,-540 808,-540 802,-540 796,-534 796,-528 796,-528 796,-516 796,-516 796,-510 802,-504 808,-504 808,-504 926,-504 926,-504 932,-504 938,-510 938,-516 938,-516 938,-528 938,-528 938,-534 932,-540 926,-540"/>
-<text text-anchor="middle" x="867" y="-519.5" font-family="sans" font-size="10.00" fill="#000000">pe_quantification_salmon</text>
-</g>
-<!-- 13->3 -->
-<g id="edge14" class="edge">
-<title>13->3</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M867.5047,-503.8314C867.7186,-496.131 867.9729,-486.9743 868.2106,-478.4166"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="871.7094,-478.5066 868.4885,-468.4133 864.7121,-478.3122 871.7094,-478.5066"/>
+<path fill="none" stroke="#78d856" stroke-width="2" d="M1093,-324C1093,-324 1027,-324 1027,-324 1021,-324 1015,-318 1015,-312 1015,-312 1015,-300 1015,-300 1015,-294 1021,-288 1027,-288 1027,-288 1093,-288 1093,-288 1099,-288 1105,-294 1105,-300 1105,-300 1105,-312 1105,-312 1105,-318 1099,-324 1093,-324"/>
+<text text-anchor="middle" x="1060" y="-303.5" font-family="sans" font-size="10.00" fill="#000000">sort_bed_4_big</text>
</g>
-<!-- 13->4 -->
-<g id="edge16" class="edge">
-<title>13->4</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M913.1786,-503.8314C937.9801,-494.0734 968.725,-481.977 994.7843,-471.7242"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="996.1292,-474.9563 1004.1534,-468.038 993.5663,-468.4423 996.1292,-474.9563"/>
+<!-- 13->2 -->
+<g id="edge13" class="edge">
+<title>13->2</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1072.6171,-287.8314C1078.3172,-279.6232 1085.1663,-269.7606 1091.4359,-260.7323"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1094.3838,-262.6234 1097.213,-252.4133 1088.6342,-258.6306 1094.3838,-262.6234"/>
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<!-- 14 -->
<g id="node15" class="node">
<title>14</title>
-<path fill="none" stroke="#c6d856" stroke-width="2" d="M1069.5,-540C1069.5,-540 968.5,-540 968.5,-540 962.5,-540 956.5,-534 956.5,-528 956.5,-528 956.5,-516 956.5,-516 956.5,-510 962.5,-504 968.5,-504 968.5,-504 1069.5,-504 1069.5,-504 1075.5,-504 1081.5,-510 1081.5,-516 1081.5,-516 1081.5,-528 1081.5,-528 1081.5,-534 1075.5,-540 1069.5,-540"/>
-<text text-anchor="middle" x="1019" y="-519.5" font-family="sans" font-size="10.00" fill="#000000">quantification_salmon</text>
+<path fill="none" stroke="#5663d8" stroke-width="2" d="M985,-684C985,-684 905,-684 905,-684 899,-684 893,-678 893,-672 893,-672 893,-660 893,-660 893,-654 899,-648 905,-648 905,-648 985,-648 985,-648 991,-648 997,-654 997,-660 997,-660 997,-672 997,-672 997,-678 991,-684 985,-684"/>
+<text text-anchor="middle" x="945" y="-663.5" font-family="sans" font-size="10.00" fill="#000000">create_index_star</text>
</g>
-<!-- 14->3 -->
-<g id="edge13" class="edge">
-<title>14->3</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M981.1487,-503.8314C961.2654,-494.2874 936.7218,-482.5065 915.6695,-472.4013"/>
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+<!-- 14->2 -->
+<g id="edge14" class="edge">
+<title>14->2</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M997.02,-653.2739C1056.8712,-635.1562 1147,-595.6465 1147,-522 1147,-522 1147,-522 1147,-378 1147,-336.4385 1132.3628,-290.1923 1121.501,-261.5961"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1124.7492,-260.2919 1117.8467,-252.254 1118.2302,-262.8419 1124.7492,-260.2919"/>
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-<!-- 14->4 -->
-<g id="edge15" class="edge">
-<title>14->4</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1026.8226,-503.8314C1030.2109,-495.9617 1034.2541,-486.5712 1038.0076,-477.8533"/>
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+<!-- 24 -->
+<g id="node25" class="node">
+<title>24</title>
+<path fill="none" stroke="#569ad8" stroke-width="2" d="M297.5,-612C297.5,-612 200.5,-612 200.5,-612 194.5,-612 188.5,-606 188.5,-600 188.5,-600 188.5,-588 188.5,-588 188.5,-582 194.5,-576 200.5,-576 200.5,-576 297.5,-576 297.5,-576 303.5,-576 309.5,-582 309.5,-588 309.5,-588 309.5,-600 309.5,-600 309.5,-606 303.5,-612 297.5,-612"/>
+<text text-anchor="middle" x="249" y="-591.5" font-family="sans" font-size="10.00" fill="#000000">create_index_salmon</text>
+</g>
+<!-- 14->24 -->
+<g id="edge42" class="edge">
+<title>14->24</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M892.9715,-660.6177C769.7407,-647.8697 459.9154,-615.8188 319.7851,-601.3226"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="319.8963,-597.8155 309.5892,-600.2678 319.1759,-604.7783 319.8963,-597.8155"/>
+</g>
+<!-- 32 -->
+<g id="node33" class="node">
+<title>32</title>
+<path fill="none" stroke="#d8bc56" stroke-width="2" d="M995.5,-612C995.5,-612 894.5,-612 894.5,-612 888.5,-612 882.5,-606 882.5,-600 882.5,-600 882.5,-588 882.5,-588 882.5,-582 888.5,-576 894.5,-576 894.5,-576 995.5,-576 995.5,-576 1001.5,-576 1007.5,-582 1007.5,-588 1007.5,-588 1007.5,-600 1007.5,-600 1007.5,-606 1001.5,-612 995.5,-612"/>
+<text text-anchor="middle" x="945" y="-591.5" font-family="sans" font-size="10.00" fill="#000000">pe_map_genome_star</text>
+</g>
+<!-- 14->32 -->
+<g id="edge56" class="edge">
+<title>14->32</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M945,-647.8314C945,-640.131 945,-630.9743 945,-622.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="948.5001,-622.4132 945,-612.4133 941.5001,-622.4133 948.5001,-622.4132"/>
+</g>
+<!-- 35 -->
+<g id="node36" class="node">
+<title>35</title>
+<path fill="none" stroke="#56d8d0" stroke-width="2" d="M852.5,-612C852.5,-612 769.5,-612 769.5,-612 763.5,-612 757.5,-606 757.5,-600 757.5,-600 757.5,-588 757.5,-588 757.5,-582 763.5,-576 769.5,-576 769.5,-576 852.5,-576 852.5,-576 858.5,-576 864.5,-582 864.5,-588 864.5,-588 864.5,-600 864.5,-600 864.5,-606 858.5,-612 852.5,-612"/>
+<text text-anchor="middle" x="811" y="-591.5" font-family="sans" font-size="10.00" fill="#000000">map_genome_star</text>
+</g>
+<!-- 14->35 -->
+<g id="edge60" class="edge">
+<title>14->35</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M911.1861,-647.8314C893.7293,-638.4516 872.2513,-626.9112 853.6648,-616.9244"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="855.2686,-613.8129 844.803,-612.1628 851.9554,-619.9792 855.2686,-613.8129"/>
+</g>
+<!-- 36 -->
+<g id="node37" class="node">
+<title>36</title>
+<path fill="none" stroke="#56d8b1" stroke-width="2" d="M943,-396C943,-396 851,-396 851,-396 845,-396 839,-390 839,-384 839,-384 839,-372 839,-372 839,-366 845,-360 851,-360 851,-360 943,-360 943,-360 949,-360 955,-366 955,-372 955,-372 955,-384 955,-384 955,-390 949,-396 943,-396"/>
+<text text-anchor="middle" x="897" y="-375.5" font-family="sans" font-size="10.00" fill="#000000">generate_alfa_index</text>
+</g>
+<!-- 14->36 -->
+<g id="edge61" class="edge">
+<title>14->36</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M973.2988,-647.8492C987.2857,-638.1424 1003.9233,-625.4374 1017,-612 1054.0212,-573.9578 1079.6148,-555.7965 1068,-504 1060.2568,-469.469 1059.832,-456.1879 1034,-432 1023.1018,-421.7955 993.631,-409.6621 964.8031,-399.4839"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="965.6739,-396.0815 955.0791,-396.1128 963.381,-402.6953 965.6739,-396.0815"/>
</g>
<!-- 15 -->
<g id="node16" class="node">
<title>15</title>
-<path fill="none" stroke="#56b1d8" stroke-width="2" d="M309,-828C309,-828 279,-828 279,-828 273,-828 267,-822 267,-816 267,-816 267,-804 267,-804 267,-798 273,-792 279,-792 279,-792 309,-792 309,-792 315,-792 321,-798 321,-804 321,-804 321,-816 321,-816 321,-822 315,-828 309,-828"/>
-<text text-anchor="middle" x="294" y="-807.5" font-family="sans" font-size="10.00" fill="#000000">start</text>
-</g>
-<!-- 15->5 -->
-<g id="edge17" class="edge">
-<title>15->5</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M266.9948,-808.5749C196.9765,-803.2851 15,-778.6966 15,-666 15,-666 15,-666 15,-522 15,-481.7369 19.7166,-435.3594 23.2358,-406.3596"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="26.7452,-406.5021 24.5136,-396.145 19.7993,-405.6332 26.7452,-406.5021"/>
+<path fill="none" stroke="#d8c356" stroke-width="2" d="M324,-540C324,-540 206,-540 206,-540 200,-540 194,-534 194,-528 194,-528 194,-516 194,-516 194,-510 200,-504 206,-504 206,-504 324,-504 324,-504 330,-504 336,-510 336,-516 336,-516 336,-528 336,-528 336,-534 330,-540 324,-540"/>
+<text text-anchor="middle" x="265" y="-519.5" font-family="sans" font-size="10.00" fill="#000000">pe_quantification_salmon</text>
</g>
-<!-- 23 -->
-<g id="node24" class="node">
-<title>23</title>
-<path fill="none" stroke="#56d86b" stroke-width="2" d="M365.5,-756C365.5,-756 222.5,-756 222.5,-756 216.5,-756 210.5,-750 210.5,-744 210.5,-744 210.5,-732 210.5,-732 210.5,-726 216.5,-720 222.5,-720 222.5,-720 365.5,-720 365.5,-720 371.5,-720 377.5,-726 377.5,-732 377.5,-732 377.5,-744 377.5,-744 377.5,-750 371.5,-756 365.5,-756"/>
-<text text-anchor="middle" x="294" y="-735.5" font-family="sans" font-size="10.00" fill="#000000">pe_remove_adapters_cutadapt</text>
-</g>
-<!-- 15->23 -->
-<g id="edge37" class="edge">
-<title>15->23</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M294,-791.8314C294,-784.131 294,-774.9743 294,-766.4166"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="297.5001,-766.4132 294,-756.4133 290.5001,-766.4133 297.5001,-766.4132"/>
-</g>
-<!-- 25 -->
-<g id="node26" class="node">
-<title>25</title>
-<path fill="none" stroke="#d8cb56" stroke-width="2" d="M677,-756C677,-756 551,-756 551,-756 545,-756 539,-750 539,-744 539,-744 539,-732 539,-732 539,-726 545,-720 551,-720 551,-720 677,-720 677,-720 683,-720 689,-726 689,-732 689,-732 689,-744 689,-744 689,-750 683,-756 677,-756"/>
-<text text-anchor="middle" x="614" y="-735.5" font-family="sans" font-size="10.00" fill="#000000">remove_adapters_cutadapt</text>
+<!-- 15->3 -->
+<g id="edge15" class="edge">
+<title>15->3</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M217.3073,-503.8314C191.6927,-494.0734 159.9398,-481.977 133.026,-471.7242"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="133.9406,-468.3273 123.3497,-468.038 131.4486,-474.8687 133.9406,-468.3273"/>
</g>
-<!-- 15->25 -->
-<g id="edge38" class="edge">
-<title>15->25</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M321.0072,-803.9234C366.3899,-793.7123 459.7683,-772.7021 528.9702,-757.1317"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="530.0085,-760.4857 538.9963,-754.8758 528.4719,-753.6564 530.0085,-760.4857"/>
+<!-- 15->4 -->
+<g id="edge17" class="edge">
+<title>15->4</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M262.9813,-503.8314C262.1257,-496.131 261.1083,-486.9743 260.1574,-478.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="263.6289,-477.9656 259.0459,-468.4133 256.6717,-478.7386 263.6289,-477.9656"/>
</g>
<!-- 16 -->
<g id="node17" class="node">
<title>16</title>
-<path fill="none" stroke="#78d856" stroke-width="2" d="M517,-684C517,-684 389,-684 389,-684 383,-684 377,-678 377,-672 377,-672 377,-660 377,-660 377,-654 383,-648 389,-648 389,-648 517,-648 517,-648 523,-648 529,-654 529,-660 529,-660 529,-672 529,-672 529,-678 523,-684 517,-684"/>
-<text text-anchor="middle" x="453" y="-663.5" font-family="sans" font-size="10.00" fill="#000000">pe_remove_polya_cutadapt</text>
-</g>
-<!-- 16->6 -->
-<g id="edge18" class="edge">
-<title>16->6</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M376.6672,-648.6626C331.0858,-638.3097 272.973,-625.1106 225.2716,-614.2762"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="225.7858,-610.8039 215.2589,-612.002 224.2353,-617.63 225.7858,-610.8039"/>
+<path fill="none" stroke="#5692d8" stroke-width="2" d="M163.5,-540C163.5,-540 62.5,-540 62.5,-540 56.5,-540 50.5,-534 50.5,-528 50.5,-528 50.5,-516 50.5,-516 50.5,-510 56.5,-504 62.5,-504 62.5,-504 163.5,-504 163.5,-504 169.5,-504 175.5,-510 175.5,-516 175.5,-516 175.5,-528 175.5,-528 175.5,-534 169.5,-540 163.5,-540"/>
+<text text-anchor="middle" x="113" y="-519.5" font-family="sans" font-size="10.00" fill="#000000">quantification_salmon</text>
</g>
-<!-- 16->13 -->
-<g id="edge25" class="edge">
-<title>16->13</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M529.0444,-649.6106C597.3012,-634.8201 687.9868,-614.9393 696,-612 744.2839,-594.2888 796.0604,-565.5158 829.832,-545.2804"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="831.694,-548.2447 838.439,-540.0742 828.071,-542.2552 831.694,-548.2447"/>
+<!-- 16->3 -->
+<g id="edge16" class="edge">
+<title>16->3</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M103.6633,-503.8314C99.5757,-495.8771 94.6896,-486.369 90.1691,-477.5723"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="93.1461,-475.7078 85.4624,-468.4133 86.9201,-478.9074 93.1461,-475.7078"/>
</g>
-<!-- 16->30 -->
-<g id="edge49" class="edge">
-<title>16->30</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M464.6077,-647.8314C469.7978,-639.7079 476.0232,-629.9637 481.7425,-621.0118"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="484.8015,-622.7246 487.236,-612.4133 478.9026,-618.9559 484.8015,-622.7246"/>
+<!-- 16->4 -->
+<g id="edge18" class="edge">
+<title>16->4</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M149.3373,-503.8314C168.3396,-494.3302 191.7758,-482.6121 211.9252,-472.5374"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="213.545,-475.6407 220.924,-468.038 210.4145,-469.3797 213.545,-475.6407"/>
</g>
<!-- 17 -->
<g id="node18" class="node">
<title>17</title>
-<path fill="none" stroke="#5663d8" stroke-width="2" d="M346.5,-684C346.5,-684 249.5,-684 249.5,-684 243.5,-684 237.5,-678 237.5,-672 237.5,-672 237.5,-660 237.5,-660 237.5,-654 243.5,-648 249.5,-648 249.5,-648 346.5,-648 346.5,-648 352.5,-648 358.5,-654 358.5,-660 358.5,-660 358.5,-672 358.5,-672 358.5,-678 352.5,-684 346.5,-684"/>
-<text text-anchor="middle" x="298" y="-663.5" font-family="sans" font-size="10.00" fill="#000000">create_index_kallisto</text>
-</g>
-<!-- 17->6 -->
-<g id="edge19" class="edge">
-<title>17->6</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M257.1206,-647.8314C235.454,-638.2018 208.6637,-626.295 185.7922,-616.1299"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="187.1451,-612.9011 176.5855,-612.038 184.3021,-619.2978 187.1451,-612.9011"/>
+<path fill="none" stroke="#97d856" stroke-width="2" d="M646,-828C646,-828 616,-828 616,-828 610,-828 604,-822 604,-816 604,-816 604,-804 604,-804 604,-798 610,-792 616,-792 616,-792 646,-792 646,-792 652,-792 658,-798 658,-804 658,-804 658,-816 658,-816 658,-822 652,-828 646,-828"/>
+<text text-anchor="middle" x="631" y="-807.5" font-family="sans" font-size="10.00" fill="#000000">start</text>
</g>
<!-- 17->7 -->
-<g id="edge20" class="edge">
+<g id="edge23" class="edge">
<title>17->7</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M306.832,-647.8314C310.6986,-639.8771 315.3206,-630.369 319.5968,-621.5723"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="322.8249,-622.9371 324.0491,-612.4133 316.5293,-619.8768 322.8249,-622.9371"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M658.1064,-808.9708C770.368,-803.9871 1193,-777.8007 1193,-666 1193,-666 1193,-666 1193,-522 1193,-481.7977 1196.5375,-435.4047 1199.1768,-406.385"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1202.6864,-406.4457 1200.1352,-396.1626 1195.717,-405.7923 1202.6864,-406.4457"/>
+</g>
+<!-- 25 -->
+<g id="node26" class="node">
+<title>25</title>
+<path fill="none" stroke="#d89c56" stroke-width="2" d="M702.5,-756C702.5,-756 559.5,-756 559.5,-756 553.5,-756 547.5,-750 547.5,-744 547.5,-744 547.5,-732 547.5,-732 547.5,-726 553.5,-720 559.5,-720 559.5,-720 702.5,-720 702.5,-720 708.5,-720 714.5,-726 714.5,-732 714.5,-732 714.5,-744 714.5,-744 714.5,-750 708.5,-756 702.5,-756"/>
+<text text-anchor="middle" x="631" y="-735.5" font-family="sans" font-size="10.00" fill="#000000">pe_remove_adapters_cutadapt</text>
+</g>
+<!-- 17->25 -->
+<g id="edge43" class="edge">
+<title>17->25</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M631,-791.8314C631,-784.131 631,-774.9743 631,-766.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="634.5001,-766.4132 631,-756.4133 627.5001,-766.4133 634.5001,-766.4132"/>
+</g>
+<!-- 27 -->
+<g id="node28" class="node">
+<title>27</title>
+<path fill="none" stroke="#56a9d8" stroke-width="2" d="M375,-756C375,-756 249,-756 249,-756 243,-756 237,-750 237,-744 237,-744 237,-732 237,-732 237,-726 243,-720 249,-720 249,-720 375,-720 375,-720 381,-720 387,-726 387,-732 387,-732 387,-744 387,-744 387,-750 381,-756 375,-756"/>
+<text text-anchor="middle" x="312" y="-735.5" font-family="sans" font-size="10.00" fill="#000000">remove_adapters_cutadapt</text>
+</g>
+<!-- 17->27 -->
+<g id="edge44" class="edge">
+<title>17->27</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M603.8022,-803.8613C558.5659,-793.6512 466.0433,-772.7684 397.2464,-757.2406"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="397.8018,-753.778 387.2766,-754.9903 396.2606,-760.6062 397.8018,-753.778"/>
</g>
<!-- 18 -->
<g id="node19" class="node">
<title>18</title>
-<path fill="none" stroke="#56d8b9" stroke-width="2" d="M669,-684C669,-684 559,-684 559,-684 553,-684 547,-678 547,-672 547,-672 547,-660 547,-660 547,-654 553,-648 559,-648 559,-648 669,-648 669,-648 675,-648 681,-654 681,-660 681,-660 681,-672 681,-672 681,-678 675,-684 669,-684"/>
-<text text-anchor="middle" x="614" y="-663.5" font-family="sans" font-size="10.00" fill="#000000">remove_polya_cutadapt</text>
+<path fill="none" stroke="#d8d356" stroke-width="2" d="M665,-684C665,-684 537,-684 537,-684 531,-684 525,-678 525,-672 525,-672 525,-660 525,-660 525,-654 531,-648 537,-648 537,-648 665,-648 665,-648 671,-648 677,-654 677,-660 677,-660 677,-672 677,-672 677,-678 671,-684 665,-684"/>
+<text text-anchor="middle" x="601" y="-663.5" font-family="sans" font-size="10.00" fill="#000000">pe_remove_polya_cutadapt</text>
</g>
-<!-- 18->7 -->
-<g id="edge21" class="edge">
-<title>18->7</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M546.6935,-648.7542C506.7096,-638.5092 455.7534,-625.4528 413.6292,-614.6594"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="414.2344,-611.2015 403.6786,-612.1098 412.4969,-617.9825 414.2344,-611.2015"/>
+<!-- 18->8 -->
+<g id="edge24" class="edge">
+<title>18->8</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M595.3306,-647.8704C588.0535,-623.5963 575.7953,-579.0581 571,-540 555.0812,-410.3404 561.499,-253.7868 565.1423,-190.5482"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="568.6583,-190.3842 565.7631,-180.1926 561.6709,-189.9652 568.6583,-190.3842"/>
</g>
-<!-- 18->14 -->
-<g id="edge28" class="edge">
-<title>18->14</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M681.1792,-649.6297C735.4104,-636.1652 804.6626,-618.3114 817,-612 839.4944,-600.4926 838.918,-588.2802 861,-576 887.6283,-561.1915 919.0252,-549.4402 946.7861,-540.7318"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="947.9014,-544.0508 956.4401,-537.7785 945.8536,-537.357 947.9014,-544.0508"/>
+<!-- 18->15 -->
+<g id="edge31" class="edge">
+<title>18->15</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M558.7856,-647.9081C497.2161,-621.5212 382.9067,-572.5315 316.4826,-544.064"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="317.6119,-540.7401 307.0417,-540.0179 314.8544,-547.1741 317.6119,-540.7401"/>
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-<!-- 18->33 -->
-<g id="edge54" class="edge">
-<title>18->33</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M618.7945,-647.8314C620.8489,-640.0463 623.296,-630.7729 625.5756,-622.1347"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="628.9735,-622.9753 628.1409,-612.4133 622.2052,-621.1892 628.9735,-622.9753"/>
+<!-- 18->32 -->
+<g id="edge55" class="edge">
+<title>18->32</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M677.1308,-652.061C729.5514,-642.2029 801.0165,-628.2533 872.2723,-612.3398"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="873.3339,-615.6886 882.3234,-610.0815 871.7994,-608.8589 873.3339,-615.6886"/>
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<!-- 19 -->
<g id="node20" class="node">
<title>19</title>
-<path fill="none" stroke="#56d88a" stroke-width="2" d="M319.5,-396C319.5,-396 236.5,-396 236.5,-396 230.5,-396 224.5,-390 224.5,-384 224.5,-384 224.5,-372 224.5,-372 224.5,-366 230.5,-360 236.5,-360 236.5,-360 319.5,-360 319.5,-360 325.5,-360 331.5,-366 331.5,-372 331.5,-372 331.5,-384 331.5,-384 331.5,-390 325.5,-396 319.5,-396"/>
-<text text-anchor="middle" x="278" y="-375.5" font-family="sans" font-size="10.00" fill="#000000">merge_TIN_scores</text>
+<path fill="none" stroke="#61d856" stroke-width="2" d="M509.5,-252C509.5,-252 412.5,-252 412.5,-252 406.5,-252 400.5,-246 400.5,-240 400.5,-240 400.5,-228 400.5,-228 400.5,-222 406.5,-216 412.5,-216 412.5,-216 509.5,-216 509.5,-216 515.5,-216 521.5,-222 521.5,-228 521.5,-228 521.5,-240 521.5,-240 521.5,-246 515.5,-252 509.5,-252"/>
+<text text-anchor="middle" x="461" y="-231.5" font-family="sans" font-size="10.00" fill="#000000">create_index_kallisto</text>
</g>
<!-- 19->8 -->
-<g id="edge22" class="edge">
+<g id="edge25" class="edge">
<title>19->8</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M273.6939,-359.7623C267.8691,-335.0928 257.4252,-290.8598 250.6048,-261.9731"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="253.9755,-261.0177 248.2712,-252.0896 247.1628,-262.6263 253.9755,-261.0177"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M487.7483,-215.8314C501.0553,-206.7927 517.316,-195.7476 531.6375,-186.0198"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="533.9547,-188.677 540.2603,-180.1628 530.0215,-182.8864 533.9547,-188.677"/>
+</g>
+<!-- 19->9 -->
+<g id="edge27" class="edge">
+<title>19->9</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M438.0369,-215.8314C426.8285,-206.9632 413.1791,-196.1637 401.0561,-186.5718"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="402.9697,-183.6229 392.9558,-180.1628 398.6263,-189.1125 402.9697,-183.6229"/>
</g>
<!-- 20 -->
<g id="node21" class="node">
<title>20</title>
-<path fill="none" stroke="#d87556" stroke-width="2" d="M518,-252C518,-252 426,-252 426,-252 420,-252 414,-246 414,-240 414,-240 414,-228 414,-228 414,-222 420,-216 426,-216 426,-216 518,-216 518,-216 524,-216 530,-222 530,-228 530,-228 530,-240 530,-240 530,-246 524,-252 518,-252"/>
-<text text-anchor="middle" x="472" y="-231.5" font-family="sans" font-size="10.00" fill="#000000">alfa_qc_all_samples</text>
+<path fill="none" stroke="#afd856" stroke-width="2" d="M427,-684C427,-684 317,-684 317,-684 311,-684 305,-678 305,-672 305,-672 305,-660 305,-660 305,-654 311,-648 317,-648 317,-648 427,-648 427,-648 433,-648 439,-654 439,-660 439,-660 439,-672 439,-672 439,-678 433,-684 427,-684"/>
+<text text-anchor="middle" x="372" y="-663.5" font-family="sans" font-size="10.00" fill="#000000">remove_polya_cutadapt</text>
</g>
<!-- 20->9 -->
-<g id="edge23" class="edge">
+<g id="edge26" class="edge">
<title>20->9</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M422.2918,-215.9243C395.2241,-206.0815 361.5561,-193.8386 333.1451,-183.5073"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="334.3227,-180.2114 323.7286,-180.0831 331.9305,-186.7899 334.3227,-180.2114"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M372,-647.8146C372,-620.4983 372,-567.25 372,-522 372,-522 372,-522 372,-306 372,-265.8721 371.2139,-219.4602 370.6274,-190.416"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="374.1218,-190.1092 370.4144,-180.1843 367.1234,-190.255 374.1218,-190.1092"/>
+</g>
+<!-- 20->16 -->
+<g id="edge33" class="edge">
+<title>20->16</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M304.8785,-649.5161C253.503,-636.5164 189.6749,-619.3885 179,-612 155.8934,-596.007 137.7849,-569.2491 126.4275,-549.0565"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="129.3804,-547.1587 121.5465,-540.0256 123.2223,-550.4871 129.3804,-547.1587"/>
+</g>
+<!-- 20->35 -->
+<g id="edge59" class="edge">
+<title>20->35</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M439.1525,-654.9864C522.9656,-641.2403 665.2549,-617.9035 747.383,-604.4338"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="748.0352,-607.8736 757.3369,-602.8012 746.9022,-600.9659 748.0352,-607.8736"/>
</g>
<!-- 21 -->
<g id="node22" class="node">
<title>21</title>
-<path fill="none" stroke="#d85656" stroke-width="2" d="M591,-396C591,-396 469,-396 469,-396 463,-396 457,-390 457,-384 457,-384 457,-372 457,-372 457,-366 463,-360 469,-360 469,-360 591,-360 591,-360 597,-360 603,-366 603,-372 603,-372 603,-384 603,-384 603,-390 597,-396 591,-396"/>
-<text text-anchor="middle" x="530" y="-375.5" font-family="sans" font-size="10.00" fill="#000000">rename_star_rpm_for_alfa</text>
-</g>
-<!-- 21->11 -->
-<g id="edge24" class="edge">
-<title>21->11</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M561.7951,-359.8314C578.0605,-350.5368 598.0386,-339.1208 615.4051,-329.1971"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="617.2691,-332.1631 624.2151,-324.1628 613.7961,-326.0854 617.2691,-332.1631"/>
+<path fill="none" stroke="#56d8d8" stroke-width="2" d="M808.5,-396C808.5,-396 725.5,-396 725.5,-396 719.5,-396 713.5,-390 713.5,-384 713.5,-384 713.5,-372 713.5,-372 713.5,-366 719.5,-360 725.5,-360 725.5,-360 808.5,-360 808.5,-360 814.5,-360 820.5,-366 820.5,-372 820.5,-372 820.5,-384 820.5,-384 820.5,-390 814.5,-396 808.5,-396"/>
+<text text-anchor="middle" x="767" y="-375.5" font-family="sans" font-size="10.00" fill="#000000">merge_TIN_scores</text>
</g>
-<!-- 27 -->
-<g id="node28" class="node">
-<title>27</title>
-<path fill="none" stroke="#56d8a9" stroke-width="2" d="M545,-324C545,-324 515,-324 515,-324 509,-324 503,-318 503,-312 503,-312 503,-300 503,-300 503,-294 509,-288 515,-288 515,-288 545,-288 545,-288 551,-288 557,-294 557,-300 557,-300 557,-312 557,-312 557,-318 551,-324 545,-324"/>
-<text text-anchor="middle" x="530" y="-303.5" font-family="sans" font-size="10.00" fill="#000000">alfa_qc</text>
-</g>
-<!-- 21->27 -->
-<g id="edge43" class="edge">
-<title>21->27</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M530,-359.8314C530,-352.131 530,-342.9743 530,-334.4166"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="533.5001,-334.4132 530,-324.4133 526.5001,-334.4133 533.5001,-334.4132"/>
-</g>
-<!-- 22->13 -->
-<g id="edge26" class="edge">
-<title>22->13</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M914.1024,-575.8314C906.7722,-567.454 897.934,-557.3531 889.9031,-548.1749"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="892.3307,-545.6343 883.1116,-540.4133 887.0627,-550.2438 892.3307,-545.6343"/>
+<!-- 21->10 -->
+<g id="edge28" class="edge">
+<title>21->10</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M775.3273,-359.8314C778.973,-351.8771 783.3309,-342.369 787.3627,-333.5723"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="790.5757,-334.9622 791.5606,-324.4133 784.2123,-332.0456 790.5757,-334.9622"/>
</g>
-<!-- 22->14 -->
-<g id="edge27" class="edge">
-<title>22->14</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M952.4585,-575.8314C963.4205,-566.9632 976.7699,-556.1637 988.6265,-546.5718"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="990.9755,-549.1734 996.5487,-540.1628 986.5729,-543.7313 990.9755,-549.1734"/>
+<!-- 22 -->
+<g id="node23" class="node">
+<title>22</title>
+<path fill="none" stroke="#d87d56" stroke-width="2" d="M970,-252C970,-252 878,-252 878,-252 872,-252 866,-246 866,-240 866,-240 866,-228 866,-228 866,-222 872,-216 878,-216 878,-216 970,-216 970,-216 976,-216 982,-222 982,-228 982,-228 982,-240 982,-240 982,-246 976,-252 970,-252"/>
+<text text-anchor="middle" x="924" y="-231.5" font-family="sans" font-size="10.00" fill="#000000">alfa_qc_all_samples</text>
</g>
-<!-- 23->16 -->
+<!-- 22->11 -->
<g id="edge29" class="edge">
-<title>23->16</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M334.1224,-719.8314C355.2932,-710.2446 381.4483,-698.4008 403.8303,-688.2655"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="405.5003,-691.3515 413.1661,-684.038 402.6128,-684.9748 405.5003,-691.3515"/>
+<title>22->11</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M923.7477,-215.8314C923.6407,-208.131 923.5135,-198.9743 923.3947,-190.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="926.8944,-190.3637 923.2557,-180.4133 919.8951,-190.4609 926.8944,-190.3637"/>
</g>
-<!-- 24 -->
-<g id="node25" class="node">
-<title>24</title>
-<path fill="none" stroke="#5692d8" stroke-width="2" d="M508.5,-756C508.5,-756 407.5,-756 407.5,-756 401.5,-756 395.5,-750 395.5,-744 395.5,-744 395.5,-732 395.5,-732 395.5,-726 401.5,-720 407.5,-720 407.5,-720 508.5,-720 508.5,-720 514.5,-720 520.5,-726 520.5,-732 520.5,-732 520.5,-744 520.5,-744 520.5,-750 514.5,-756 508.5,-756"/>
-<text text-anchor="middle" x="458" y="-735.5" font-family="sans" font-size="10.00" fill="#000000">extract_transcriptome</text>
+<!-- 23 -->
+<g id="node24" class="node">
+<title>23</title>
+<path fill="none" stroke="#d86656" stroke-width="2" d="M1107,-396C1107,-396 985,-396 985,-396 979,-396 973,-390 973,-384 973,-384 973,-372 973,-372 973,-366 979,-360 985,-360 985,-360 1107,-360 1107,-360 1113,-360 1119,-366 1119,-372 1119,-372 1119,-384 1119,-384 1119,-390 1113,-396 1107,-396"/>
+<text text-anchor="middle" x="1046" y="-375.5" font-family="sans" font-size="10.00" fill="#000000">rename_star_rpm_for_alfa</text>
</g>
-<!-- 24->17 -->
+<!-- 23->13 -->
<g id="edge30" class="edge">
-<title>24->17</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M417.6252,-719.8314C396.3213,-710.2446 370.0017,-698.4008 347.4789,-688.2655"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="348.6399,-684.95 338.0844,-684.038 345.7674,-691.3334 348.6399,-684.95"/>
+<title>23->13</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1049.5328,-359.8314C1051.0301,-352.131 1052.8105,-342.9743 1054.4745,-334.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1057.9465,-334.8975 1056.4196,-324.4133 1051.0752,-333.5614 1057.9465,-334.8975"/>
</g>
<!-- 29 -->
<g id="node30" class="node">
<title>29</title>
-<path fill="none" stroke="#70d856" stroke-width="2" d="M1027,-684C1027,-684 833,-684 833,-684 827,-684 821,-678 821,-672 821,-672 821,-660 821,-660 821,-654 827,-648 833,-648 833,-648 1027,-648 1027,-648 1033,-648 1039,-654 1039,-660 1039,-660 1039,-672 1039,-672 1039,-678 1033,-684 1027,-684"/>
-<text text-anchor="middle" x="930" y="-663.5" font-family="sans" font-size="10.00" fill="#000000">concatenate_transcriptome_and_genome</text>
+<path fill="none" stroke="#56d8a2" stroke-width="2" d="M939,-324C939,-324 909,-324 909,-324 903,-324 897,-318 897,-312 897,-312 897,-300 897,-300 897,-294 903,-288 909,-288 909,-288 939,-288 939,-288 945,-288 951,-294 951,-300 951,-300 951,-312 951,-312 951,-318 945,-324 939,-324"/>
+<text text-anchor="middle" x="924" y="-303.5" font-family="sans" font-size="10.00" fill="#000000">alfa_qc</text>
</g>
-<!-- 24->29 -->
-<g id="edge48" class="edge">
-<title>24->29</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M520.7325,-721.8538C523.859,-721.1946 526.961,-720.5718 530,-720 651.0189,-697.2303 685.1517,-701.2979 810.7194,-684.1497"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="811.2969,-687.6032 820.7227,-682.7654 810.3373,-680.6693 811.2969,-687.6032"/>
+<!-- 23->29 -->
+<g id="edge49" class="edge">
+<title>23->29</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1015.2142,-359.8314C998.3832,-349.8983 977.4465,-337.5422 959.8783,-327.1741"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="961.4289,-324.0251 951.0379,-321.9568 957.8711,-330.0536 961.4289,-324.0251"/>
+</g>
+<!-- 24->15 -->
+<g id="edge32" class="edge">
+<title>24->15</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M253.0375,-575.8314C254.7487,-568.131 256.7835,-558.9743 258.6852,-550.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="262.1554,-550.9344 260.9082,-540.4133 255.3221,-549.4159 262.1554,-550.9344"/>
+</g>
+<!-- 24->16 -->
+<g id="edge34" class="edge">
+<title>24->16</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M214.6815,-575.8314C196.9641,-566.4516 175.1655,-554.9112 156.3016,-544.9244"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="157.7831,-541.7485 147.3076,-540.1628 154.5078,-547.935 157.7831,-541.7485"/>
</g>
<!-- 25->18 -->
-<g id="edge31" class="edge">
+<g id="edge35" class="edge">
<title>25->18</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M614,-719.8314C614,-712.131 614,-702.9743 614,-694.4166"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="617.5001,-694.4132 614,-684.4133 610.5001,-694.4133 617.5001,-694.4132"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M623.4297,-719.8314C620.1507,-711.9617 616.238,-702.5712 612.6055,-693.8533"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="615.7492,-692.2979 608.6722,-684.4133 609.2876,-694.9902 615.7492,-692.2979"/>
</g>
<!-- 26 -->
<g id="node27" class="node">
<title>26</title>
-<path fill="none" stroke="#97d856" stroke-width="2" d="M338.5,-468C338.5,-468 243.5,-468 243.5,-468 237.5,-468 231.5,-462 231.5,-456 231.5,-456 231.5,-444 231.5,-444 231.5,-438 237.5,-432 243.5,-432 243.5,-432 338.5,-432 338.5,-432 344.5,-432 350.5,-438 350.5,-444 350.5,-444 350.5,-456 350.5,-456 350.5,-462 344.5,-468 338.5,-468"/>
-<text text-anchor="middle" x="291" y="-447.5" font-family="sans" font-size="10.00" fill="#000000">calculate_TIN_scores</text>
+<path fill="none" stroke="#5673d8" stroke-width="2" d="M517.5,-756C517.5,-756 416.5,-756 416.5,-756 410.5,-756 404.5,-750 404.5,-744 404.5,-744 404.5,-732 404.5,-732 404.5,-726 410.5,-720 416.5,-720 416.5,-720 517.5,-720 517.5,-720 523.5,-720 529.5,-726 529.5,-732 529.5,-732 529.5,-744 529.5,-744 529.5,-750 523.5,-756 517.5,-756"/>
+<text text-anchor="middle" x="467" y="-735.5" font-family="sans" font-size="10.00" fill="#000000">extract_transcriptome</text>
</g>
<!-- 26->19 -->
-<g id="edge32" class="edge">
+<g id="edge36" class="edge">
<title>26->19</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M287.7196,-431.8314C286.3292,-424.131 284.6759,-414.9743 283.1308,-406.4166"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="286.5458,-405.6322 281.3246,-396.4133 279.6572,-406.8761 286.5458,-405.6322"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M467,-719.8146C467,-692.4983 467,-639.25 467,-594 467,-594 467,-594 467,-378 467,-337.8412 464.6417,-291.4372 462.8821,-262.4031"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="466.3599,-261.9376 462.2432,-252.1753 459.3736,-262.3741 466.3599,-261.9376"/>
+</g>
+<!-- 31 -->
+<g id="node32" class="node">
+<title>31</title>
+<path fill="none" stroke="#a7d856" stroke-width="2" d="M275,-684C275,-684 81,-684 81,-684 75,-684 69,-678 69,-672 69,-672 69,-660 69,-660 69,-654 75,-648 81,-648 81,-648 275,-648 275,-648 281,-648 287,-654 287,-660 287,-660 287,-672 287,-672 287,-678 281,-684 275,-684"/>
+<text text-anchor="middle" x="178" y="-663.5" font-family="sans" font-size="10.00" fill="#000000">concatenate_transcriptome_and_genome</text>
+</g>
+<!-- 26->31 -->
+<g id="edge54" class="edge">
+<title>26->31</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M404.2848,-722.0806C401.4853,-721.3762 398.7137,-720.6801 396,-720 351.4509,-708.8355 301.7459,-696.5129 261.0607,-686.4615"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="261.7363,-683.0233 251.1888,-684.0234 260.0579,-689.8191 261.7363,-683.0233"/>
</g>
<!-- 27->20 -->
-<g id="edge33" class="edge">
+<g id="edge37" class="edge">
<title>27->20</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M515.3642,-287.8314C508.6839,-279.5386 500.6432,-269.557 493.3096,-260.4533"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="495.8319,-258.0052 486.8329,-252.4133 490.3806,-262.3965 495.8319,-258.0052"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M327.1405,-719.8314C334.1217,-711.454 342.5391,-701.3531 350.1876,-692.1749"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="352.9425,-694.3362 356.6556,-684.4133 347.5649,-689.8548 352.9425,-694.3362"/>
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<!-- 28 -->
<g id="node29" class="node">
<title>28</title>
-<path fill="none" stroke="#d8a456" stroke-width="2" d="M609,-468C609,-468 573,-468 573,-468 567,-468 561,-462 561,-456 561,-456 561,-444 561,-444 561,-438 567,-432 573,-432 573,-432 609,-432 609,-432 615,-432 621,-438 621,-444 621,-444 621,-456 621,-456 621,-462 615,-468 609,-468"/>
-<text text-anchor="middle" x="591" y="-447.5" font-family="sans" font-size="10.00" fill="#000000">star_rpm</text>
+<path fill="none" stroke="#d85656" stroke-width="2" d="M814.5,-468C814.5,-468 719.5,-468 719.5,-468 713.5,-468 707.5,-462 707.5,-456 707.5,-456 707.5,-444 707.5,-444 707.5,-438 713.5,-432 719.5,-432 719.5,-432 814.5,-432 814.5,-432 820.5,-432 826.5,-438 826.5,-444 826.5,-444 826.5,-456 826.5,-456 826.5,-462 820.5,-468 814.5,-468"/>
+<text text-anchor="middle" x="767" y="-447.5" font-family="sans" font-size="10.00" fill="#000000">calculate_TIN_scores</text>
</g>
<!-- 28->21 -->
-<g id="edge34" class="edge">
+<g id="edge38" class="edge">
<title>28->21</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M575.6071,-431.8314C568.5096,-423.454 559.952,-413.3531 552.176,-404.1749"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="554.7348,-401.7807 545.6001,-396.4133 549.3939,-406.3056 554.7348,-401.7807"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M767,-431.8314C767,-424.131 767,-414.9743 767,-406.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="770.5001,-406.4132 767,-396.4133 763.5001,-406.4133 770.5001,-406.4132"/>
</g>
<!-- 29->22 -->
-<g id="edge36" class="edge">
+<g id="edge39" class="edge">
<title>29->22</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M930,-647.8314C930,-640.131 930,-630.9743 930,-622.4166"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="933.5001,-622.4132 930,-612.4133 926.5001,-622.4133 933.5001,-622.4132"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M924,-287.8314C924,-280.131 924,-270.9743 924,-262.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="927.5001,-262.4132 924,-252.4133 920.5001,-262.4133 927.5001,-262.4132"/>
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-<!-- 30->26 -->
-<g id="edge40" class="edge">
-<title>30->26</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M436.2442,-577.9722C433.1239,-577.2817 430.0296,-576.6199 427,-576 377.3918,-565.85 234.8551,-578.5298 202,-540 191.6184,-527.8253 194.1512,-517.9426 202,-504 209.2034,-491.2038 220.7994,-481.0907 233.2742,-473.2465"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="235.1189,-476.2227 242.0078,-468.1733 231.6028,-470.1698 235.1189,-476.2227"/>
-</g>
-<!-- 30->28 -->
-<g id="edge46" class="edge">
-<title>30->28</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M552.7084,-575.7905C568.8649,-567.5107 584.7454,-555.9057 594,-540 604.8131,-521.4157 603.1421,-496.8239 599.2798,-478.0433"/>
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-</g>
-<!-- 31 -->
-<g id="node32" class="node">
-<title>31</title>
-<path fill="none" stroke="#56d89a" stroke-width="2" d="M573,-540C573,-540 401,-540 401,-540 395,-540 389,-534 389,-528 389,-528 389,-516 389,-516 389,-510 395,-504 401,-504 401,-504 573,-504 573,-504 579,-504 585,-510 585,-516 585,-516 585,-528 585,-528 585,-534 579,-540 573,-540"/>
-<text text-anchor="middle" x="487" y="-519.5" font-family="sans" font-size="10.00" fill="#000000">index_genomic_alignment_samtools</text>
+<!-- 30 -->
+<g id="node31" class="node">
+<title>30</title>
+<path fill="none" stroke="#56d87b" stroke-width="2" d="M1013,-468C1013,-468 977,-468 977,-468 971,-468 965,-462 965,-456 965,-456 965,-444 965,-444 965,-438 971,-432 977,-432 977,-432 1013,-432 1013,-432 1019,-432 1025,-438 1025,-444 1025,-444 1025,-456 1025,-456 1025,-462 1019,-468 1013,-468"/>
+<text text-anchor="middle" x="995" y="-447.5" font-family="sans" font-size="10.00" fill="#000000">star_rpm</text>
</g>
-<!-- 30->31 -->
-<g id="edge52" class="edge">
-<title>30->31</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M495.9719,-575.8314C494.6885,-568.131 493.1624,-558.9743 491.7361,-550.4166"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="495.1653,-549.7018 490.0689,-540.4133 488.2606,-550.8526 495.1653,-549.7018"/>
+<!-- 30->23 -->
+<g id="edge40" class="edge">
+<title>30->23</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1007.8695,-431.8314C1013.6835,-423.6232 1020.6696,-413.7606 1027.0646,-404.7323"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1030.0331,-406.5966 1032.9573,-396.4133 1024.321,-402.5505 1030.0331,-406.5966"/>
</g>
-<!-- 31->26 -->
-<g id="edge42" class="edge">
-<title>31->26</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M437.7939,-503.9243C411.1161,-494.1243 377.9614,-481.945 349.9148,-471.6422"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="350.8199,-468.246 340.2263,-468.0831 348.4062,-474.8167 350.8199,-468.246"/>
+<!-- 31->24 -->
+<g id="edge41" class="edge">
+<title>31->24</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M195.9163,-647.8314C204.3442,-639.2848 214.541,-628.9443 223.736,-619.6198"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="226.3131,-621.9912 230.8425,-612.4133 221.3289,-617.0761 226.3131,-621.9912"/>
</g>
-<!-- 31->28 -->
-<g id="edge47" class="edge">
-<title>31->28</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M513.2436,-503.8314C526.2995,-494.7927 542.2535,-483.7476 556.3047,-474.0198"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="558.5351,-476.7326 564.7648,-468.1628 554.5506,-470.9773 558.5351,-476.7326"/>
+<!-- 32->28 -->
+<g id="edge48" class="edge">
+<title>32->28</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M898.6506,-575.9617C878.7822,-566.9259 856.046,-554.7466 838,-540 815.9494,-521.9809 796.3677,-495.9884 783.3837,-476.5649"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="786.2925,-474.6179 777.8971,-468.155 780.4298,-478.4427 786.2925,-474.6179"/>
</g>
-<!-- 32 -->
-<g id="node33" class="node">
-<title>32</title>
-<path fill="none" stroke="#61d856" stroke-width="2" d="M359,-540C359,-540 223,-540 223,-540 217,-540 211,-534 211,-528 211,-528 211,-516 211,-516 211,-510 217,-504 223,-504 223,-504 359,-504 359,-504 365,-504 371,-510 371,-516 371,-516 371,-528 371,-528 371,-534 365,-540 359,-540"/>
-<text text-anchor="middle" x="291" y="-519.5" font-family="sans" font-size="10.00" fill="#000000">extract_transcripts_as_bed12</text>
+<!-- 32->30 -->
+<g id="edge53" class="edge">
+<title>32->30</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1007.5603,-576.2456C1024.9625,-568.1131 1041.8571,-556.4803 1052,-540 1060.3863,-526.3739 1058.3221,-518.698 1052,-504 1047.2509,-492.9589 1039.0115,-483.1176 1030.2494,-474.9593"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1032.339,-472.1388 1022.4894,-468.2354 1027.755,-477.4291 1032.339,-472.1388"/>
</g>
-<!-- 32->26 -->
-<g id="edge41" class="edge">
-<title>32->26</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M291,-503.8314C291,-496.131 291,-486.9743 291,-478.4166"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="294.5001,-478.4132 291,-468.4133 287.5001,-478.4133 294.5001,-478.4132"/>
+<!-- 33 -->
+<g id="node34" class="node">
+<title>33</title>
+<path fill="none" stroke="#56d85b" stroke-width="2" d="M1031,-540C1031,-540 859,-540 859,-540 853,-540 847,-534 847,-528 847,-528 847,-516 847,-516 847,-510 853,-504 859,-504 859,-504 1031,-504 1031,-504 1037,-504 1043,-510 1043,-516 1043,-516 1043,-528 1043,-528 1043,-534 1037,-540 1031,-540"/>
+<text text-anchor="middle" x="945" y="-519.5" font-family="sans" font-size="10.00" fill="#000000">index_genomic_alignment_samtools</text>
</g>
-<!-- 33->26 -->
-<g id="edge39" class="edge">
-<title>33->26</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M630.2977,-575.6979C626.2231,-554.9601 616.4396,-521.746 594,-504 558.7533,-476.1257 439.0231,-461.5688 361.0402,-454.8624"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="361.0572,-451.3517 350.8003,-454.0061 360.4738,-458.3274 361.0572,-451.3517"/>
+<!-- 32->33 -->
+<g id="edge58" class="edge">
+<title>32->33</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M945,-575.8314C945,-568.131 945,-558.9743 945,-550.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="948.5001,-550.4132 945,-540.4133 941.5001,-550.4133 948.5001,-550.4132"/>
</g>
<!-- 33->28 -->
<g id="edge45" class="edge">
<title>33->28</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M647.947,-575.85C661.321,-557.2624 677.0963,-527.8017 665,-504 657.4342,-489.1129 643.6258,-477.3535 629.9685,-468.6606"/>
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+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M900.0831,-503.8314C876.065,-494.1162 846.3166,-482.0831 821.0408,-471.8592"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="822.1767,-468.5432 811.5939,-468.038 819.5518,-475.0325 822.1767,-468.5432"/>
</g>
-<!-- 33->31 -->
+<!-- 33->30 -->
<g id="edge51" class="edge">
-<title>33->31</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M596.158,-575.8314C576.8918,-566.3302 553.1301,-554.6121 532.7008,-544.5374"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="534.0938,-541.3219 523.577,-540.038 530.9977,-547.6 534.0938,-541.3219"/>
+<title>33->30</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M957.6171,-503.8314C963.3172,-495.6232 970.1663,-485.7606 976.4359,-476.7323"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="979.3838,-478.6234 982.213,-468.4133 973.6342,-474.6306 979.3838,-478.6234"/>
</g>
-<!-- 34->27 -->
-<g id="edge44" class="edge">
-<title>34->27</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M641.401,-359.8314C618.3665,-348.7006 589.0355,-334.5272 566.2526,-323.5181"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="567.7689,-320.3636 557.2422,-319.164 564.7233,-326.6663 567.7689,-320.3636"/>
+<!-- 34 -->
+<g id="node35" class="node">
+<title>34</title>
+<path fill="none" stroke="#d88d56" stroke-width="2" d="M741,-540C741,-540 605,-540 605,-540 599,-540 593,-534 593,-528 593,-528 593,-516 593,-516 593,-510 599,-504 605,-504 605,-504 741,-504 741,-504 747,-504 753,-510 753,-516 753,-516 753,-528 753,-528 753,-534 747,-540 741,-540"/>
+<text text-anchor="middle" x="673" y="-519.5" font-family="sans" font-size="10.00" fill="#000000">extract_transcripts_as_bed12</text>
+</g>
+<!-- 34->28 -->
+<g id="edge47" class="edge">
+<title>34->28</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M696.7202,-503.8314C708.4094,-494.8779 722.6688,-483.9558 735.2809,-474.2955"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="737.4769,-477.0222 743.2874,-468.1628 733.2203,-471.4651 737.4769,-477.0222"/>
+</g>
+<!-- 35->28 -->
+<g id="edge46" class="edge">
+<title>35->28</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M757.2532,-588.8041C697.0784,-581.7456 605.1884,-566.8201 584,-540 548.3016,-494.8132 631.8376,-470.715 697.5067,-459.1486"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="698.1838,-462.5838 707.4602,-457.4652 697.0165,-455.6819 698.1838,-462.5838"/>
+</g>
+<!-- 35->30 -->
+<g id="edge52" class="edge">
+<title>35->30</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M811.7077,-575.6902C813.4544,-555.5713 819.2369,-523.5255 838,-504 868.811,-471.937 919.5025,-458.9075 954.9243,-453.6152"/>
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+</g>
+<!-- 35->33 -->
+<g id="edge57" class="edge">
+<title>35->33</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M844.8139,-575.8314C862.2707,-566.4516 883.7487,-554.9112 902.3352,-544.9244"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="904.0446,-547.9792 911.197,-540.1628 900.7314,-541.8129 904.0446,-547.9792"/>
+</g>
+<!-- 36->29 -->
+<g id="edge50" class="edge">
+<title>36->29</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M903.8132,-359.8314C906.7644,-351.9617 910.2858,-342.5712 913.555,-333.8533"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="916.8609,-335.0055 917.095,-324.4133 910.3066,-332.5476 916.8609,-335.0055"/>
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</svg>
diff --git a/pipeline_documentation.md b/pipeline_documentation.md
index 6dea08609c37872cedd22feebd3eacee282a4d16..e9b582a05fb7774c7ff0d7ab4dcbb7a4e326ecdb 100644
--- a/pipeline_documentation.md
+++ b/pipeline_documentation.md
@@ -30,6 +30,8 @@ on installation and usage please see [here](README.md).
- [**plot_TIN_scores**](#plot_tin_scores)
- [**salmon_quantmerge_genes**](#salmon_quantmerge_genes)
- [**salmon_quantmerge_transcripts**](#salmon_quantmerge_transcripts)
+ - [**kallisto_merge_genes**](#kallisto_merge_genes)
+ - [**kallisto_merge_transcripts**](#kallisto_merge_transcripts)
- [**generate_alfa_index**](#generate_alfa_index)
- [**alfa_qc**](#alfa_qc)
- [**alfa_qc_all_samples**](#alfa_qc_all_samples)
@@ -37,7 +39,7 @@ on installation and usage please see [here](README.md).
- [**prepare_multiqc_config**](#prepare_multiqc_config)
- [**multiqc_report**](#multiqc_report)
- [**finish**](#finish)
- - [**Sequencing mode-specific**](#sequencing-mode-specific)
+ - [**Sequencing mode-specific**](#sequencing-mode-specific)
- [**remove_adapters_cutadapt**](#remove_adapters_cutadapt)
- [**remove_polya_cutadapt**](#remove_polya_cutadapt)
- [**map_genome_star**](#map_genome_star)
@@ -416,6 +418,36 @@ Merge transcript-level expression estimates for all samples with
- Transcript read count table (custom `.tsv`); used in
[**multiqc_report**](#multiqc_report)
+#### `kallisto_merge_genes`
+
+Merge gene-level expression estimates for all samples with
+[custom script][custom-script-merge-kallisto].
+
+> Rule is run once per sequencing mode
+
+- **Input**
+ - Transcript expression tables (custom `.h5`) for samples of same sequencing
+ mode; from [**genome_quantification_kallisto**](#genome_quantification_kallisto)
+ - Gene annotation file (custom `.gtf`)
+- **Output**
+ - Gene TPM table (custom `.tsv`)
+ - Gene read count table (custom `.tsv`)
+ - Mapping gene/transcript IDs table (custom `.tsv`)
+
+#### `kallisto_merge_transcripts`
+
+Merge transcript-level expression estimates for all samples with
+[custom script][custom-script-merge-kallisto].
+
+> Rule is run once per sequencing mode
+
+- **Input**
+ - Transcript expression tables (custom `.h5`) for samples of same sequencing
+ mode; from [**genome_quantification_kallisto**](#genome_quantification_kallisto)
+- **Output**
+ - Transcript TPM table (custom `.tsv`)
+ - Transcript read count table (custom `.tsv`)
+
#### `generate_alfa_index`
Create index for [**ALFA**](#third-party-software-used).
@@ -681,6 +713,7 @@ Generate pseudoalignments of reads to transcripts with
[code-star]: <https://github.com/alexdobin/STAR>
[custom-script-gtf-to-bed12]: <https://git.scicore.unibas.ch/zavolan_group/tools/gtf_transcript_type_to_bed12>
[custom-script-tin]: <https://git.scicore.unibas.ch/zavolan_group/tools/tin_score_calculation>
+[custom-script-merge-kallisto]: <https://github.com/zavolanlab/merge_kallisto>
[docs-alfa]: <https://github.com/biocompibens/ALFA#manual>
[docs-bedgraphtobigwig]: <http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/>
[docs-bedtools]: <https://bedtools.readthedocs.io/en/latest/>
diff --git a/tests/test_integration_workflow/expected_output.files b/tests/test_integration_workflow/expected_output.files
index cc9d90b0700ba426f21e12e4016bfd6e39bf9c6a..e1cdb51cc4fa398ce9ed25f6c8a498823521be30 100644
--- a/tests/test_integration_workflow/expected_output.files
+++ b/tests/test_integration_workflow/expected_output.files
@@ -83,8 +83,8 @@ results/alfa_indexes/homo_sapiens/75/ALFA/sorted_genes.stranded.ALFA_index
results/alfa_indexes/homo_sapiens/75/ALFA/sorted_genes.unstranded.ALFA_index
results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/UniqueMultiple/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.UniqueMultiple.minus.bg
results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/UniqueMultiple/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.UniqueMultiple.plus.bg
-results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/Unique/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Signal.Unique.out.minus.bg
-results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/Unique/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Signal.Unique.out.plus.bg
+results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/Unique/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.Unique.minus.bg
+results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/Unique/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.Unique.plus.bg
results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/UniqueMultiple/synthetic_10_reads_paired_synthetic_10_reads_paired.UniqueMultiple.minus.bg
results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/UniqueMultiple/synthetic_10_reads_paired_synthetic_10_reads_paired.UniqueMultiple.plus.bg
results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/Unique/synthetic_10_reads_paired_synthetic_10_reads_paired.Unique.minus.bg
@@ -106,3 +106,8 @@ results/multiqc_summary/multiqc_data/multiqc_cutadapt.txt
results/multiqc_summary/multiqc_data/multiqc_star.txt
results/multiqc_summary/multiqc_data/multiqc_kallisto.txt
results/multiqc_summary/multiqc_data/multiqc_general_stats.txt
+results/summary_kallisto/tx2geneID.tsv
+results/summary_kallisto/genes_counts.tsv
+results/summary_kallisto/transcripts_counts.tsv
+results/summary_kallisto/transcripts_tpm.tsv
+results/summary_kallisto/genes_tpm.tsv
\ No newline at end of file
diff --git a/tests/test_integration_workflow/expected_output.md5 b/tests/test_integration_workflow/expected_output.md5
index f8f074ee41f58d23057567fc86fc3357fe8ff9c8..92429556e2a1db6434184fade06aac4a0130337b 100644
--- a/tests/test_integration_workflow/expected_output.md5
+++ b/tests/test_integration_workflow/expected_output.md5
@@ -101,8 +101,13 @@ ed3428feeb7257b0a69ead76a417e339 results/samples/synthetic_10_reads_mate_1_synt
ec5aab1b79e7880dfa590e5bc7db5232 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/bigWig/UniqueMultiple/synthetic_10_reads_paired_synthetic_10_reads_paired_UniqueMultiple_plus.bw
69e2bf688165e9fb7c9c49a8763f5632 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/bigWig/Unique/synthetic_10_reads_paired_synthetic_10_reads_paired_Unique_minus.bw
ec5aab1b79e7880dfa590e5bc7db5232 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/bigWig/Unique/synthetic_10_reads_paired_synthetic_10_reads_paired_Unique_plus.bw
+ba090b1b4a2473891de97493d3244956 results/multiqc_summary/multiqc_data/multiqc_fastqc.txt
3e4db5fad83e162bcc19abbe81333a95 results/multiqc_summary/multiqc_data/multiqc_cutadapt.txt
0c6363588cf6ff74d49f27c164185918 results/multiqc_summary/multiqc_data/multiqc_star.txt
dd81441ca97912a62292d317af2c107c results/multiqc_summary/multiqc_data/multiqc_kallisto.txt
-ba090b1b4a2473891de97493d3244956 results/multiqc_summary/multiqc_data/multiqc_fastqc.txt
0703b4cb7ec2abfab13ccd5f58c2d536 results/multiqc_summary/multiqc_data/multiqc_general_stats.txt
+9f22fcd1b38d9dd692e77cb27f2e52f2 results/summary_kallisto/tx2geneID.tsv
+a9514da3fe2c94b9dca71d9e0160be69 results/summary_kallisto/genes_counts.tsv
+0d288e71d017a090152384fd915dc2a1 results/summary_kallisto/transcripts_counts.tsv
+58a075e4e938d690748b556141912d1c results/summary_kallisto/transcripts_tpm.tsv
+8f29696ede8e5d290513f56d3a0b4bff results/summary_kallisto/genes_tpm.tsv
diff --git a/tests/test_integration_workflow_multiple_lanes/expected_output.md5 b/tests/test_integration_workflow_multiple_lanes/expected_output.md5
index f8f074ee41f58d23057567fc86fc3357fe8ff9c8..7a6ae82d02eb20ee568017f8150bc7a671dadc4c 100644
--- a/tests/test_integration_workflow_multiple_lanes/expected_output.md5
+++ b/tests/test_integration_workflow_multiple_lanes/expected_output.md5
@@ -106,3 +106,8 @@ ec5aab1b79e7880dfa590e5bc7db5232 results/samples/synthetic_10_reads_paired_synt
dd81441ca97912a62292d317af2c107c results/multiqc_summary/multiqc_data/multiqc_kallisto.txt
ba090b1b4a2473891de97493d3244956 results/multiqc_summary/multiqc_data/multiqc_fastqc.txt
0703b4cb7ec2abfab13ccd5f58c2d536 results/multiqc_summary/multiqc_data/multiqc_general_stats.txt
+9f22fcd1b38d9dd692e77cb27f2e52f2 results/summary_kallisto/tx2geneID.tsv
+a9514da3fe2c94b9dca71d9e0160be69 results/summary_kallisto/genes_counts.tsv
+0d288e71d017a090152384fd915dc2a1 results/summary_kallisto/transcripts_counts.tsv
+58a075e4e938d690748b556141912d1c results/summary_kallisto/transcripts_tpm.tsv
+8f29696ede8e5d290513f56d3a0b4bff results/summary_kallisto/genes_tpm.tsv