From 44826db4653f7efa5a029afe03f83bd908062e9a Mon Sep 17 00:00:00 2001
From: Alex Kanitz <alexander.kanitz@unibas.ch>
Date: Fri, 12 Jun 2020 12:50:14 +0200
Subject: [PATCH] fix(prepare_inputs): support relative paths
---
.gitlab-ci.yml | 4 +-
README.md | 4 +-
images/dag_test_workflow.svg | 280 +++++-----
images/rule_graph.svg | 124 ++---
...epare_inputs.labkey_to_snakemake.dict.tsv} | 0
...bkey_to_snakemake.py => prepare_inputs.py} | 514 +++++++++---------
.../expected_output.md5 | 2 -
.../expected_output.md5 | 0
.../test.sh | 4 +-
.../expected_output.md5 | 2 +
.../input_table.tsv | 0
.../test.sh | 6 +-
12 files changed, 478 insertions(+), 462 deletions(-)
rename scripts/{labkey_to_snakemake.dict.tsv => prepare_inputs.labkey_to_snakemake.dict.tsv} (100%)
rename scripts/{labkey_to_snakemake.py => prepare_inputs.py} (96%)
delete mode 100644 tests/test_scripts_labkey_to_snakemake_table/expected_output.md5
rename tests/{test_scripts_labkey_to_snakemake_api => test_scripts_prepare_inputs_labkey}/expected_output.md5 (100%)
rename tests/{test_scripts_labkey_to_snakemake_api => test_scripts_prepare_inputs_labkey}/test.sh (91%)
create mode 100644 tests/test_scripts_prepare_inputs_table/expected_output.md5
rename tests/{test_scripts_labkey_to_snakemake_table => test_scripts_prepare_inputs_table}/input_table.tsv (100%)
rename tests/{test_scripts_labkey_to_snakemake_table => test_scripts_prepare_inputs_table}/test.sh (85%)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index dfb1dd4..64fdc8f 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -12,8 +12,8 @@ test:
# add code quality tests here
# add unit tests here
# add script tests here
- #- bash tests/test_scripts_labkey_to_snakemake_table/test.sh
- #- bash tests/test_scripts_labkey_to_snakemake_api/test.sh
+ - bash tests/test_scripts_prepare_inputs_table/test.sh
+ - bash tests/test_scripts_prepare_inputs_labkey/test.sh
- bash tests/test_alfa/test.sh
# add integration tests here
- bash tests/test_create_dag_image/test.sh
diff --git a/README.md b/README.md
index c53835a..6c76bbc 100644
--- a/README.md
+++ b/README.md
@@ -254,10 +254,10 @@ replacing the placeholders with the appropriate values (check out the
help screen with option '--help' for further options and information):
```bash
- python scripts/labkey_to_snakemake.py \
+ python scripts/prepare_inputs.py \
--labkey-domain="my.labkey.service.io"
--labkey-domain="/my/project/path"
- --input-to-output-mapping="scripts/labkey_to_snakemake.dict.tsv" \
+ --input-to-output-mapping="scripts/prepare_inputs.labkey_to_snakemake.dict.tsv" \
--resources-dir="/path/to/my/genome/resources" \
--output-table="config/my_run/samples.tsv" \
--config_file="config/my_run/config.yaml" \
diff --git a/images/dag_test_workflow.svg b/images/dag_test_workflow.svg
index bcd33c5..dcbb2f6 100644
--- a/images/dag_test_workflow.svg
+++ b/images/dag_test_workflow.svg
@@ -12,37 +12,37 @@
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<g id="node1" class="node">
<title>0</title>
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<text text-anchor="middle" x="1471.5" y="-15.5" font-family="sans" font-size="10.00" fill="#000000">finish</text>
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<title>2</title>
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<title>3</title>
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@@ -54,7 +54,7 @@
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@@ -66,7 +66,7 @@
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@@ -78,7 +78,7 @@
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<g id="node7" class="node">
<title>6</title>
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@@ -90,7 +90,7 @@
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<g id="node8" class="node">
<title>7</title>
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@@ -102,7 +102,7 @@
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<g id="node9" class="node">
<title>8</title>
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@@ -114,7 +114,7 @@
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@@ -126,138 +126,138 @@
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-<text text-anchor="middle" x="707.5" y="-82" font-family="sans" font-size="10.00" fill="#000000">salmon_merge_on: tpm</text>
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<g id="edge38" class="edge">
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<!-- 31->11 -->
<g id="edge40" class="edge">
<title>31->11</title>
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<title>32->13</title>
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</g>
<!-- 33 -->
<g id="node34" class="node">
<title>33</title>
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+<path fill="none" stroke="#d8a456" stroke-width="2" d="M313,-838C313,-838 12,-838 12,-838 6,-838 0,-832 0,-826 0,-826 0,-809 0,-809 0,-803 6,-797 12,-797 12,-797 313,-797 313,-797 319,-797 325,-803 325,-809 325,-809 325,-826 325,-826 325,-832 319,-838 313,-838"/>
<text text-anchor="middle" x="162.5" y="-826" font-family="sans" font-size="10.00" fill="#000000">start</text>
<text text-anchor="middle" x="162.5" y="-815" font-family="sans" font-size="10.00" fill="#000000">mate: fq1</text>
<text text-anchor="middle" x="162.5" y="-804" font-family="sans" font-size="10.00" fill="#000000">sample: synthetic_10_reads_paired_synthetic_10_reads_paired</text>
@@ -557,7 +557,7 @@
<!-- 47 -->
<g id="node48" class="node">
<title>47</title>
-<path fill="none" stroke="#d8ac56" stroke-width="2" d="M409,-761C409,-761 266,-761 266,-761 260,-761 254,-755 254,-749 254,-749 254,-737 254,-737 254,-731 260,-725 266,-725 266,-725 409,-725 409,-725 415,-725 421,-731 421,-737 421,-737 421,-749 421,-749 421,-755 415,-761 409,-761"/>
+<path fill="none" stroke="#97d856" stroke-width="2" d="M409,-761C409,-761 266,-761 266,-761 260,-761 254,-755 254,-749 254,-749 254,-737 254,-737 254,-731 260,-725 266,-725 266,-725 409,-725 409,-725 415,-725 421,-731 421,-737 421,-737 421,-749 421,-749 421,-755 415,-761 409,-761"/>
<text text-anchor="middle" x="337.5" y="-740.5" font-family="sans" font-size="10.00" fill="#000000">pe_remove_adapters_cutadapt</text>
</g>
<!-- 33->47 -->
@@ -569,7 +569,7 @@
<!-- 34 -->
<g id="node35" class="node">
<title>34</title>
-<path fill="none" stroke="#56d8d8" stroke-width="2" d="M676,-838C676,-838 363,-838 363,-838 357,-838 351,-832 351,-826 351,-826 351,-809 351,-809 351,-803 357,-797 363,-797 363,-797 676,-797 676,-797 682,-797 688,-803 688,-809 688,-809 688,-826 688,-826 688,-832 682,-838 676,-838"/>
+<path fill="none" stroke="#d8a456" stroke-width="2" d="M676,-838C676,-838 363,-838 363,-838 357,-838 351,-832 351,-826 351,-826 351,-809 351,-809 351,-803 357,-797 363,-797 363,-797 676,-797 676,-797 682,-797 688,-803 688,-809 688,-809 688,-826 688,-826 688,-832 682,-838 676,-838"/>
<text text-anchor="middle" x="519.5" y="-826" font-family="sans" font-size="10.00" fill="#000000">start</text>
<text text-anchor="middle" x="519.5" y="-815" font-family="sans" font-size="10.00" fill="#000000">mate: fq1</text>
<text text-anchor="middle" x="519.5" y="-804" font-family="sans" font-size="10.00" fill="#000000">sample: synthetic_10_reads_mate_1_synthetic_10_reads_mate_1</text>
@@ -583,7 +583,7 @@
<!-- 49 -->
<g id="node50" class="node">
<title>49</title>
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+<path fill="none" stroke="#56d8a9" stroke-width="2" d="M583.5,-761C583.5,-761 457.5,-761 457.5,-761 451.5,-761 445.5,-755 445.5,-749 445.5,-749 445.5,-737 445.5,-737 445.5,-731 451.5,-725 457.5,-725 457.5,-725 583.5,-725 583.5,-725 589.5,-725 595.5,-731 595.5,-737 595.5,-737 595.5,-749 595.5,-749 595.5,-755 589.5,-761 583.5,-761"/>
<text text-anchor="middle" x="520.5" y="-740.5" font-family="sans" font-size="10.00" fill="#000000">remove_adapters_cutadapt</text>
</g>
<!-- 34->49 -->
@@ -595,7 +595,7 @@
<!-- 35 -->
<g id="node36" class="node">
<title>35</title>
-<path fill="none" stroke="#56d8d8" stroke-width="2" d="M1070,-838C1070,-838 769,-838 769,-838 763,-838 757,-832 757,-826 757,-826 757,-809 757,-809 757,-803 763,-797 769,-797 769,-797 1070,-797 1070,-797 1076,-797 1082,-803 1082,-809 1082,-809 1082,-826 1082,-826 1082,-832 1076,-838 1070,-838"/>
+<path fill="none" stroke="#d8a456" stroke-width="2" d="M1070,-838C1070,-838 769,-838 769,-838 763,-838 757,-832 757,-826 757,-826 757,-809 757,-809 757,-803 763,-797 769,-797 769,-797 1070,-797 1070,-797 1076,-797 1082,-803 1082,-809 1082,-809 1082,-826 1082,-826 1082,-832 1076,-838 1070,-838"/>
<text text-anchor="middle" x="919.5" y="-826" font-family="sans" font-size="10.00" fill="#000000">start</text>
<text text-anchor="middle" x="919.5" y="-815" font-family="sans" font-size="10.00" fill="#000000">mate: fq2</text>
<text text-anchor="middle" x="919.5" y="-804" font-family="sans" font-size="10.00" fill="#000000">sample: synthetic_10_reads_paired_synthetic_10_reads_paired</text>
@@ -615,20 +615,20 @@
<!-- 36 -->
<g id="node37" class="node">
<title>36</title>
-<path fill="none" stroke="#56d8c9" stroke-width="2" d="M401.5,-686.5C401.5,-686.5 273.5,-686.5 273.5,-686.5 267.5,-686.5 261.5,-680.5 261.5,-674.5 261.5,-674.5 261.5,-662.5 261.5,-662.5 261.5,-656.5 267.5,-650.5 273.5,-650.5 273.5,-650.5 401.5,-650.5 401.5,-650.5 407.5,-650.5 413.5,-656.5 413.5,-662.5 413.5,-662.5 413.5,-674.5 413.5,-674.5 413.5,-680.5 407.5,-686.5 401.5,-686.5"/>
+<path fill="none" stroke="#d6d856" stroke-width="2" d="M401.5,-686.5C401.5,-686.5 273.5,-686.5 273.5,-686.5 267.5,-686.5 261.5,-680.5 261.5,-674.5 261.5,-674.5 261.5,-662.5 261.5,-662.5 261.5,-656.5 267.5,-650.5 273.5,-650.5 273.5,-650.5 401.5,-650.5 401.5,-650.5 407.5,-650.5 413.5,-656.5 413.5,-662.5 413.5,-662.5 413.5,-674.5 413.5,-674.5 413.5,-680.5 407.5,-686.5 401.5,-686.5"/>
<text text-anchor="middle" x="337.5" y="-666" font-family="sans" font-size="10.00" fill="#000000">pe_remove_polya_cutadapt</text>
</g>
<!-- 36->17 -->
<g id="edge49" class="edge">
<title>36->17</title>
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+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M327.9567,-650.0941C314.7473,-622.8634 292.5,-569.8923 292.5,-522 292.5,-522 292.5,-522 292.5,-378 292.5,-337.1184 290.3827,-323.0052 311.5,-288 318.3169,-276.7 328.3685,-266.6739 338.54,-258.4217"/>
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<!-- 36->31 -->
<g id="edge64" class="edge">
<title>36->31</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M319.0796,-650.4784C294.6271,-624.5348 254.5,-574.0336 254.5,-522 254.5,-522 254.5,-522 254.5,-306 254.5,-265.2078 241.9874,-243.0737 272.5,-216 310.8481,-181.974 681.4824,-185.0552 732.5,-180 754.7947,-177.7909 778.9112,-175.052 801.1518,-172.3828"/>
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+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M319.0796,-650.4784C294.6271,-624.5348 254.5,-574.0336 254.5,-522 254.5,-522 254.5,-522 254.5,-306 254.5,-265.1184 242.7763,-242.9697 273.5,-216 312.0289,-182.1788 682.4824,-185.0552 733.5,-180 755.6815,-177.8021 779.6664,-175.0798 801.8129,-172.4235"/>
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<!-- 36->59 -->
<g id="edge106" class="edge">
@@ -639,38 +639,38 @@
<!-- 37 -->
<g id="node38" class="node">
<title>37</title>
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+<path fill="none" stroke="#d87556" stroke-width="2" d="M430,-324C430,-324 333,-324 333,-324 327,-324 321,-318 321,-312 321,-312 321,-300 321,-300 321,-294 327,-288 333,-288 333,-288 430,-288 430,-288 436,-288 442,-294 442,-300 442,-300 442,-312 442,-312 442,-318 436,-324 430,-324"/>
<text text-anchor="middle" x="381.5" y="-303.5" font-family="sans" font-size="10.00" fill="#000000">create_index_kallisto</text>
</g>
<!-- 37->17 -->
<g id="edge50" class="edge">
<title>37->17</title>
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-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="381.3529,-262.088 377.0344,-252.4133 374.3771,-262.6694 381.3529,-262.088"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M380.2383,-287.8314C379.7035,-280.131 379.0677,-270.9743 378.4734,-262.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="381.9632,-262.1467 377.7787,-252.4133 374.98,-262.6317 381.9632,-262.1467"/>
</g>
<!-- 37->18 -->
<g id="edge52" class="edge">
<title>37->18</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M429.6974,-287.8314C455.6966,-278.0306 487.9536,-265.8709 515.2281,-255.5894"/>
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+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="517.2643,-258.8264 525.3987,-252.038 514.8064,-252.2721 517.2643,-258.8264"/>
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<!-- 38 -->
<g id="node39" class="node">
<title>38</title>
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+<path fill="none" stroke="#d8ac56" stroke-width="2" d="M577.5,-686.5C577.5,-686.5 467.5,-686.5 467.5,-686.5 461.5,-686.5 455.5,-680.5 455.5,-674.5 455.5,-674.5 455.5,-662.5 455.5,-662.5 455.5,-656.5 461.5,-650.5 467.5,-650.5 467.5,-650.5 577.5,-650.5 577.5,-650.5 583.5,-650.5 589.5,-656.5 589.5,-662.5 589.5,-662.5 589.5,-674.5 589.5,-674.5 589.5,-680.5 583.5,-686.5 577.5,-686.5"/>
<text text-anchor="middle" x="522.5" y="-666" font-family="sans" font-size="10.00" fill="#000000">remove_polya_cutadapt</text>
</g>
<!-- 38->18 -->
<g id="edge51" class="edge">
<title>38->18</title>
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</g>
<!-- 38->32 -->
<g id="edge66" class="edge">
<title>38->32</title>
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+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M525.0999,-650.0328C530.2013,-618.2821 543.6371,-552.1246 572.5,-504 651.0069,-373.1014 700.9451,-352.0338 839.5,-288 883.5197,-267.6561 901.2249,-277.4553 942.5,-252 970.4016,-234.7925 996.7068,-207.9663 1014.1727,-188.0741"/>
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<!-- 38->62 -->
<g id="edge109" class="edge">
@@ -681,19 +681,19 @@
<!-- 39 -->
<g id="node40" class="node">
<title>39</title>
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<text text-anchor="middle" x="778.5" y="-375.5" font-family="sans" font-size="10.00" fill="#000000">merge_TIN_scores</text>
</g>
<!-- 39->19 -->
<g id="edge53" class="edge">
<title>39->19</title>
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+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M770.0625,-359.9555C752.3504,-322.0762 711.2049,-234.0818 690.2531,-189.274"/>
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</g>
<!-- 40 -->
<g id="node41" class="node">
<title>40</title>
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+<path fill="none" stroke="#5663d8" stroke-width="2" d="M1260.5,-252C1260.5,-252 1168.5,-252 1168.5,-252 1162.5,-252 1156.5,-246 1156.5,-240 1156.5,-240 1156.5,-228 1156.5,-228 1156.5,-222 1162.5,-216 1168.5,-216 1168.5,-216 1260.5,-216 1260.5,-216 1266.5,-216 1272.5,-222 1272.5,-228 1272.5,-228 1272.5,-240 1272.5,-240 1272.5,-246 1266.5,-252 1260.5,-252"/>
<text text-anchor="middle" x="1214.5" y="-231.5" font-family="sans" font-size="10.00" fill="#000000">alfa_qc_all_samples</text>
</g>
<!-- 40->20 -->
@@ -705,7 +705,7 @@
<!-- 41 -->
<g id="node42" class="node">
<title>41</title>
-<path fill="none" stroke="#56b1d8" stroke-width="2" d="M1394.5,-252C1394.5,-252 1302.5,-252 1302.5,-252 1296.5,-252 1290.5,-246 1290.5,-240 1290.5,-240 1290.5,-228 1290.5,-228 1290.5,-222 1296.5,-216 1302.5,-216 1302.5,-216 1394.5,-216 1394.5,-216 1400.5,-216 1406.5,-222 1406.5,-228 1406.5,-228 1406.5,-240 1406.5,-240 1406.5,-246 1400.5,-252 1394.5,-252"/>
+<path fill="none" stroke="#5663d8" stroke-width="2" d="M1394.5,-252C1394.5,-252 1302.5,-252 1302.5,-252 1296.5,-252 1290.5,-246 1290.5,-240 1290.5,-240 1290.5,-228 1290.5,-228 1290.5,-222 1296.5,-216 1302.5,-216 1302.5,-216 1394.5,-216 1394.5,-216 1400.5,-216 1406.5,-222 1406.5,-228 1406.5,-228 1406.5,-240 1406.5,-240 1406.5,-246 1400.5,-252 1394.5,-252"/>
<text text-anchor="middle" x="1348.5" y="-231.5" font-family="sans" font-size="10.00" fill="#000000">alfa_qc_all_samples</text>
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<!-- 41->20 -->
@@ -717,7 +717,7 @@
<!-- 42 -->
<g id="node43" class="node">
<title>42</title>
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<text text-anchor="middle" x="961.5" y="-381" font-family="sans" font-size="10.00" fill="#000000">rename_star_rpm_for_alfa</text>
<text text-anchor="middle" x="961.5" y="-370" font-family="sans" font-size="10.00" fill="#000000">unique: Unique</text>
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@@ -736,7 +736,7 @@
<!-- 52 -->
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<title>46->31</title>
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<text text-anchor="middle" x="390.5" y="-381" font-family="sans" font-size="10.00" fill="#000000">extract_transcriptome</text>
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diff --git a/images/rule_graph.svg b/images/rule_graph.svg
index 79aa749..cb260f5 100644
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<g id="node4" class="node">
<title>3</title>
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+<g id="edge1" class="edge">
<title>3->0</title>
<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M865.892,-431.8777C861.4984,-404.6417 854,-351.4948 854,-306 854,-306 854,-306 854,-162 854,-121.2235 843.4119,-75.0472 835.4967,-46.2247"/>
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@@ -54,11 +54,11 @@
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<g id="node5" class="node">
<title>4</title>
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</g>
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+<g id="edge4" class="edge">
<title>4->0</title>
<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1032.0737,-431.7434C1008.7654,-405.9886 971,-356.4717 971,-306 971,-306 971,-306 971,-162 971,-101.0638 905.7286,-56.9075 863.0745,-34.5576"/>
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@@ -66,11 +66,11 @@
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<g id="node6" class="node">
<title>5</title>
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<text text-anchor="middle" x="27" y="-375.5" font-family="sans" font-size="10.00" fill="#000000">fastqc</text>
</g>
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+<g id="edge9" class="edge">
<title>5->1</title>
<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M27.5291,-359.7719C29.6541,-317.3835 40.2588,-210.7263 93,-144 104.2897,-129.7166 120.4546,-118.6219 136.3599,-110.3072"/>
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@@ -78,11 +78,11 @@
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<g id="node7" class="node">
<title>6</title>
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<text text-anchor="middle" x="136" y="-591.5" font-family="sans" font-size="10.00" fill="#000000">pe_genome_quantification_kallisto</text>
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<title>6->1</title>
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@@ -90,11 +90,11 @@
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<g id="node8" class="node">
<title>7</title>
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</g>
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+<g id="edge7" class="edge">
<title>7->1</title>
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@@ -102,11 +102,11 @@
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</g>
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+<g id="edge10" class="edge">
<title>8->1</title>
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@@ -114,11 +114,11 @@
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<g id="node10" class="node">
<title>9</title>
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+<g id="edge6" class="edge">
<title>9->1</title>
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@@ -126,11 +126,11 @@
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<title>10</title>
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@@ -138,7 +138,7 @@
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@@ -150,7 +150,7 @@
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@@ -162,11 +162,11 @@
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<g id="node23" class="node">
<title>22</title>
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@@ -174,11 +174,11 @@
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<title>30</title>
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<title>13</title>
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<!-- 13->3 -->
@@ -228,7 +228,7 @@
<!-- 14 -->
<g id="node15" class="node">
<title>14</title>
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<text text-anchor="middle" x="1019" y="-519.5" font-family="sans" font-size="10.00" fill="#000000">quantification_salmon</text>
</g>
<!-- 14->3 -->
@@ -246,19 +246,19 @@
<!-- 15 -->
<g id="node16" class="node">
<title>15</title>
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<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>
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<!-- 23 -->
<g id="node24" class="node">
<title>23</title>
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</g>
<!-- 15->23 -->
@@ -270,7 +270,7 @@
<!-- 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"/>
+<path fill="none" stroke="#56c1d8" 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>
</g>
<!-- 15->25 -->
@@ -282,7 +282,7 @@
<!-- 16 -->
<g id="node17" class="node">
<title>16</title>
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+<path fill="none" stroke="#d88556" 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 -->
@@ -292,13 +292,13 @@
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</g>
<!-- 16->13 -->
-<g id="edge25" class="edge">
+<g id="edge26" 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"/>
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</g>
<!-- 16->30 -->
-<g id="edge49" class="edge">
+<g id="edge50" 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"/>
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@@ -306,7 +306,7 @@
<!-- 17 -->
<g id="node18" class="node">
<title>17</title>
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+<path fill="none" stroke="#d6d856" 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 -->
@@ -316,7 +316,7 @@
<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"/>
</g>
<!-- 17->7 -->
-<g id="edge20" class="edge">
+<g id="edge21" 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"/>
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@@ -324,11 +324,11 @@
<!-- 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"/>
+<path fill="none" stroke="#5673d8" 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>
</g>
<!-- 18->7 -->
-<g id="edge21" class="edge">
+<g id="edge20" 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"/>
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@@ -348,7 +348,7 @@
<!-- 19 -->
<g id="node20" class="node">
<title>19</title>
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+<path fill="none" stroke="#d85656" 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>
</g>
<!-- 19->8 -->
@@ -360,7 +360,7 @@
<!-- 20 -->
<g id="node21" class="node">
<title>20</title>
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+<path fill="none" stroke="#56d88a" 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>
</g>
<!-- 20->9 -->
@@ -372,7 +372,7 @@
<!-- 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"/>
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<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 -->
@@ -384,17 +384,17 @@
<!-- 27 -->
<g id="node28" class="node">
<title>27</title>
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<text text-anchor="middle" x="530" y="-303.5" font-family="sans" font-size="10.00" fill="#000000">alfa_qc</text>
</g>
<!-- 21->27 -->
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+<g id="edge44" 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"/>
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<!-- 22->13 -->
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+<g id="edge25" class="edge">
<title>22->13</title>
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@@ -414,7 +414,7 @@
<!-- 24 -->
<g id="node25" class="node">
<title>24</title>
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<!-- 24->17 -->
@@ -426,7 +426,7 @@
<!-- 29 -->
<g id="node30" class="node">
<title>29</title>
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<!-- 24->29 -->
@@ -444,7 +444,7 @@
<!-- 26 -->
<g id="node27" class="node">
<title>26</title>
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<!-- 26->19 -->
@@ -462,7 +462,7 @@
<!-- 28 -->
<g id="node29" class="node">
<title>28</title>
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@@ -472,13 +472,13 @@
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<!-- 29->22 -->
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+<g id="edge35" class="edge">
<title>29->22</title>
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+<g id="edge41" class="edge">
<title>30->26</title>
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@@ -492,7 +492,7 @@
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<title>31</title>
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@@ -502,13 +502,13 @@
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@@ -516,23 +516,23 @@
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<text text-anchor="middle" x="291" y="-519.5" font-family="sans" font-size="10.00" fill="#000000">extract_transcripts_as_bed12</text>
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diff --git a/scripts/labkey_to_snakemake.dict.tsv b/scripts/prepare_inputs.labkey_to_snakemake.dict.tsv
similarity index 100%
rename from scripts/labkey_to_snakemake.dict.tsv
rename to scripts/prepare_inputs.labkey_to_snakemake.dict.tsv
diff --git a/scripts/labkey_to_snakemake.py b/scripts/prepare_inputs.py
similarity index 96%
rename from scripts/labkey_to_snakemake.py
rename to scripts/prepare_inputs.py
index 6cce1e4..4ac90ab 100755
--- a/scripts/labkey_to_snakemake.py
+++ b/scripts/prepare_inputs.py
@@ -3,6 +3,7 @@
"""Create input table and config for Rhea."""
import argparse
+from functools import partial
import gzip
import logging
import math
@@ -17,244 +18,6 @@ import pandas as pd
logger = logging.getLogger(__name__)
-def main():
- """
- Create input table and config for Rhea.
- """
- args = parse_cli_args()
-
- setup_logging(
- logger=logger,
- verbose=args.verbose,
- debug=args.debug,
- )
-
- # get input table from LabKey or CLI
- if args.labkey_domain:
- logger.info(
- f"Fetching input table from LabKey instance "
- "'{args.labkey_domain}'..."
- )
- input_table = fetch_labkey_table(
- domain=args.labkey_domain,
- container_path=args.labkey_path,
- query_name=args.table,
- )
- labkey_table = expand_path(
- '.'.join([args.output_table.name, "labkey"])
- )
- input_table.to_csv(
- labkey_table,
- sep='\t',
- index=False,
- )
- from_api = True
- else:
- logger.info(f"Reading input table from file '{args.table}'...")
- input_table = pd.read_csv(
- args.table,
- header=0,
- sep='\t',
- index_col=None,
- comment='#',
- engine='python',
- )
- from_api = False
-
- # get LabKey to Snakemake sample table field mappings
- input_dict = pd.read_csv(
- args.input_to_output_mapping,
- header=0,
- sep='\t',
- index_col=None,
- comment='#',
- engine='python',
- )
- args.input_to_output_mapping.close()
- input_dict.set_index('snakemake', inplace=True, drop=True)
-
- # create Snakemake table
- logger.info("Creating Snakemake input table...")
- snakemake_table = pd.DataFrame()
-
- for index, row in input_table.iterrows():
-
- # extract data from LabKey-like table
- lk_replicate_name = row[input_dict.loc['replicate_name', 'labkey']]
- lk_condition = row[input_dict.loc['condition', 'labkey']]
- lk_seqmode = row[input_dict.loc['seqmode', 'labkey']]
- lk_fastq_path = row[input_dict.loc['fastq_path', 'labkey']]
- lk_fq1 = row[input_dict.loc['fq1', 'labkey']]
- lk_fq2 = row[input_dict.loc['fq2', 'labkey']]
- lk_fq1_3p = row[input_dict.loc['fq1_3p', 'labkey']]
- lk_fq1_5p = row[input_dict.loc['fq1_5p', 'labkey']]
- lk_fq2_3p = row[input_dict.loc['fq2_3p', 'labkey']]
- lk_fq2_5p = row[input_dict.loc['fq2_5p', 'labkey']]
- lk_organism = row[input_dict.loc['organism', 'labkey']]
- lk_sd = row[input_dict.loc['sd', 'labkey']]
- lk_mean = row[input_dict.loc['mean', 'labkey']]
- lk_mate1_direction = row[input_dict.loc['mate1_direction', 'labkey']]
- lk_mate2_direction = row[input_dict.loc['mate2_direction', 'labkey']]
-
- # extract, infer or convert to Snakemake input format
- if from_api and not os.path.isabs(lk_fastq_path):
- anchor = os.getcwd()
- logger.warning(
- f"[WARNING] Don't know how to interpret relative paths "
- "inside LabKey table. Trying with current working directory "
- f"'{anchor}' as an anchor, but it may be better to use"
- "absolute paths wherever possible..."
- )
- else:
- anchor = os.path.abspath(os.path.dirname(args.table))
- sample = "_".join([lk_replicate_name, lk_condition])
- if lk_seqmode == 'PAIRED':
- seqmode = 'pe'
- fq2 = expand_path(
- lk_fastq_path,
- lk_fq2,
- anchor=anchor,
- )
- elif lk_seqmode == 'SINGLE':
- seqmode = 'se'
- fq2 = "XXXXXXXXXXXXXXX"
- else:
- logger.error(
- f"[ERROR] Illegal sequencing mode '{lk_seqmode}' in row "
- f"{index+1}."
- )
- sys.exit("Execution aborted.")
- fq1 = expand_path(
- lk_fastq_path,
- lk_fq1,
- anchor=anchor,
- )
- read_length = get_read_length(fq1)
- index_size = read_length - 1
- kmer = kmer_from_read_length(read_length)
- fq1_3p = lk_fq1_3p
- fq1_5p = lk_fq1_5p
- fq2_3p = lk_fq2_3p
- fq2_5p = lk_fq2_5p
- organism = lk_organism.replace(' ', '_').lower()
- gtf = expand_path(
- args.resources_dir,
- organism,
- 'annotation.gtf',
- )
- genome = expand_path(
- args.resources_dir,
- organism,
- 'genome.fa',
- )
- sd = lk_sd
- mean = lk_mean
- fq1_polya_3p, fq1_polya_5p = get_polya_adapter_seqs(lk_mate1_direction)
- fq2_polya_3p, fq2_polya_5p = get_polya_adapter_seqs(lk_mate2_direction)
- kallisto_directionality = get_strand_param_kallisto(lk_mate1_direction)
- alfa_directionality = get_strand_param_alfa(lk_mate1_direction)
- alfa_plus, alfa_minus = get_strand_names_alfa(lk_mate1_direction)
-
- # construct row in Snakemake input table
- snakemake_table.loc[index, 'sample'] = sample
- snakemake_table.loc[index, 'seqmode'] = seqmode
- snakemake_table.loc[index, 'fq1'] = fq1
- snakemake_table.loc[index, 'fq2'] = fq2
- snakemake_table.loc[index, 'index_size'] = index_size
- snakemake_table.loc[index, 'kmer'] = kmer
- snakemake_table.loc[index, 'fq1_3p'] = fq1_3p
- snakemake_table.loc[index, 'fq1_5p'] = fq1_5p
- snakemake_table.loc[index, 'fq2_3p'] = fq2_3p
- snakemake_table.loc[index, 'fq2_5p'] = fq2_5p
- snakemake_table.loc[index, 'organism'] = organism
- snakemake_table.loc[index, 'gtf'] = gtf
- snakemake_table.loc[index, 'genome'] = genome
- snakemake_table.loc[index, 'sd'] = sd
- snakemake_table.loc[index, 'mean'] = mean
- snakemake_table.loc[index, 'kallisto_directionality'] = \
- kallisto_directionality
- snakemake_table.loc[index, 'alfa_directionality'] = alfa_directionality
- snakemake_table.loc[index, 'alfa_plus'] = alfa_plus
- snakemake_table.loc[index, 'alfa_minus'] = alfa_minus
-
- # add CLI argument-dependent parameters
- snakemake_table.loc[index, 'multimappers'] = args.multimappers
- snakemake_table.loc[index, 'soft_clip'] = args.soft_clip
- snakemake_table.loc[index, 'pass_mode'] = args.pass_mode
- snakemake_table.loc[index, 'libtype'] = args.libtype
- if args.trim_polya is True:
- snakemake_table.loc[index, 'fq1_polya_3p'] = fq1_polya_3p
- snakemake_table.loc[index, 'fq1_polya_5p'] = fq1_polya_5p
- snakemake_table.loc[index, 'fq2_polya_3p'] = fq2_polya_3p
- snakemake_table.loc[index, 'fq2_polya_5p'] = fq2_polya_5p
-
- # adjust sample table format
- snakemake_table.fillna('XXXXXXXXXXXXXXX', inplace=True)
- snakemake_table = snakemake_table.astype(
- {
- "sd": int,
- "mean": int,
- "multimappers": int,
- "kmer": int,
- "index_size": int,
- }
- )
-
- # write Snakemake sample table
- logger.info("Writing Snakemake input table...")
- snakemake_table.to_csv(
- args.output_table,
- sep='\t',
- header=True,
- index=False)
- args.output_table.close()
-
- # compile entries for Snakemake config file
- logger.info("Creating Snakemake config file...")
- results_dir = expand_path(
- args.output_dir,
- "results",
- )
- log_dir = expand_path(
- args.output_dir,
- "logs",
- )
- kallisto_indexes = expand_path(
- results_dir,
- "kallisto_indexes",
- )
- salmon_indexes = expand_path(
- results_dir,
- "salmon_indexes",
- )
- star_indexes = expand_path(
- results_dir,
- "star_indexes",
- )
- alfa_indexes = expand_path(
- results_dir,
- "alfa_indexes",
- )
-
- # write Snakemake config file
- logger.info("Writing Snakemake config file...")
- config_file_content = f'''---
- samples: "{expand_path(args.output_table.name)}"
- output_dir: "{results_dir}"
- log_dir: "{log_dir}"
- kallisto_indexes: "{kallisto_indexes}"
- salmon_indexes: "{salmon_indexes}"
- star_indexes: "{star_indexes}"
- alfa_indexes: "{alfa_indexes}"
- report_description: "{args.description}"
- report_logo: "{args.logo}"
- report_url: "{args.url}"
-...
-'''
- args.config_file.write(config_file_content)
- args.config_file.close()
-
-
def parse_cli_args() -> argparse.Namespace:
"""
Parses command line arguments.
@@ -298,7 +61,7 @@ def parse_cli_args() -> argparse.Namespace:
type=argparse.FileType('r'),
default=os.path.join(
os.path.dirname(__file__),
- 'labkey_to_snakemake.dict.tsv',
+ 'prepare_inputs.labkey_to_snakemake.dict.tsv',
),
help="lookup table with mappings from input (LabKey or LabKey-like) "
"to output (Snakemake) table; default: '%(default)s'",
@@ -335,6 +98,12 @@ def parse_cli_args() -> argparse.Namespace:
"(default: %(default)s)",
metavar="DIR",
)
+ parser.add_argument(
+ "--no-process-paths",
+ action="store_true",
+ default=False,
+ help="do not attempt to create absolute paths in output files",
+ )
behavior = parser.add_argument_group("workflow behavior")
behavior.add_argument(
@@ -415,7 +184,7 @@ def parse_cli_args() -> argparse.Namespace:
if args.logo:
args.logo.close()
- args.logo = os.path.abspath(args.logo.name)
+ args.logo = args.logo.name
else:
args.logo = ""
@@ -510,7 +279,7 @@ def get_read_length(file: str) -> int:
def kmer_from_read_length(
- l: int,
+ length: int,
k_max: int = 31,
k_min: int = 11,
) -> int:
@@ -523,7 +292,7 @@ def kmer_from_read_length(
https://salmon.readthedocs.io/en/latest/salmon.html#preparing-transcriptome-indices-mapping-based-mode
https://groups.google.com/d/msg/sailfish-users/fphjX7OIGzY/bMBwlCaZAgAJ
- :param l: length of read in nucleotides
+ :param length: length of read in nucleotides
:param k_max: maximum allowed k-mer size
:param k_min: minimum allowed k-mer size
@@ -531,9 +300,9 @@ def kmer_from_read_length(
where k is biggest odd integer that fulfills k < l / 2
"""
k = k_max
- if l < 2 * k_max + 1:
+ if length < 2 * k_max + 1:
# ensure kmer is smaller than half of read length
- k = math.floor((l - 1) / 2)
+ k = math.floor((length - 1) / 2)
# ensure kmer is odd
if not k % 2:
k -= 1
@@ -639,6 +408,7 @@ def expand_path(
*args: str,
anchor: str = os.getcwd(),
expand: bool = True,
+ no_abs: bool = False,
) -> str:
"""
Constructs absolute path.
@@ -654,10 +424,14 @@ def expand_path(
the path will be returned without considering the anchor
:param expand: whether environment variables and user directories (e.g,
`~`) shall be expanded
+ :param join_only: path fragments in args are joined, but no further
+ processing is done
:returns: absolute path
"""
suffix = os.path.join(*args)
+ if no_abs:
+ return suffix
if os.path.isabs(suffix):
return os.path.normpath(suffix)
if expand:
@@ -668,17 +442,257 @@ def expand_path(
)
if os.path.isabs(suffix):
return os.path.normpath(suffix)
- if expand:
- anchor = os.path.expanduser(
- os.path.expandvars(
- anchor
- )
+ anchor = os.path.expanduser(
+ os.path.expandvars(
+ anchor
)
+ )
path = os.path.join(anchor, suffix)
return os.path.normpath(path)
+def main(args):
+ """
+ Create input table and config for Rhea.
+ """
+ setup_logging(
+ logger=logger,
+ verbose=args.verbose,
+ debug=args.debug,
+ )
+
+ # get input table from LabKey or CLI
+ if args.labkey_domain:
+ logger.info(
+ f"Fetching input table from LabKey instance "
+ "'{args.labkey_domain}'..."
+ )
+ input_table = fetch_labkey_table(
+ domain=args.labkey_domain,
+ container_path=args.labkey_path,
+ query_name=args.table,
+ )
+ labkey_table = expand_path(
+ '.'.join([args.output_table.name, "labkey"])
+ )
+ input_table.to_csv(
+ labkey_table,
+ sep='\t',
+ index=False,
+ )
+ from_api = True
+ else:
+ logger.info(f"Reading input table from file '{args.table}'...")
+ input_table = pd.read_csv(
+ args.table,
+ header=0,
+ sep='\t',
+ index_col=None,
+ comment='#',
+ engine='python',
+ )
+ from_api = False
+
+ # get LabKey to Snakemake sample table field mappings
+ input_dict = pd.read_csv(
+ args.input_to_output_mapping,
+ header=0,
+ sep='\t',
+ index_col=None,
+ comment='#',
+ engine='python',
+ )
+ args.input_to_output_mapping.close()
+ input_dict.set_index('snakemake', inplace=True, drop=True)
+
+ # create Snakemake table
+ logger.info("Creating Snakemake input table...")
+ snakemake_table = pd.DataFrame()
+
+ for index, row in input_table.iterrows():
+
+ # extract data from LabKey-like table
+ lk_replicate_name = row[input_dict.loc['replicate_name', 'labkey']]
+ lk_condition = row[input_dict.loc['condition', 'labkey']]
+ lk_seqmode = row[input_dict.loc['seqmode', 'labkey']]
+ lk_fastq_path = row[input_dict.loc['fastq_path', 'labkey']]
+ lk_fq1 = row[input_dict.loc['fq1', 'labkey']]
+ lk_fq2 = row[input_dict.loc['fq2', 'labkey']]
+ lk_fq1_3p = row[input_dict.loc['fq1_3p', 'labkey']]
+ lk_fq1_5p = row[input_dict.loc['fq1_5p', 'labkey']]
+ lk_fq2_3p = row[input_dict.loc['fq2_3p', 'labkey']]
+ lk_fq2_5p = row[input_dict.loc['fq2_5p', 'labkey']]
+ lk_organism = row[input_dict.loc['organism', 'labkey']]
+ lk_sd = row[input_dict.loc['sd', 'labkey']]
+ lk_mean = row[input_dict.loc['mean', 'labkey']]
+ lk_mate1_direction = row[input_dict.loc['mate1_direction', 'labkey']]
+ lk_mate2_direction = row[input_dict.loc['mate2_direction', 'labkey']]
+
+ # extract, infer or convert to Snakemake input format
+ if from_api and not os.path.isabs(lk_fastq_path):
+ anchor = os.getcwd()
+ logger.warning(
+ f"[WARNING] Don't know how to interpret relative paths "
+ "inside LabKey table. Trying with current working directory "
+ f"'{anchor}' as an anchor, but it may be better to use"
+ "absolute paths wherever possible..."
+ )
+ else:
+ anchor = os.path.abspath(os.path.dirname(args.table))
+ sample = "_".join([lk_replicate_name, lk_condition])
+ if lk_seqmode == 'PAIRED':
+ seqmode = 'pe'
+ fq2 = expand_path(
+ lk_fastq_path,
+ lk_fq2,
+ anchor=anchor,
+ )
+ elif lk_seqmode == 'SINGLE':
+ seqmode = 'se'
+ fq2 = "XXXXXXXXXXXXXXX"
+ else:
+ logger.error(
+ f"[ERROR] Illegal sequencing mode '{lk_seqmode}' in row "
+ f"{index+1}."
+ )
+ sys.exit("Execution aborted.")
+ fq1 = expand_path(
+ lk_fastq_path,
+ lk_fq1,
+ anchor=anchor,
+ )
+ read_length = get_read_length(fq1)
+ index_size = read_length - 1
+ kmer = kmer_from_read_length(read_length)
+ fq1_3p = lk_fq1_3p
+ fq1_5p = lk_fq1_5p
+ fq2_3p = lk_fq2_3p
+ fq2_5p = lk_fq2_5p
+ organism = lk_organism.replace(' ', '_').lower()
+ gtf = expand_path(
+ args.resources_dir,
+ organism,
+ 'annotation.gtf',
+ )
+ genome = expand_path(
+ args.resources_dir,
+ organism,
+ 'genome.fa',
+ )
+ sd = lk_sd
+ mean = lk_mean
+ fq1_polya_3p, fq1_polya_5p = get_polya_adapter_seqs(lk_mate1_direction)
+ fq2_polya_3p, fq2_polya_5p = get_polya_adapter_seqs(lk_mate2_direction)
+ kallisto_directionality = get_strand_param_kallisto(lk_mate1_direction)
+ alfa_directionality = get_strand_param_alfa(lk_mate1_direction)
+ alfa_plus, alfa_minus = get_strand_names_alfa(lk_mate1_direction)
+
+ # construct row in Snakemake input table
+ snakemake_table.loc[index, 'sample'] = sample
+ snakemake_table.loc[index, 'seqmode'] = seqmode
+ snakemake_table.loc[index, 'fq1'] = fq1
+ snakemake_table.loc[index, 'fq2'] = fq2
+ snakemake_table.loc[index, 'index_size'] = index_size
+ snakemake_table.loc[index, 'kmer'] = kmer
+ snakemake_table.loc[index, 'fq1_3p'] = fq1_3p
+ snakemake_table.loc[index, 'fq1_5p'] = fq1_5p
+ snakemake_table.loc[index, 'fq2_3p'] = fq2_3p
+ snakemake_table.loc[index, 'fq2_5p'] = fq2_5p
+ snakemake_table.loc[index, 'organism'] = organism
+ snakemake_table.loc[index, 'gtf'] = gtf
+ snakemake_table.loc[index, 'genome'] = genome
+ snakemake_table.loc[index, 'sd'] = sd
+ snakemake_table.loc[index, 'mean'] = mean
+ snakemake_table.loc[index, 'kallisto_directionality'] = \
+ kallisto_directionality
+ snakemake_table.loc[index, 'alfa_directionality'] = alfa_directionality
+ snakemake_table.loc[index, 'alfa_plus'] = alfa_plus
+ snakemake_table.loc[index, 'alfa_minus'] = alfa_minus
+
+ # add CLI argument-dependent parameters
+ snakemake_table.loc[index, 'multimappers'] = args.multimappers
+ snakemake_table.loc[index, 'soft_clip'] = args.soft_clip
+ snakemake_table.loc[index, 'pass_mode'] = args.pass_mode
+ snakemake_table.loc[index, 'libtype'] = args.libtype
+ if args.trim_polya is True:
+ snakemake_table.loc[index, 'fq1_polya_3p'] = fq1_polya_3p
+ snakemake_table.loc[index, 'fq1_polya_5p'] = fq1_polya_5p
+ snakemake_table.loc[index, 'fq2_polya_3p'] = fq2_polya_3p
+ snakemake_table.loc[index, 'fq2_polya_5p'] = fq2_polya_5p
+
+ # adjust sample table format
+ snakemake_table.fillna('XXXXXXXXXXXXXXX', inplace=True)
+ snakemake_table = snakemake_table.astype(
+ {
+ "sd": int,
+ "mean": int,
+ "multimappers": int,
+ "kmer": int,
+ "index_size": int,
+ }
+ )
+
+ # write Snakemake sample table
+ logger.info("Writing Snakemake input table...")
+ snakemake_table.to_csv(
+ args.output_table,
+ sep='\t',
+ header=True,
+ index=False)
+ args.output_table.close()
+
+ # compile entries for Snakemake config file
+ logger.info("Creating Snakemake config file...")
+ results_dir = expand_path(
+ args.output_dir,
+ "results",
+ )
+ log_dir = expand_path(
+ args.output_dir,
+ "logs",
+ )
+ kallisto_indexes = expand_path(
+ results_dir,
+ "kallisto_indexes",
+ )
+ salmon_indexes = expand_path(
+ results_dir,
+ "salmon_indexes",
+ )
+ star_indexes = expand_path(
+ results_dir,
+ "star_indexes",
+ )
+ alfa_indexes = expand_path(
+ results_dir,
+ "alfa_indexes",
+ )
+
+ # write Snakemake config file
+ logger.info("Writing Snakemake config file...")
+ config_file_content = f'''---
+ samples: "{expand_path(args.output_table.name)}"
+ output_dir: "{results_dir}"
+ log_dir: "{log_dir}"
+ kallisto_indexes: "{kallisto_indexes}"
+ salmon_indexes: "{salmon_indexes}"
+ star_indexes: "{star_indexes}"
+ alfa_indexes: "{alfa_indexes}"
+ report_description: "{args.description}"
+ report_logo: "{args.logo}"
+ report_url: "{args.url}"
+...
+'''
+ args.config_file.write(config_file_content)
+ args.config_file.close()
+
+
if __name__ == '__main__':
- main()
+ args = parse_cli_args()
+
+ # Set default according to CLI arg
+ expand_path = partial(expand_path, no_abs=args.no_process_paths) # type: ignore
+
+ main(args)
logger.info("Program completed successfully.")
sys.exit(0)
diff --git a/tests/test_scripts_labkey_to_snakemake_table/expected_output.md5 b/tests/test_scripts_labkey_to_snakemake_table/expected_output.md5
deleted file mode 100644
index abbf9ab..0000000
--- a/tests/test_scripts_labkey_to_snakemake_table/expected_output.md5
+++ /dev/null
@@ -1,2 +0,0 @@
-057cbd5757ca7f0b94909eeeca531af3 config.yaml
-34422785b7cc77d1aac73d25e767dc2d samples.tsv
diff --git a/tests/test_scripts_labkey_to_snakemake_api/expected_output.md5 b/tests/test_scripts_prepare_inputs_labkey/expected_output.md5
similarity index 100%
rename from tests/test_scripts_labkey_to_snakemake_api/expected_output.md5
rename to tests/test_scripts_prepare_inputs_labkey/expected_output.md5
diff --git a/tests/test_scripts_labkey_to_snakemake_api/test.sh b/tests/test_scripts_prepare_inputs_labkey/test.sh
similarity index 91%
rename from tests/test_scripts_labkey_to_snakemake_api/test.sh
rename to tests/test_scripts_prepare_inputs_labkey/test.sh
index 4f18c42..45aea36 100755
--- a/tests/test_scripts_labkey_to_snakemake_api/test.sh
+++ b/tests/test_scripts_prepare_inputs_labkey/test.sh
@@ -30,10 +30,10 @@ password ${LABKEY_PASS}
EOF
# Run tests
-python "../../scripts/labkey_to_snakemake.py" \
+python "../../scripts/prepare_inputs.py" \
--labkey-domain="${LABKEY_HOST}" \
--labkey-path="/Zavolan Group/TEST_LABKEY" \
- --input-to-output-mapping="../../scripts/labkey_to_snakemake.dict.tsv" \
+ --input-to-output-mapping="../../scripts/prepare_inputs.labkey_to_snakemake.dict.tsv" \
--resources-dir="../input_files" \
--output-table="samples.tsv" \
--config-file="config.yaml" \
diff --git a/tests/test_scripts_prepare_inputs_table/expected_output.md5 b/tests/test_scripts_prepare_inputs_table/expected_output.md5
new file mode 100644
index 0000000..ae56572
--- /dev/null
+++ b/tests/test_scripts_prepare_inputs_table/expected_output.md5
@@ -0,0 +1,2 @@
+6be36d7527d4b1705f39d4297d5e2bd0 config.yaml
+c8dcc5a203e9046806c4090525960151 samples.tsv
diff --git a/tests/test_scripts_labkey_to_snakemake_table/input_table.tsv b/tests/test_scripts_prepare_inputs_table/input_table.tsv
similarity index 100%
rename from tests/test_scripts_labkey_to_snakemake_table/input_table.tsv
rename to tests/test_scripts_prepare_inputs_table/input_table.tsv
diff --git a/tests/test_scripts_labkey_to_snakemake_table/test.sh b/tests/test_scripts_prepare_inputs_table/test.sh
similarity index 85%
rename from tests/test_scripts_labkey_to_snakemake_table/test.sh
rename to tests/test_scripts_prepare_inputs_table/test.sh
index e60c4fc..b58dae1 100755
--- a/tests/test_scripts_labkey_to_snakemake_table/test.sh
+++ b/tests/test_scripts_prepare_inputs_table/test.sh
@@ -21,13 +21,15 @@ script_dir="$(cd "$(dirname "${BASH_SOURCE[0]}")" >/dev/null 2>&1 && pwd)"
cd $script_dir/
# Run tests
-python "../../scripts/labkey_to_snakemake.py" \
- --input-to-output-mapping="../../scripts/labkey_to_snakemake.dict.tsv" \
+python "../../scripts/prepare_inputs.py" \
+ --input-to-output-mapping="../../scripts/prepare_inputs.labkey_to_snakemake.dict.tsv" \
--resources-dir="../input_files" \
--output-table="samples.tsv" \
--config-file="config.yaml" \
--multimappers='10' \
--logo="../../images/logo.128px.png" \
+ --output-dir="." \
+ --no-process-paths \
"input_table.tsv"
--
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