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Changeset 0:e462044ece67 (2024-06-04)

Next changeset 1:da336e3ead38 (2024-06-17)

Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit 8593dacde03b50726e9ca12fa15e4a104531708c

diff -r 000000000000 -r e462044ece67 falco.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/falco.xml Tue Jun 04 14:14:49 2024 +0000

[

b'@@ -0,0 +1,219 @@\n+<tool id="falco" name="Falco" version="1.2.2+galaxy0" profile="21.05">\n+ <description>A high throughput sequence QC analysis tool</description>\n+ <xrefs>\n+ <xref type="bio.tools">falco</xref>\n+ </xrefs>\n+ <requirements>\n+ <requirement type="package" version="1.2.2">falco</requirement>\n+ </requirements>\n+ <command detect_errors="aggressive"><![CDATA[\n+ #import re\n+ #set input_name = re.sub(\'[^\\w\\-\\s]\', \'_\', str($input_file.element_identifier))\n+\n+ #if $input_file.ext.endswith(\'.gz\'):\n+ #set input_file_sl = $input_name + \'.gz\'\n+ #elif $input_file.ext.endswith(\'.bz2\'):\n+ #set input_file_sl = $input_name + \'.bz2\'\n+ #else\n+ #set input_file_sl = $input_name\n+ #end if\n+\n+ #if \'bam\' in $input_file.ext:\n+ #set format = \'bam\'\n+ #elif \'sam\' in $input_file.ext:\n+ #set format = \'sam\'\n+ #else\n+ #set format = \'fastq\'\n+ #end if\n+\n+ ln -s \'${input_file}\' \'${input_file_sl}\' &&\n+ falco\n+ #if $contaminants:\n+ --contaminants \'${contaminants}\'\n+ #end if\n+\n+ #if $adapters.dataset and str($adapters) > \'\'\n+ --adapters \'${adapters}\'\n+ #end if\n+\n+ #if $limits.dataset and str($limits) > \'\'\n+ --limits \'${limits}\'\n+ #end if\n+ --threads \\${GALAXY_SLOTS:-2}\n+ --quiet\n+ --extract\n+ ## #if $min_length:\n+ ## --min_length $min_length\n+ ## #end if\n+ $nogroup\n+ ## --kmers $kmers\n+ -f \'${format}\'\n+ \'${input_file_sl}\'\n+ -subsample $subsample\n+ $bisulfite\n+ $reverse_complement\n+\n+ ]]></command>\n+ <inputs>\n+ <param format="fastq,fastq.gz,fastq.bz2,bam,sam" name="input_file" type="data" label="Raw read data from your current history"/>\n+ <param name="contaminants" type="data" format="tabular" optional="true" label="Contaminant list" help="tab delimited file with 2 columns: name and sequence. For example: Illumina Small RNA RT Primer	CAAGCAGAAGACGGCATACGA"/>\n+ <param argument="--adapters" type="data" format="tabular" optional="true" label="Adapter list" help="List of adapters adapter sequences which will be explicity searched against the library. It should be a tab-delimited file with 2 columns: name and sequence."/>\n+ <param name="limits" type="data" format="txt" optional="true" label="Submodule and Limit specifing file" help="a file that specifies which submodules are to be executed (default=all) and also specifies the thresholds for the each submodules warning parameter."/>\n+ <param argument="--nogroup" type="boolean" truevalue="--nogroup" falsevalue="" checked="False" label="Disable grouping of bases for reads >50bp" help=" Using this option, your plots may end up a ridiculous size. You have been warned!"/>\n+ \n+ \n+ <param argument="-subs'..b'ta_nogroup_summary.txt" ftype="txt"/>\n+ <assert_command>\n+ <has_text text="--nogroup"/>\n+ </assert_command>\n+ </test>\n+ <test>\n+ <param name="input_file" value="1000trimmed.fastq"/>\n+ <param name="subsample" value="10"/>\n+ <output name="html_file" file="fastqc_report_subsample.html" ftype="html" lines_diff="2"/>\n+ <output name="text_file" file="fastqc_report_subsample.txt" ftype="txt"/>\n+ <output name="summary_file" file="fastqc_report_subsample_summary.txt" ftype="txt"/>\n+ </test>\n+ <test>\n+ <param name="input_file" value="1000trimmed.fastq"/>\n+ <param name="bisulfite" value="-bisulfite"/>\n+ <output name="html_file" file="fastqc_report_bisulfite.html" ftype="html" lines_diff="2"/>\n+ <output name="text_file" file="fastqc_report_bisulfite.txt" ftype="txt"/>\n+ <output name="summary_file" file="fastqc_report_bisulfite_summary.txt" ftype="txt"/>\n+ </test>\n+ <test>\n+ <param name="input_file" value="1000trimmed.fastq"/>\n+ <param name="reverse_complement" value="-reverse-complement"/>\n+ <output name="html_file" file="fastqc_report_reverse_complement.html" ftype="html" lines_diff="2"/>\n+ <output name="text_file" file="fastqc_report_reverse_complement.txt" ftype="txt"/>\n+ <output name="summary_file" file="fastqc_report_reverse_complement_summary.txt" ftype="txt"/>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+.. class:: infomark\n+\n+**Purpose**\n+\n+Falco is an emulation of the popular FastQC software to check large sequencing reads for common problems.\n+\n+The main functions of Falco are:\n+\n+- Import of data from BAM, SAM or FastQ/FastQ.gz files (any variant),\n+- Providing a quick overview to tell you in which areas there may be problems\n+- Summary graphs and tables to quickly assess your data\n+- Export of results to an HTML based permanent report\n+- Offline operation to allow automated generation of reports without running the interactive application\n+\n+-----\n+\n+.. class:: infomark\n+\n+**Inputs and outputs**\n+\n+Falco_ is the best place to look for documentation - it\'s very good.\n+A summary follows below for those in a tearing hurry.\n+\n+This wrapper will accept a Galaxy fastq, fastq.gz, sam or bam as the input read file to check.\n+It will also take an optional file containing a list of contaminants information, in the form of\n+a tab-delimited file with 2 columns, name and sequence. As another option the tool takes a custom\n+limits.txt file that allows setting the warning thresholds for the different modules and also specifies\n+which modules to include in the output.\n+\n+The tool produces a basic text and a HTML output file that contain all of the results, including the following:\n+\n+- Basic Statistics\n+- Per base sequence quality\n+- Per sequence quality scores\n+- Per base sequence content\n+- Per base GC content\n+- Per sequence GC content\n+- Per base N content\n+- Sequence Length Distribution\n+- Sequence Duplication Levels\n+- Overrepresented sequences\n+- Adapter Content\n+\n+All except Basic Statistics and Overrepresented sequences are plots.\n+ .. _Falco: https://github.com/smithlabcode/falco/\n+ .. _Picard-tools: https://broadinstitute.github.io/picard/\n+ ]]></help>\n+ <citations>\n+ <citation type="bibtex">\n+ @article{deSenaBrandine2021,\n+ author = {de Sena Brandine, Gabriel and Smith, Andrew D.},\n+ title = {Falco: high-speed FastQC emulation for quality control of sequencing data},\n+ journal = {F1000Research},\n+ year = {2021},\n+ volume = {8},\n+ pages = {1874},\n+ url = {https://doi.org/10.12688/f1000research.21142.2},\n+ doi = {10.12688/f1000research.21142.2},\n+ note = {Version 2; peer review: 2 approved},\n+ }\n+ \n+ </citation>\n+ </citations>\n+</tool>\n'

diff -r 000000000000 -r e462044ece67 test-data/1000trimmed.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/1000trimmed.fastq Tue Jun 04 14:14:49 2024 +0000

b"@@ -0,0 +1,19620 @@\n+@ERR005448.2 IL40_2446:5:1:0:451/2\n+ACACTCTTTCCCTACACGACGCTGTTCCATCTACACTCTTTCCCTACACGACGCTGTTCCATCT\n++\n+>?A?<8=AB?:<B<:9;ABB=<78458:?@<@>?A?<8=AB?:<B<:9;ABB=<78458:?@<@\n+@ERR005448.2 IL40_2446:5:1:0:451/2\n+ATAAAGACCAGCCTGGCCAATGTGGTGAAACCCTGTCTCTACTAAAAGTACAAAATAAAGACCAGCCTGGCCAATGTGGTGAAACCCTGTCTCTACTAAAAGTACAAA\n++\n+>?A?<8=AB?:<B<:9;ABB=<78458:?@<@@<68@@BA><>@@>8/3>9=;?>?A?<8=AB?:<B<:9;ABB=<78458:?@<@@<68@@BA><>@@>8/3>9=;?\n+@ERR005448.3 IL40_2446:5:1:0:1205/2\n+ATTCTACTCCAACT\n++\n+?:B7C;6<<;B6/7\n+@ERR005448.4 IL40_2446:5:1:0:17/2\n+CACTTCCAGATACTCCAAAAAGAGTGTTTCCAACCTGCTCTAGTAATGGGAATGCACTTCCAGATACTCCAAAAAGAGTGTTTCCAACCTGCTCTAGTAATGGGAATG\n++\n+BBBA=<=B6ABA<BB8>>@7=?>44>8;88=@=6B9??;B=6;8<:BB?@9=<ABBBA=<=B6ABA<BB8>>@7=?>44>8;88=@=6B9??;B=6;8<:BB?@9=<A\n+@ERR005448.5 IL40_2446:5:1:0:719/2\n+ATTCCATCCTT\n++\n+@>@>AA99975\n+@ERR005448.6 IL40_2446:5:1:0:156/2\n+CAGGAAAGGGCCTGGTGGGAGGTAATTGGATCATGGGGGTGGTTTCCTCCATGCCAGGAAAGGGCCTGGTGGGAGGTAATTGGATCATGGGGGTGGTTTCCTCCATGC\n++\n+<:<=;A=4=A?@?4>>?0=84=?AAA>@:8BB<;=09;?'?;4??:A@>@?A>;<:<=;A=4=A?@?4>>?0=84=?AAA>@:8BB<;=09;?'?;4??:A@>@?A>;\n+@ERR005448.8 IL40_2446:5:1:0:1162/2\n+GCTTATCAACAGAAAGCA\n++\n+0=;=;8*<;7;=8A8048\n+@ERR005448.10 IL40_2446:5:1:0:842/2\n+TGGATTCCACTCCATTCCATTGCAC\n++\n+>81>?>5>?=@?>@>?>=9;>79=6\n+@ERR005448.11 IL40_2446:5:1:0:947/2\n+AAAAAAAAAAAGCTGGGAG\n++\n+AAAAAAAA?=>:8?:;539\n+@ERR005448.12 IL40_2446:5:1:0:389/2\n+CAGAGATGTTTAATATGAGCCAGGAATTCTGCTAGGCACTTTGTGTATGTTTTACAGAGATGTTTAATATGAGCCAGGAATTCTGCTAGGCACTTTGTGTATGTTTTA\n++\n+@?559>@76>CCC@CC;A80=B>7?B?=<;><B?66;A=BC>>;>6A><;?B>>@?559>@76>CCC@CC;A80=B>7?B?=<;><B?66;A=BC>>;>6A><;?B>>\n+@ERR005448.13 IL40_2446:5:1:0:435/2\n+ACTGAATTTGGAA\n++\n+89=7)?>C;8997\n+@ERR005448.14 IL40_2446:5:1:0:552/2\n+CTTTGA\n++\n+AA?/*<\n+@ERR005448.15 IL40_2446:5:1:0:770/2\n+AAAA\n++\n+>>>6\n+@ERR005448.16 IL40_2446:5:1:0:788/2\n+AATGGCTTTGA\n++\n+>>>6;:AB8)6\n+@ERR005448.18 IL40_2446:5:1:0:1012/2\n+TGCCTACAATAGCAAATTTTGAAAAACATAGAG\n++\n+>;4?4=??@B7'8>AA>?@;8=C?C;;:>=,=5\n+@ERR005448.19 IL40_2446:5:1:0:1150/2\n+TTATATGCAAGCGAAGAAGGTAAGTA\n++\n+>=?AB8<:8438><=48;921<<00:\n+@ERR005448.20 IL40_2446:5:1:0:1254/2\n+TGTCTCTTCTCTCTTGAATTCCTGATCT\n++\n+95<AC=BB@C@AAC??<AAA:==8;?@:\n+@ERR005448.21 IL40_2446:5:1:0:1669/2\n+CAGCACCT\n++\n+8>3<A?36\n+@ERR005448.23 IL40_2446:5:1:0:57/2\n+ATGATGGTAGAGAGGACATTGTCAAAGATGCCAAAATTTTAGACTCATTGGG\n++\n+A:3??AA9>>>B99;>ABCC>>C?B=0:BA=:ABB>@99?B;39B?79;069\n+@ERR005448.24 IL40_2446:5:1:0:971/2\n+AAAATAATTCCCATTGCTATTTCTCGT\n++\n+AAB@>ACCCA>@B=<1:C>;=?>@=>6\n+@ERR005448.25 IL40_2446:5:1:0:685/2\n+TTCCATTCCACACGGGTTGGTTCCCTTGCATCCCTTTCCATTCCA\n++\n+:?A@@AAA?@@@95<:79393=:6<==4;<?7>0;9>973;4<35\n+@ERR005448.26 IL40_2446:5:1:0:311/2\n+GCTGACTGATAGGCCCCACTCGCGGTA\n++\n+=?99?=<><?>33==?=A@=<6@7475\n+@ERR005448.27 IL40_2446:5:1:0:528/2\n+AGACTGGATTAAGAAAATGTGGCACATATACACCATGGAATACTATGCA\n++\n+BACB<.;;?C@:=ABC@891:6<AAAB=3>@?8;<79=9>=<??<@9-7\n+@ERR005448.28 IL40_2446:5:1:0:315/2\n+AACTTTTACTATCTGTACCATTCCTGTACTCTGACATTACCTGGTTATGTCTGAAACTTTTACTATCTGTACCATTCCTGTACTCTGACATTACCTGGTTATGTCTG\n++\n+AAC?CA@?=ABB=A;>@><?B?;7;78C??C:6<A@B@;:@B>;6>>;53=854AAC?CA@?=ABB=A;>@><?B?;7;78C??C:6<A@B@;:@B>;6>>;53=85\n+@ERR005448.29 IL40_2446:5:1:0:1616/2\n+TATAATCTTAATGGGATCCATCATTGACCAAAATGCAGCCCATCATTGACCAAATATAATCTTAATGGGATCCATCATTGACCAAAATGCAGCCCATCATTGACCAAA\n++\n+C>:@ACCBCCC=8677B>?C?6>:@:@=;=@CC=6:>863:@<<=<609<;?;BC>:@ACCBCCC=8677B>?C?6>:@:@=;=@CC=6:>863:@<<=<609<;?;B\n+@ERR005448.30 IL40_2446:5:1:0:852/2\n+TGATGTGTG\n++\n+?6<?:9/75\n+@ERR005448.31 IL40_2446:5:1:0:1684/2\n+AGAAGGATACCGACTGGA\n++\n+=/;>85:A>;:4=<<446\n+@ERR005448.32 IL40_2446:5:1:1:881/2\n+GTCTAGGAATTTATTTATTTTCCCTATATTTTTCAGTTCACTAGCATATAGTTGGTCTAGGAATTTATTTATTTTCCCTATATTTTTCAGTTCACTAGCATATAGTTG\n++\n+C7?6>B@==8>>8@CCA@A=@<>>@@ACCACB:::;3A5=4?>3><8=CA=826C7?6>B@==8>>8@CCA@A=@<>>@@ACCACB:::;3A5=4?>3><8=CA=826\n+@ERR005448.33 IL40_2446:5:1:1:412/2\n+GTCCCAGGGCCCAGAAGAGCTTGTGGCCTCCTTGCAGACATCAGTAGTGGCCCCGTCCCAGGGCCCAGAAGAGCTTGTGGCCTCCTTGCAGACATCAGTAGTGGCCCC\n++\n+<8>A?=5929@@><=?7?9@A<4:49>A?>AA;289<?>:;9<:3?6969<<8<<8>A?=5929@@><=?7?9"..b"=A49@@@BB@A>@;;?A:7=\n+@CONTAMINATED-SEQ\n+ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT\n++\n+>@;;?A:7=AAAB<<B<=AAB@A;0?BBAB><'=A49@@@BB@A>@;;?A:7=AAAB<<B<=AAB@A;0?BBAB><'=A49@@@BB@A>@;;?A:7=\n+@CONTAMINATED-SEQ\n+ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT\n++\n+>@;;?A:7=AAAB<<B<=AAB@A;0?BBAB><'=A49@@@BB@A>@;;?A:7=AAAB<<B<=AAB@A;0?BBAB><'=A49@@@BB@A>@;;?A:7=\n+@CONTAMINATED-SEQ\n+ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT\n++\n+>@;;?A:7=AAAB<<B<=AAB@A;0?BBAB><'=A49@@@BB@A>@;;?A:7=AAAB<<B<=AAB@A;0?BBAB><'=A49@@@BB@A>@;;?A:7=\n+@CONTAMINATED-SEQ\n+ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT\n++\n+>@;;?A:7=AAAB<<B<=AAB@A;0?BBAB><'=A49@@@BB@A>@;;?A:7=AAAB<<B<=AAB@A;0?BBAB><'=A49@@@BB@A>@;;?A:7=\n+@CONTAMINATED-SEQ\n+ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT\n++\n+>@;;?A:7=AAAB<<B<=AAB@A;0?BBAB><'=A49@@@BB@A>@;;?A:7=AAAB<<B<=AAB@A;0?BBAB><'=A49@@@BB@A>@;;?A:7=\n+@CONTAMINATED-SEQ\n+ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT\n++\n+>@;;?A:7=AAAB<<B<=AAB@A;0?BBAB><'=A49@@@BB@A>@;;?A:7=AAAB<<B<=AAB@A;0?BBAB><'=A49@@@BB@A>@;;?A:7=\n+@CONTAMINATED-SEQ\n+ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT\n++\n+>@;;?A:7=AAAB<<B<=AAB@A;0?BBAB><'=A49@@@BB@A>@;;?A:7=AAAB<<B<=AAB@A;0?BBAB><'=A49@@@BB@A>@;;?A:7=\n+@CONTAMINATED-SEQ\n+ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT\n++\n+>@;;?A:7=AAAB<<B<=AAB@A;0?BBAB><'=A49@@@BB@A>@;;?A:7=AAAB<<B<=AAB@A;0?BBAB><'=A49@@@BB@A>@;;?A:7=\n+@CONTAMINATED-SEQ\n+ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT\n++\n+>@;;?A:7=AAAB<<B<=AAB@A;0?BBAB><'=A49@@@BB@A>@;;?A:7=AAAB<<B<=AAB@A;0?BBAB><'=A49@@@BB@A>@;;?A:7=\n+@CONTAMINATED-SEQ\n+ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT\n++\n+>@;;?A:7=AAAB<<B<=AAB@A;0?BBAB><'=A49@@@BB@A>@;;?A:7=AAAB<<B<=AAB@A;0?BBAB><'=A49@@@BB@A>@;;?A:7=\n+@CONTAMINATED-SEQ\n+ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT\n++\n+>@;;?A:7=AAAB<<B<=AAB@A;0?BBAB><'=A49@@@BB@A>@;;?A:7=AAAB<<B<=AAB@A;0?BBAB><'=A49@@@BB@A>@;;?A:7=\n+@CONTAMINATED-SEQ\n+ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT\n++\n+>@;;?A:7=AAAB<<B<=AAB@A;0?BBAB><'=A49@@@BB@A>@;;?A:7=AAAB<<B<=AAB@A;0?BBAB><'=A49@@@BB@A>@;;?A:7=\n+@CONTAMINATED-SEQ\n+ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT\n++\n+>@;;?A:7=AAAB<<B<=AAB@A;0?BBAB><'=A49@@@BB@A>@;;?A:7=AAAB<<B<=AAB@A;0?BBAB><'=A49@@@BB@A>@;;?A:7=\n+@CONTAMINATED-SEQ\n+ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT\n++\n+>@;;?A:7=AAAB<<B<=AAB@A;0?BBAB><'=A49@@@BB@A>@;;?A:7=AAAB<<B<=AAB@A;0?BBAB><'=A49@@@BB@A>@;;?A:7=\n+@CONTAMINATED-SEQ\n+ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT\n++\n+>@;;?A:7=AAAB<<B<=AAB@A;0?BBAB><'=A49@@@BB@A>@;;?A:7=AAAB<<B<=AAB@A;0?BBAB><'=A49@@@BB@A>@;;?A:7=\n+@CONTAMINATED-SEQ\n+ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT\n++\n+>@;;?A:7=AAAB<<B<=AAB@A;0?BBAB><'=A49@@@BB@A>@;;?A:7=AAAB<<B<=AAB@A;0?BBAB><'=A49@@@BB@A>@;;?A:7=\n+@CONTAMINATED-SEQ\n+ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT\n++\n+>@;;?A:7=AAAB<<B<=AAB@A;0?BBAB><'=A49@@@BB@A>@;;?A:7=AAAB<<B<=AAB@A;0?BBAB><'=A49@@@BB@A>@;;?A:7=\n+@CONTAMINATED-SEQ\n+ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT\n++\n+>@;;?A:7=AAAB<<B<=AAB@A;0?BBAB><'=A49@@@BB@A>@;;?A:7=AAAB<<B<=AAB@A;0?BBAB><'=A49@@@BB@A>@;;?A:7=\n"

diff -r 000000000000 -r e462044ece67 test-data/1000trimmed.fastq.bz2

Binary file test-data/1000trimmed.fastq.bz2 has changed

diff -r 000000000000 -r e462044ece67 test-data/1000trimmed.fastq.gz

Binary file test-data/1000trimmed.fastq.gz has changed

diff -r 000000000000 -r e462044ece67 test-data/adapter_list.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/adapter_list.txt Tue Jun 04 14:14:49 2024 +0000

[

@@ -0,0 +1,26 @@
+# This file contains a set of sequence fragments which will be explicitly
+# searched against your library. The reporting will be similar to the
+# Kmer plot, except that every sequence in this list will be shown so
+# you can use this to judge the level of adapter read-through even if those
+# adapter sequences aren't picked out by the Kmer module.
+#
+# Since every sequence here will be analysed and the results plotted it
+# doesn't make any sense to include duplicate sequences, or to add too
+# many sequences since your plot will end up a mess.
+#
+# You can add more sequences to the file by putting one line per entry
+# and specifying a name[tab]sequence. If the contaminant you add is
+# likely to be of use to others please consider sending it to the FastQ
+# authors, either via a bug report at www.bioinformatics.babraham.ac.uk/bugzilla/
+# or by directly emailing simon.andrews@babraham.ac.uk so other users of
+# the program can benefit.
+#
+# For the time being it's going to be easier to interpret this plot if all
+# of the sequences provided are the same length, so we've gone with 12bp
+# fragments for now.
+
+Illumina Universal Adapter AGATCGGAAGAG
+Illumina Small RNA 3 prime Adapter TGGAATTCTCGG
+Illumina Small RNA 5 prime Adapter GATCGTCGGACT
+Nextera Transposase Sequence CTGTCTCTTATA
+SOLID Small RNA Adapter CGCCTTGGCCGT

diff -r 000000000000 -r e462044ece67 test-data/contaminant_list.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/contaminant_list.txt Tue Jun 04 14:14:49 2024 +0000

[

b"@@ -0,0 +1,192 @@\n+# This file contains a list of potential contaminants which are\r\n+# frequently found in high throughput sequencing reactions. These\r\n+# are mostly sequences of adapters / primers used in the various\r\n+# sequencing chemistries.\r\n+# \r\n+# Please DO NOT rely on these sequences to design your own oligos, some\r\n+# of them are truncated at ambiguous positions, and none of them are\r\n+# definitive sequences from the manufacturers so don't blame us if you\r\n+# try to use them and they don't work.\r\n+#\r\n+# You can add more sequences to the file by putting one line per entry\r\n+# and specifying a name[tab]sequence. If the contaminant you add is \r\n+# likely to be of use to others please consider sending it to the FastQ\r\n+# authors, either via a bug report at www.bioinformatics.babraham.ac.uk/bugzilla/\r\n+# or by directly emailing simon.andrews@babraham.ac.uk so other users of\r\n+# the program can benefit.\r\n+\r\n+Illumina Single End Adapter 1\t\t\t\t\tGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG\r\n+Illumina Single End Adapter 2\t\t\t\t\tCAAGCAGAAGACGGCATACGAGCTCTTCCGATCT\r\n+Illumina Single End PCR Primer 1\t\t\t\tAATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT\r\n+Illumina Single End PCR Primer 2\t\t\t\tCAAGCAGAAGACGGCATACGAGCTCTTCCGATCT\r\n+Illumina Single End Sequencing Primer\t\t\tACACTCTTTCCCTACACGACGCTCTTCCGATCT\r\n+\r\n+Illumina Paired End Adapter 1\t\t\t\t\tACACTCTTTCCCTACACGACGCTCTTCCGATCT\r\n+Illumina Paired End Adapter 2\t\t\t\t\tGATCGGAAGAGCGGTTCAGCAGGAATGCCGAG\r\n+Illumina Paried End PCR Primer 1\t\t\t\tAATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT\r\n+Illumina Paired End PCR Primer 2\t\t\t\tCAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT\r\n+Illumina Paried End Sequencing Primer 1\t\t\tACACTCTTTCCCTACACGACGCTCTTCCGATCT\r\n+Illumina Paired End Sequencing Primer 2\t\t\tCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT\r\n+\r\n+Illumina DpnII expression Adapter 1\t\t\t\tACAGGTTCAGAGTTCTACAGTCCGAC\r\n+Illumina DpnII expression Adapter 2\t\t\t\tCAAGCAGAAGACGGCATACGA\r\n+Illumina DpnII expression PCR Primer 1\t\t\tCAAGCAGAAGACGGCATACGA\r\n+Illumina DpnII expression PCR Primer 2\t\t\tAATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA\r\n+Illumina DpnII expression Sequencing Primer\t\tCGACAGGTTCAGAGTTCTACAGTCCGACGATC\r\n+\r\n+Illumina NlaIII expression Adapter 1\t\t\tACAGGTTCAGAGTTCTACAGTCCGACATG\r\n+Illumina NlaIII expression Adapter 2\t\t\tCAAGCAGAAGACGGCATACGA\r\n+Illumina NlaIII expression PCR Primer 1\t\t\tCAAGCAGAAGACGGCATACGA\r\n+Illumina NlaIII expression PCR Primer 2\t\t\tAATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA\r\n+Illumina NlaIII expression Sequencing Primer\tCCGACAGGTTCAGAGTTCTACAGTCCGACATG\r\n+\r\n+Illumina Small RNA Adapter 1\t\t\t\t\tGTTCAGAGTTCTACAGTCCGACGATC\r\n+Illumina Small RNA Adapter 2\t\t\t\t\tTGGAATTCTCGGGTGCCAAGG\r\n+Illumina Small RNA RT Primer\t\t\t\t\tCAAGCAGAAGACGGCATACGA\r\n+Illumina Small RNA PCR Primer 2\t\t\t\t\tAATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA\r\n+Illumina Small RNA Sequencing Primer\t\t\tCGACAGGTTCAGAGTTCTACAGTCCGACGATC\r\n+\r\n+Illumina Multiplexing Adapter 1\t\t\t\t\tGATCGGAAGAGCACACGTCT\r\n+Illumina Multiplexing Adapter 2\t\t\t\t\tACACTCTTTCCCTACACGACGCTCTTCCGATCT\r\n+Illumina Multiplexing PCR Primer 1.01\t\t\tAATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT\r\n+Illumina Multiplexing PCR Primer 2.01\t\t\tGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT\r\n+Illumina Multiplexing Read1 Sequencing Primer\tACACTCTTTCCCTACACGACGCTCTTCCGATCT\r\n+Illumina Multiplexing Index Sequencing Primer\tGATCGGAAGAGCACACGTCTGAACTCCAGTCAC\r\n+Illumina Multiplexing Read2 Sequencing Primer\tGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT\r\n+\r\n+Illumina PCR Primer Index 1\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATCGTGATGTGACTGGAGTTC\r\n+Illumina PCR Primer Index 2\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATACATCGGTGACTGGAGTTC\r\n+Illumina PCR Primer Index 3\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATGCCTAAGTGACTGGAGTTC\r\n+Illumina PCR Primer Index 4\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATTGGTCAGTGACTGGAGTTC\r\n+Illumina PCR Primer Index 5\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATCACTGTGTGACTGGAGTTC\r\n+Illumina PCR Primer Index 6\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATATTGGCGTGACTGGAGTTC\r\n+Illumina PCR Primer Index 7\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATGATCTGGTGACTGGAGTT"..b"CA\r\n+RNA PCR Primer, Index 21\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATCGAAACGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\r\n+RNA PCR Primer, Index 22\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATCGTACGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\r\n+RNA PCR Primer, Index 23\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATCCACTCGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\r\n+RNA PCR Primer, Index 24\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATGCTACCGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\r\n+RNA PCR Primer, Index 25\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATATCAGTGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\r\n+RNA PCR Primer, Index 26\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATGCTCATGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\r\n+RNA PCR Primer, Index 27\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATAGGAATGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\r\n+RNA PCR Primer, Index 28\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATCTTTTGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\r\n+RNA PCR Primer, Index 29\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATTAGTTGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\r\n+RNA PCR Primer, Index 30\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATCCGGTGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\r\n+RNA PCR Primer, Index 31\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATATCGTGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\r\n+RNA PCR Primer, Index 32\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATTGAGTGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\r\n+RNA PCR Primer, Index 33\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATCGCCTGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\r\n+RNA PCR Primer, Index 34\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATGCCATGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\r\n+RNA PCR Primer, Index 35\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATAAAATGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\r\n+RNA PCR Primer, Index 36\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATTGTTGGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\r\n+RNA PCR Primer, Index 37\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATATTCCGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\r\n+RNA PCR Primer, Index 38\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATAGCTAGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\r\n+RNA PCR Primer, Index 39\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATGTATAGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\r\n+RNA PCR Primer, Index 40\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATTCTGAGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\r\n+RNA PCR Primer, Index 41\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATGTCGTCGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\r\n+RNA PCR Primer, Index 42\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATCGATTAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\r\n+RNA PCR Primer, Index 43\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATGCTGTAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\r\n+RNA PCR Primer, Index 44\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATATTATAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\r\n+RNA PCR Primer, Index 45\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATGAATGAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\r\n+RNA PCR Primer, Index 46\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATTCGGGAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\r\n+RNA PCR Primer, Index 47\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATCTTCGAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\r\n+RNA PCR Primer, Index 48\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATTGCCGAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\r\n+\r\n+ABI Dynabead EcoP Oligo\t\t\t\t\t\t\tCTGATCTAGAGGTACCGGATCCCAGCAGT\r\n+ABI Solid3 Adapter A\t\t\t\t\t\t\tCTGCCCCGGGTTCCTCATTCTCTCAGCAGCATG\r\n+ABI Solid3 Adapter B\t\t\t\t\t\t\tCCACTACGCCTCCGCTTTCCTCTCTATGGGCAGTCGGTGAT\r\n+ABI Solid3 5' AMP Primer\t\t\t\t\t\tCCACTACGCCTCCGCTTTCCTCTCTATG\r\n+ABI Solid3 3' AMP Primer\t\t\t\t\t\tCTGCCCCGGGTTCCTCATTCT\r\n+ABI Solid3 EF1 alpha Sense Primer\t\t\t\tCATGTGTGTTGAGAGCTTC\r\n+ABI Solid3 EF1 alpha Antisense Primer\t\t\tGAAAACCAAAGTGGTCCAC\r\n+ABI Solid3 GAPDH Forward Primer\t\t\t\t\tTTAGCACCCCTGGCCAAGG\r\n+ABI Solid3 GAPDH Reverse Primer\t\t\t\t\tCTTACTCCTTGGAGGCCATG\r\n+\r\n+\r\n+\r\n+Clontech Universal Primer Mix Short\t\t\t\tCTAATACGACTCACTATAGGGC\r\n+Clontech Universal Primer Mix Long\t\t\t\tCTAATACGACTCACTATAGGGCAAGCAGTGGTATCAACGCAGAGT\r\n+Clontech SMARTer II A Oligonucleotide\t\t\tAAGCAGTGGTATCAACGCAGAGTAC\r\n+Clontech SMART CDS Primer II A\t\t\t\t\tAAGCAGTGGTATCAACGCAGAGTACT\r\n+Clontech_Universal_Primer_Mix_Short CTAATACGACTCACTATAGGGC\r\n+Clontech_Universal_Primer_Mix_Long CTAATACGACTCACTATAGGGCAAGCAGTGGTATCAACGCAGAGT\r\n+Clontech_SMARTer_II_A_Oligonucleotide AAGCAGTGGTATCAACGCAGAGTAC\r\n+Clontech_SMART_CDS_Primer_II_A AAGCAGTGGTATCAACGCAGAGTACT\r\n+Clontech_SMART_CDS_Primer_II_A ACGTACTCTGCGTTGATACCACTGCTTCCGCGGACAGGCGTGTAGATCTCGGTGGTCGC\r\n+Clontech_SMART_CDS_Primer_II_A GAGTACGTACTCTGCGTTGATACCACTGCTTCCGCGGACAGGCGTGTAGATCTCGGTGGT\r\n+\r\n"

diff -r 000000000000 -r e462044ece67 test-data/fastqc_adapters.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fastqc_adapters.txt Tue Jun 04 14:14:49 2024 +0000

[

b"@@ -0,0 +1,170 @@\n+# This file contains a list of potential contaminants which are\n+# frequently found in high throughput sequencing reactions. These\n+# are mostly sequences of adapters / primers used in the various\n+# sequencing chemistries.\n+# \n+# Please DO NOT rely on these sequences to design your own oligos, some\n+# of them are truncated at ambiguous positions, and none of them are\n+# definitive sequences from the manufacturers so don't blame us if you\n+# try to use them and they don't work.\n+#\n+# You can add more sequences to the file by putting one line per entry\n+# and specifying a name[tab]sequence. If the contaminant you add is \n+# likely to be of use to others please consider sending it to the FastQ\n+# authors, either via a bug report at www.bioinformatics.bbsrc.ac.uk/bugzilla/\n+# or by directly emailing simon.andrews@bbsrc.ac.uk so other users of\n+# the program can benefit.\n+\n+Illumina Single End Apapter 1\t\t\t\t\tACACTCTTTCCCTACACGACGCTGTTCCATCT\n+Illumina Single End Apapter 2\t\t\t\t\tCAAGCAGAAGACGGCATACGAGCTCTTCCGATCT\n+Illumina Single End PCR Primer 1\t\t\t\tAATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT\n+Illumina Single End PCR Primer 2\t\t\t\tCAAGCAGAAGACGGCATACGAGCTCTTCCGATCT\n+Illumina Single End Sequencing Primer\t\t\tACACTCTTTCCCTACACGACGCTCTTCCGATCT\n+\n+Illumina Paired End Adapter 1\t\t\t\t\tACACTCTTTCCCTACACGACGCTCTTCCGATCT\n+Illumina Paired End Adapter 2\t\t\t\t\tCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT\n+Illumina Paried End PCR Primer 1\t\t\t\tAATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT\n+Illumina Paired End PCR Primer 2\t\t\t\tCAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT\n+Illumina Paried End Sequencing Primer 1\t\t\tACACTCTTTCCCTACACGACGCTCTTCCGATCT\n+Illumina Paired End Sequencing Primer 2\t\t\tCGGTCTCGGCATTCCTACTGAACCGCTCTTCCGATCT\n+\n+Illumina DpnII expression Adapter 1\t\t\t\tACAGGTTCAGAGTTCTACAGTCCGAC\n+Illumina DpnII expression Adapter 2\t\t\t\tCAAGCAGAAGACGGCATACGA\n+Illumina DpnII expression PCR Primer 1\t\t\tCAAGCAGAAGACGGCATACGA\n+Illumina DpnII expression PCR Primer 2\t\t\tAATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA\n+Illumina DpnII expression Sequencing Primer\t\tCGACAGGTTCAGAGTTCTACAGTCCGACGATC\n+\n+Illumina NlaIII expression Adapter 1\t\t\tACAGGTTCAGAGTTCTACAGTCCGACATG\n+Illumina NlaIII expression Adapter 2\t\t\tCAAGCAGAAGACGGCATACGA\n+Illumina NlaIII expression PCR Primer 1\t\t\tCAAGCAGAAGACGGCATACGA\n+Illumina NlaIII expression PCR Primer 2\t\t\tAATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA\n+Illumina NlaIII expression Sequencing Primer\tCCGACAGGTTCAGAGTTCTACAGTCCGACATG\n+\n+Illumina Small RNA Adapter 1\t\t\t\t\tGTTCAGAGTTCTACAGTCCGACGATC\n+Illumina Small RNA Adapter 2\t\t\t\t\tTCGTATGCCGTCTTCTGCTTGT\n+Illumina Small RNA RT Primer\t\t\t\t\tCAAGCAGAAGACGGCATACGA\n+Illumina Small RNA PCR Primer 1\t\t\t\t\tCAAGCAGAAGACGGCATACGA\n+Illumina Small RNA PCR Primer 2\t\t\t\t\tAATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA\n+Illumina Small RNA Sequencing Primer\t\t\tCGACAGGTTCAGAGTTCTACAGTCCGACGATC\n+\n+Illumina Multiplexing Adapter 1\t\t\t\t\tGATCGGAAGAGCACACGTCT\n+Illumina Multiplexing Adapter 2\t\t\t\t\tACACTCTTTCCCTACACGACGCTCTTCCGATCT\n+Illumina Multiplexing PCR Primer 1.01\t\t\tAATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT\n+Illumina Multiplexing PCR Primer 2.01\t\t\tGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT\n+Illumina Multiplexing Read1 Sequencing Primer\tACACTCTTTCCCTACACGACGCTCTTCCGATCT\n+Illumina Multiplexing Index Sequencing Primer\tGATCGGAAGAGCACACGTCTGAACTCCAGTCAC\n+Illumina Multiplexing Read2 Sequencing Primer\tGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT\n+\n+Illumina PCR Primer Index 1\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATCGTGATGTGACTGGAGTTC\n+Illumina PCR Primer Index 2\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATACATCGGTGACTGGAGTTC\n+Illumina PCR Primer Index 3\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATGCCTAAGTGACTGGAGTTC\n+Illumina PCR Primer Index 4\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATTGGTCAGTGACTGGAGTTC\n+Illumina PCR Primer Index 5\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATCACTGTGTGACTGGAGTTC\n+Illumina PCR Primer Index 6\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATATTGGCGTGACTGGAGTTC\n+Illumina PCR Primer Index 7\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATGATCTGGTGACTGGAGTTC\n+Illum"..b"AAGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n+RNA PCR Primer, Index 13\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATTTGACTGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n+RNA PCR Primer, Index 14\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATGGAACTGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n+RNA PCR Primer, Index 15\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATTGACATGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n+RNA PCR Primer, Index 16\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATGGACGGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n+RNA PCR Primer, Index 17\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATCTCTACGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n+RNA PCR Primer, Index 18\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATGCGGACGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n+RNA PCR Primer, Index 19\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATTTTCACGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n+RNA PCR Primer, Index 20\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATGGCCACGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n+RNA PCR Primer, Index 21\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATCGAAACGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n+RNA PCR Primer, Index 22\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATCGTACGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n+RNA PCR Primer, Index 23\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATCCACTCGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n+RNA PCR Primer, Index 24\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATGCTACCGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n+RNA PCR Primer, Index 25\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATATCAGTGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n+RNA PCR Primer, Index 26\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATGCTCATGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n+RNA PCR Primer, Index 27\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATAGGAATGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n+RNA PCR Primer, Index 28\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATCTTTTGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n+RNA PCR Primer, Index 29\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATTAGTTGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n+RNA PCR Primer, Index 30\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATCCGGTGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n+RNA PCR Primer, Index 31\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATATCGTGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n+RNA PCR Primer, Index 32\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATTGAGTGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n+RNA PCR Primer, Index 33\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATCGCCTGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n+RNA PCR Primer, Index 34\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATGCCATGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n+RNA PCR Primer, Index 35\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATAAAATGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n+RNA PCR Primer, Index 36\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATTGTTGGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n+RNA PCR Primer, Index 37\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATATTCCGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n+RNA PCR Primer, Index 38\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATAGCTAGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n+RNA PCR Primer, Index 39\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATGTATAGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n+RNA PCR Primer, Index 40\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATTCTGAGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n+RNA PCR Primer, Index 41\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATGTCGTCGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n+RNA PCR Primer, Index 42\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATCGATTAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n+RNA PCR Primer, Index 43\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATGCTGTAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n+RNA PCR Primer, Index 44\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATATTATAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n+RNA PCR Primer, Index 45\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATGAATGAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n+RNA PCR Primer, Index 46\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATTCGGGAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n+RNA PCR Primer, Index 47\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATCTTCGAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n+RNA PCR Primer, Index 48\t\t\t\t\t\tCAAGCAGAAGACGGCATACGAGATTGCCGAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n+\n+ABI Dynabead EcoP Oligo\t\t\t\t\t\t\tCTGATCTAGAGGTACCGGATCCCAGCAGT\n+ABI Solid3 Adapter A\t\t\t\t\t\t\tCTGCCCCGGGTTCCTCATTCTCTCAGCAGCATG\n+ABI Solid3 Adapter B\t\t\t\t\t\t\tCCACTACGCCTCCGCTTTCCTCTCTATGGGCAGTCGGTGAT\n+ABI Solid3 5' AMP Primer\t\t\t\t\t\tCCACTACGCCTCCGCTTTCCTCTCTATG\n+ABI Solid3 3' AMP Primer\t\t\t\t\t\tCTGCCCCGGGTTCCTCATTCT\n+ABI Solid3 EF1 alpha Sense Primer\t\t\t\tCATGTGTGTTGAGAGCTTC\n+ABI Solid3 EF1 alpha Antisense Primer\t\t\tGAAAACCAAAGTGGTCCAC\n+ABI Solid3 GAPDH Forward Primer\t\t\t\t\tTTAGCACCCCTGGCCAAGG\n+ABI Solid3 GAPDH Reverse Primer\t\t\t\t\tCTTACTCCTTGGAGGCCATG\n"

diff -r 000000000000 -r e462044ece67 test-data/fastqc_contaminants.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fastqc_contaminants.txt Tue Jun 04 14:14:49 2024 +0000

[

@@ -0,0 +1,17 @@
+# This file contains a list of potential contaminants which are
+# frequently found in high throughput sequencing reactions. These
+# are mostly sequences of adapters / primers used in the various
+# sequencing chemistries.
+#
+# Please DO NOT rely on these sequences to design your own oligos, some
+# of them are truncated at ambiguous positions, and none of them are
+# definitive sequences from the manufacturers so don't blame us if you
+# try to use them and they don't work.
+#
+# You can add more sequences to the file by putting one line per entry
+# and specifying a name[tab]sequence. If the contaminant you add is
+# likely to be of use to others please consider sending it to the FastQ
+# authors, either via a bug report at www.bioinformatics.bbsrc.ac.uk/bugzilla/
+# or by directly emailing simon.andrews@bbsrc.ac.uk so other users of
+# the program can benefit.
+TestContaminant ATGCATGCATGCATGCATGCATGC

diff -r 000000000000 -r e462044ece67 test-data/fastqc_customlimits.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fastqc_customlimits.txt Tue Jun 04 14:14:49 2024 +0000

@@ -0,0 +1,84 @@
+# For each of the modules you can choose to not run that
+# module at all by setting the value below to 1 for the
+# modules you want to remove.
+duplication ignore 0
+kmer ignore 0
+n_content ignore 0
+overrepresented ignore 0
+quality_base ignore 0
+sequence ignore 0
+gc_sequence ignore 0
+quality_sequence ignore 0
+tile ignore 0
+sequence_length ignore 0
+adapter ignore 0
+
+# For the duplication module the value is the percentage
+# remaining after deduplication.  Measured levels below
+# these limits trigger the warning / error.
+duplication warn 70
+duplication error 50
+
+# For the kmer module the filter is on the -log10 binomial
+# pvalue for the most significant Kmer, so 5 would be
+# 10^-5 = p<0.00001
+kmer warn 2
+kmer error 5
+
+# For the N module the filter is on the percentage of Ns
+# at any position in the library
+n_content warn 5
+n_content error 20
+
+# For the overrepresented seqs the warn value sets the
+# threshold for the overrepresented sequences to be reported
+# at all as the proportion of the library which must be seen
+# as a single sequence
+overrepresented warn 0.1
+overrepresented error 1
+
+# The per base quality filter uses two values, one for the value
+# of the lower quartile, and the other for the value of the
+# median quality.  Failing either of these will trigger the alert
+quality_base_lower warn 10
+quality_base_lower error 5
+quality_base_median warn 25
+quality_base_median error 20
+
+# The per base sequence content module tests the maximum deviation
+# between A and T or C and G
+sequence warn 10
+sequence error 20
+
+# The per sequence GC content tests the maximum deviation between
+# the theoretical distribution and the real distribution
+gc_sequence warn 15
+gc_sequence error 30
+
+# The per sequence quality module tests the phred score which is
+# most frequently observed
+quality_sequence warn 27
+quality_sequence error 20
+
+# The per tile module tests the maximum phred score loss between
+# and individual tile and the average for that base across all tiles
+tile warn 5
+tile error 10
+
+# The sequence length module tests are binary, so the values here
+# simply turn them on or off.  The actual tests warn if you have
+# sequences of different length, and error if you have sequences
+# of zero length.
+
+sequence_length warn 1
+sequence_length error 1
+
+# The adapter module's warnings and errors are based on the
+# percentage of reads in the library which have been observed
+# to contain an adapter associated Kmer at any point
+
+adapter warn 5
+adapter error 10
+
+
+

diff -r 000000000000 -r e462044ece67 test-data/fastqc_data.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fastqc_data.txt Tue Jun 04 14:14:49 2024 +0000

b'@@ -0,0 +1,1710 @@\n+##Falco\t1.2.2\n+>>Basic Statistics\tpass\n+#Measure\tValue\n+Filename\t1000trimmed_fastq\n+File type\tConventional base calls\n+Encoding\tSanger / Illumina 1.9\n+Total Sequences\t4905\n+Sequences flagged as poor quality\t0\n+Sequence length\t1-108\n+%GC\t41\n+>>END_MODULE\n+>>Per base sequence quality\tpass\n+#Base\tMean\tMedian\tLower Quartile\tUpper Quartile\t10th Percentile\t90th Percentile\n+1\t29.2828\t31\t27\t33\t23\t34\n+2\t28.8329\t30\t27\t32\t22\t33\n+3\t28.897\t30\t27\t32\t23\t34\n+4\t29.0068\t30\t27\t32\t23\t34\n+5\t28.9378\t30\t27\t32\t22\t34\n+6\t29.0029\t30\t27\t32\t23\t34\n+7\t28.8998\t30\t27\t32\t22\t34\n+8\t28.9007\t30\t27\t32\t22\t33\n+9\t28.7546\t30\t27\t32\t22\t34\n+10-11\t28.8221\t30\t27\t32\t22.5\t33\n+12-13\t28.749\t30\t26.5\t32\t22\t33\n+14-15\t28.5337\t30\t26\t32\t22\t33.5\n+16-17\t28.5266\t30\t26\t32\t22\t33\n+18-19\t28.6834\t30\t26\t32\t22.5\t33\n+20-21\t28.3701\t29.5\t26\t32\t22\t33\n+22-23\t28.1859\t29\t26\t32\t22\t33\n+24-25\t28.1301\t29\t26\t32\t21.5\t33\n+26-27\t28.0758\t29\t26\t32\t21.5\t33\n+28-29\t27.828\t29\t25\t32\t21\t33\n+30-31\t27.7928\t29\t25\t31.5\t21\t33\n+32-33\t27.491\t28\t25\t31\t21\t33\n+34-35\t27.3572\t28\t24.5\t31\t21\t33\n+36-37\t27.0622\t28\t24\t31\t20.5\t33\n+38-39\t27.238\t28\t24\t31\t21\t33\n+40-41\t27.029\t28\t24\t31\t20.5\t33\n+42-43\t26.9086\t27\t24\t31\t20.5\t33\n+44-45\t26.632\t27\t24\t30\t20\t32\n+46-47\t26.8304\t27.5\t24\t31\t20.5\t32\n+48-49\t26.4317\t27\t23.5\t30\t20\t32\n+50-51\t26.219\t27\t23\t30\t20\t32\n+52-53\t25.9257\t26.5\t22.5\t29.5\t19.5\t31.5\n+54-55\t27.9952\t29.5\t25.5\t31.5\t20.5\t33\n+56-57\t30.4109\t31.5\t28.5\t33\t25.5\t34\n+58-59\t30.4084\t31.5\t28.5\t33\t26\t34\n+60-61\t30.4448\t31.5\t29\t33\t26\t34\n+62-63\t30.4404\t31.5\t29\t33\t25.5\t34\n+64-65\t30.4417\t31.5\t29\t33\t25.5\t34\n+66-67\t30.5114\t32\t29\t33\t25.5\t34\n+68-69\t30.0512\t31\t28\t33\t24.5\t34\n+70-71\t30.2761\t31\t29\t33\t25\t34\n+72-73\t30.3855\t31.5\t29\t33\t25.5\t34\n+74-75\t30.2135\t31\t28.5\t33\t25.5\t34\n+76-77\t29.6789\t31\t28\t33\t24.5\t34\n+78-79\t30.0191\t31\t28\t33\t24.5\t34\n+80-81\t29.6642\t31\t27.5\t33\t24\t34\n+82-83\t29.6535\t31\t28\t32.5\t24.5\t34\n+84-85\t29.4256\t30.5\t27\t32\t24\t34\n+86-87\t29.3406\t30\t27\t32.5\t24\t34\n+88-89\t28.7857\t30\t27\t32\t22.5\t33.5\n+90-91\t28.6675\t29.5\t26\t32\t23\t33\n+92-93\t28.5659\t29\t26\t32\t23\t33\n+94-95\t28.2717\t29\t26\t32\t22.5\t33\n+96-97\t27.9496\t29\t25.5\t31\t22\t33\n+98-99\t27.3152\t28\t25\t31\t21.5\t33\n+100-101\t27.6147\t28\t25\t31\t21.5\t33\n+102-103\t27.1962\t28\t24.5\t31\t21\t33\n+104-105\t26.8709\t27.5\t24\t31\t20\t32.5\n+106-107\t26.3676\t27\t23.5\t30\t20.5\t32\n+108\t27.5651\t28\t24\t31\t22\t33\n+>>END_MODULE\n+>>Per tile sequence quality\tfail\n+#Tile\tBase\tMean\n+0\t1\t-29.4857\n+0\t2\t-28.7721\n+0\t3\t-28.5832\n+0\t4\t-28.7282\n+0\t5\t-28.9662\n+0\t6\t-28.9765\n+0\t7\t-29.0324\n+0\t8\t-28.9563\n+0\t9\t-28.4479\n+0\t10\t-28.2935\n+0\t11\t-28.6264\n+0\t12\t-28.711\n+0\t13\t-28.5163\n+0\t14\t-28.3915\n+0\t15\t-28.2392\n+0\t16\t-28.5304\n+0\t17\t-28.3975\n+0\t18\t-28.5859\n+0\t19\t-28.6272\n+0\t20\t-28.1273\n+0\t21\t-28.2058\n+0\t22\t-28.1046\n+0\t23\t-28.3908\n+0\t24\t-28.0801\n+0\t25\t-28.0111\n+0\t26\t-27.9571\n+0\t27\t-28.1062\n+0\t28\t-27.7915\n+0\t29\t-27.6043\n+0\t30\t-27.7709\n+0\t31\t-27.5781\n+0\t32\t-27.8211\n+0\t33\t-27.6197\n+0\t34\t-27.447\n+0\t35\t-27.3368\n+0\t36\t-27.2226\n+0\t37\t-27.2582\n+0\t38\t-27.2825\n+0\t39\t-26.7901\n+0\t40\t-26.9377\n+0\t41\t-27.17\n+0\t42\t-27.1488\n+0\t43\t-26.1931\n+0\t44\t-26.6119\n+0\t45\t-26.5613\n+0\t46\t-26.7864\n+0\t47\t-26.3367\n+0\t48\t-26.2903\n+0\t49\t-25.7095\n+0\t50\t-26.3457\n+0\t51\t-26.0927\n+0\t52\t-25.7055\n+0\t53\t-24.9716\n+0\t54\t-26\n+0\t55\t-30.4161\n+0\t56\t-30.3869\n+0\t57\t-30.1825\n+0\t58\t-29.6569\n+0\t59\t-30.0876\n+0\t60\t-30.146\n+0\t61\t-30.4891\n+0\t62\t-30.9197\n+0\t63\t-30.0511\n+0\t64\t-29.5255\n+0\t65\t-30.0956\n+0\t66\t-30.4559\n+0\t67\t-30.0588\n+0\t68\t-30.1176\n+0\t69\t-29.9853\n+0\t70\t-30.4191\n+0\t71\t-30.1029\n+0\t72\t-30.2206\n+0\t73\t-30.2132\n+0\t74\t-29.2721\n+0\t75\t-29.25\n+0\t76\t-29.7206\n+0\t77\t-29.8015\n+0\t78\t-29.7794\n+0\t79\t-29.6838\n+0\t80\t-29.5956\n+0\t81\t-29.4412\n+0\t82\t-29.3824\n+0\t83\t-29.375\n+0\t84\t-29.6176\n+0\t85\t-29.1544\n+0\t86\t-29.2059\n+0\t87\t-29.0074\n+0\t88\t-28.8162\n+0\t89\t-28.3603\n+0\t90\t-28.0809\n+0\t91\t-28.8309\n+0\t92\t-28.5882\n+0\t93\t-28.1618\n+0\t94\t-27.8897\n+0\t95\t-28.0074\n+0\t96\t-28.1471\n+0\t97\t-27.6471\n+0\t98\t-27.5662\n+0\t99\t-27.4485\n+0\t100\t-27.4044\n+0\t101\t-26.9265\n+0\t102\t-27.2132\n+0\t103\t-26.5882\n+0\t104\t-26.8603\n+0\t105\t-26.2868\n+0\t106\t-26.0588\n+0\t107\t-25.1343\n+0\t108\t-27.2314\n+1\t1\t0.904969\n+1\t2\t0.618551\n+1\t3\t0.463713\n+1\t4\t-0.165716\n+1\t5\t-0.0790766\n+1\t6\t0.136407\n+'..b'Base\tN-Count\n+1\t0\n+2\t0\n+3\t0\n+4\t0\n+5\t0\n+6\t0\n+7\t0\n+8\t0\n+9\t0\n+10-11\t0\n+12-13\t0\n+14-15\t0\n+16-17\t0\n+18-19\t0\n+20-21\t0\n+22-23\t0\n+24-25\t0\n+26-27\t0\n+28-29\t0\n+30-31\t0\n+32-33\t0\n+34-35\t0\n+36-37\t0\n+38-39\t0\n+40-41\t0\n+42-43\t0\n+44-45\t0\n+46-47\t0\n+48-49\t0\n+50-51\t0\n+52-53\t0\n+54-55\t0\n+56-57\t0\n+58-59\t0\n+60-61\t0\n+62-63\t0\n+64-65\t0\n+66-67\t0\n+68-69\t0\n+70-71\t0\n+72-73\t0\n+74-75\t0\n+76-77\t0\n+78-79\t0\n+80-81\t0\n+82-83\t0\n+84-85\t0\n+86-87\t0\n+88-89\t0\n+90-91\t0\n+92-93\t0\n+94-95\t0\n+96-97\t0\n+98-99\t0\n+100-101\t0\n+102-103\t0\n+104-105\t0\n+106-107\t0\n+108\t0\n+>>END_MODULE\n+>>Sequence Length Distribution\twarn\n+#Length\tCount\n+1\t3.0\n+2\t11.0\n+3\t28.0\n+4\t56.0\n+5\t43.0\n+6\t52.0\n+7\t39.0\n+8\t56.0\n+9\t60.0\n+10\t57.0\n+11\t43.0\n+12\t46.0\n+13\t45.0\n+14\t66.0\n+15\t59.0\n+16\t49.0\n+17\t73.0\n+18\t54.0\n+19\t44.0\n+20\t52.0\n+21\t73.0\n+22\t72.0\n+23\t68.0\n+24\t56.0\n+25\t86.0\n+26\t92.0\n+27\t75.0\n+28\t69.0\n+29\t74.0\n+30\t96.0\n+31\t72.0\n+32\t81.0\n+33\t65.0\n+34\t87.0\n+35\t86.0\n+36\t87.0\n+37\t100.0\n+38\t82.0\n+39\t78.0\n+40\t76.0\n+41\t79.0\n+42\t88.0\n+43\t83.0\n+44\t75.0\n+45\t74.0\n+46\t72.0\n+47\t84.0\n+48\t74.0\n+49\t81.0\n+50\t91.0\n+51\t80.0\n+52\t98.0\n+53\t43.0\n+54\t8.0\n+55\t4.0\n+56\t1.0\n+64\t1.0\n+97\t1.0\n+98\t32.0\n+106\t34.0\n+107\t169.0\n+108\t1122.0\n+>>END_MODULE\n+>>Sequence Duplication Levels\tpass\n+#Total Deduplicated Percentage\t98.736\n+#Duplication Level\tPercentage of deduplicated\tPercentage of total\n+1\t99.4425\t98.1855\n+2\t0.474912\t0.937819\n+3\t0.0412967\t0.122324\n+4\t0.0206484\t0.0815494\n+5\t0\t0\n+6\t0\t0\n+7\t0\t0\n+8\t0\t0\n+9\t0\t0\n+>10\t0.0206484\t0.672783\n+>50\t0\t0\n+>100\t0\t0\n+>500\t0\t0\n+>1k\t0\t0\n+>5k\t0\t0\n+>10k+\t0\t0\n+>>END_MODULE\n+>>Overrepresented sequences\twarn\n+#Sequence\tCount\tPercentage\tPossible Source\n+ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT\t33\t0.672783\tNo Hit\n+>>END_MODULE\n+>>Adapter Content\tpass\n+#Position\tIllumina Universal Adapter\tIllumina Small RNA 3 prime Adapter\tIllumina Small RNA 5 prime Adapter\tNextera Transposase Sequence\tSOLID Small RNA Adapter\n+1\t0\t0\t0\t0\t0\n+2\t0\t0\t0\t0\t0\n+3\t0\t0\t0\t0\t0\n+4\t0\t0\t0\t0\t0\n+5\t0\t0\t0\t0\t0\n+6\t0\t0\t0\t0\t0\n+7\t0\t0\t0\t0\t0\n+8\t0\t0\t0\t0\t0\n+9\t0\t0\t0\t0\t0\n+10\t0\t0\t0\t0\t0\n+11\t0\t0\t0\t0\t0\n+12\t0\t0\t0\t0\t0\n+13\t0\t0\t0\t0\t0\n+14\t0\t0\t0\t0\t0\n+15\t0\t0\t0\t0\t0\n+16\t0\t0\t0\t0\t0\n+17\t0\t0\t0\t0\t0\n+18\t0\t0\t0\t0\t0\n+19\t0\t0\t0\t0\t0\n+20\t0.122324\t0\t0\t0\t0\n+21\t0.122324\t0\t0\t0\t0\n+22\t0.122324\t0\t0\t0\t0\n+23\t0.122324\t0\t0\t0\t0\n+24\t0.122324\t0\t0\t0\t0\n+25\t0.122324\t0\t0\t0\t0\n+26\t0.122324\t0\t0\t0\t0\n+27\t0.142712\t0\t0\t0\t0\n+28\t0.183486\t0\t0\t0\t0\n+29\t0.224261\t0\t0\t0\t0\n+30\t0.224261\t0\t0\t0\t0\n+31\t0.224261\t0\t0\t0\t0\n+32\t0.224261\t0\t0\t0\t0\n+33\t0.224261\t0\t0\t0\t0\n+34\t0.224261\t0\t0\t0\t0\n+35\t0.265036\t0\t0\t0\t0\n+36\t0.285423\t0\t0\t0\t0\n+37\t0.326198\t0\t0\t0\t0\n+38\t0.407747\t0\t0\t0\t0\n+39\t0.468909\t0\t0\t0\t0\n+40\t0.468909\t0\t0\t0\t0\n+41\t0.468909\t0\t0\t0\t0\n+42\t0.468909\t0\t0\t0\t0\n+43\t0.468909\t0\t0\t0\t0\n+44\t0.468909\t0\t0\t0\t0\n+45\t0.468909\t0\t0\t0\t0\n+46\t0.468909\t0\t0\t0\t0\n+47\t0.468909\t0\t0\t0\t0\n+48\t0.468909\t0\t0\t0\t0\n+49\t0.468909\t0\t0\t0\t0\n+50\t0.468909\t0\t0\t0\t0\n+51\t0.468909\t0\t0\t0\t0\n+52\t0.468909\t0\t0\t0\t0\n+53\t0.468909\t0\t0\t0\t0\n+54\t0.468909\t0\t0\t0\t0\n+55\t0.468909\t0\t0\t0\t0\n+56\t0.468909\t0\t0\t0\t0\n+57\t0.468909\t0\t0\t0\t0\n+58\t0.468909\t0\t0\t0\t0\n+59\t0.468909\t0\t0\t0\t0\n+60\t0.468909\t0\t0\t0\t0\n+61\t0.468909\t0\t0\t0\t0\n+62\t0.468909\t0\t0\t0\t0\n+63\t0.468909\t0\t0\t0\t0\n+64\t0.468909\t0\t0\t0\t0\n+65\t0.468909\t0\t0\t0\t0\n+66\t0.468909\t0\t0\t0\t0\n+67\t0.468909\t0\t0\t0\t0\n+68\t0.468909\t0\t0\t0\t0\n+69\t0.468909\t0\t0\t0\t0\n+70\t0.468909\t0\t0\t0\t0\n+71\t0.468909\t0\t0\t0\t0\n+72\t0.468909\t0\t0\t0\t0\n+73\t0.468909\t0\t0\t0\t0\n+74\t0.489297\t0\t0\t0\t0\n+75\t0.489297\t0\t0\t0\t0\n+76\t0.489297\t0\t0\t0\t0\n+77\t0.489297\t0\t0\t0\t0\n+78\t0.489297\t0\t0\t0\t0\n+79\t0.489297\t0\t0\t0\t0\n+80\t0.489297\t0\t0\t0\t0\n+81\t0.489297\t0\t0\t0\t0\n+82\t0.489297\t0\t0\t0\t0\n+83\t0.509684\t0\t0\t0\t0\n+84\t0.509684\t0\t0\t0\t0\n+85\t0.509684\t0\t0\t0\t0\n+86\t0.509684\t0\t0\t0\t0\n+87\t0.509684\t0\t0\t0\t0\n+88\t0.509684\t0\t0\t0\t0\n+89\t0.509684\t0\t0\t0\t0\n+90\t0.509684\t0\t0\t0\t0\n+91\t0.509684\t0\t0\t0\t0\n+92\t0.570846\t0\t0\t0\t0\n+93\t0.632008\t0\t0\t0\t0\n+94\t0.632008\t0\t0\t0\t0\n+95\t0.632008\t0\t0\t0\t0\n+96\t0.632008\t0\t0\t0\t0\n+97\t0.632008\t0\t0\t0\t0\n+98\t0.632008\t0\t0\t0\t0\n+99\t0.632008\t0\t0\t0\t0\n+100\t0.632008\t0\t0\t0\t0\n+101\t0.632008\t0\t0\t0\t0\n+102\t0.632008\t0\t0\t0\t0\n+103\t0.632008\t0\t0\t0\t0\n+104\t0.632008\t0\t0\t0\t0\n+105\t0.632008\t0\t0\t0\t0\n+106\t0.632008\t0\t0\t0\t0\n+107\t0.632008\t0\t0\t0\t0\n+108\t0.632008\t0\t0\t0\t0\n+>>END_MODULE\n'

diff -r 000000000000 -r e462044ece67 test-data/fastqc_data_adapters.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fastqc_data_adapters.txt Tue Jun 04 14:14:49 2024 +0000

diff -r 000000000000 -r e462044ece67 test-data/fastqc_data_adapters_summary.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fastqc_data_adapters_summary.txt Tue Jun 04 14:14:49 2024 +0000

@@ -0,0 +1,11 @@
+PASS Basic Statistics 1000trimmed_fastq
+PASS Per base sequence quality 1000trimmed_fastq
+FAIL Per tile sequence quality 1000trimmed_fastq
+PASS Per sequence quality scores 1000trimmed_fastq
+FAIL Per base sequence content 1000trimmed_fastq
+WARN Per sequence GC content 1000trimmed_fastq
+PASS Per base N content 1000trimmed_fastq
+WARN Sequence Length Distribution 1000trimmed_fastq
+PASS Sequence Duplication Levels 1000trimmed_fastq
+WARN Overrepresented sequences 1000trimmed_fastq
+PASS Adapter Content 1000trimmed_fastq

diff -r 000000000000 -r e462044ece67 test-data/fastqc_data_contaminant_summary.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fastqc_data_contaminant_summary.txt Tue Jun 04 14:14:49 2024 +0000

diff -r 000000000000 -r e462044ece67 test-data/fastqc_data_contaminants.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fastqc_data_contaminants.txt Tue Jun 04 14:14:49 2024 +0000

diff -r 000000000000 -r e462044ece67 test-data/fastqc_data_customlimits.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fastqc_data_customlimits.txt Tue Jun 04 14:14:49 2024 +0000

diff -r 000000000000 -r e462044ece67 test-data/fastqc_data_customlimits_summary.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fastqc_data_customlimits_summary.txt Tue Jun 04 14:14:49 2024 +0000

diff -r 000000000000 -r e462044ece67 test-data/fastqc_data_hisat.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fastqc_data_hisat.txt Tue Jun 04 14:14:49 2024 +0000

b'@@ -0,0 +1,448 @@\n+##FastQC\t0.12.1\n+>>Basic Statistics\tpass\n+#Measure\tValue\n+Filename\thisat_output_1_bam\n+File type\tConventional base calls\n+Encoding\tSanger / Illumina 1.9\n+Total Sequences\t20\n+Total Bases\t1.4 kbp\n+Sequences flagged as poor quality\t0\n+Sequence length\t70\n+%GC\t43\n+>>END_MODULE\n+>>Per base sequence quality\tpass\n+#Base\tMean\tMedian\tLower Quartile\tUpper Quartile\t10th Percentile\t90th Percentile\n+1\t17.0\tNaN\tNaN\tNaN\tNaN\tNaN\n+2\t17.0\tNaN\tNaN\tNaN\tNaN\tNaN\n+3\t17.0\tNaN\tNaN\tNaN\tNaN\tNaN\n+4\t17.0\tNaN\tNaN\tNaN\tNaN\tNaN\n+5\t17.0\tNaN\tNaN\tNaN\tNaN\tNaN\n+6\t17.0\tNaN\tNaN\tNaN\tNaN\tNaN\n+7\t17.0\tNaN\tNaN\tNaN\tNaN\tNaN\n+8\t17.0\tNaN\tNaN\tNaN\tNaN\tNaN\n+9\t17.0\tNaN\tNaN\tNaN\tNaN\tNaN\n+10\t17.0\tNaN\tNaN\tNaN\tNaN\tNaN\n+11\t17.0\tNaN\tNaN\tNaN\tNaN\tNaN\n+12\t17.0\tNaN\tNaN\tNaN\tNaN\tNaN\n+13\t17.0\tNaN\tNaN\tNaN\tNaN\tNaN\n+14\t17.0\tNaN\tNaN\tNaN\tNaN\tNaN\n+15\t17.0\tNaN\tNaN\tNaN\tNaN\tNaN\n+16\t17.0\tNaN\tNaN\tNaN\tNaN\tNaN\n+17\t17.0\tNaN\tNaN\tNaN\tNaN\tNaN\n+18\t17.0\tNaN\tNaN\tNaN\tNaN\tNaN\n+19\t17.0\tNaN\tNaN\tNaN\tNaN\tNaN\n+20\t17.0\tNaN\tNaN\tNaN\tNaN\tNaN\n+21\t17.0\tNaN\tNaN\tNaN\tNaN\tNaN\n+22\t17.0\tNaN\tNaN\tNaN\tNaN\tNaN\n+23\t17.0\tNaN\tNaN\tNaN\tNaN\tNaN\n+24\t17.0\tNaN\tNaN\tNaN\tNaN\tNaN\n+25\t17.0\tNaN\tNaN\tNaN\tNaN\tNaN\n+26\t17.0\tNaN\tNaN\tNaN\tNaN\tNaN\n+27\t17.0\tNaN\tNaN\tNaN\tNaN\tNaN\n+28\t17.0\tNaN\tNaN\tNaN\tNaN\tNaN\n+29\t17.0\tNaN\tNaN\tNaN\tNaN\tNaN\n+30\t17.0\tNaN\tNaN\tNaN\tNaN\tNaN\n+31\t17.0\tNaN\tNaN\tNaN\tNaN\tNaN\n+32\t17.0\tNaN\tNaN\tNaN\tNaN\tNaN\n+33\t17.0\tNaN\tNaN\tNaN\tNaN\tNaN\n+34\t17.0\tNaN\tNaN\tNaN\tNaN\tNaN\n+35\t17.0\tNaN\tNaN\tNaN\tNaN\tNaN\n+36\t17.0\tNaN\tNaN\tNaN\tNaN\tNaN\n+37\t17.0\tNaN\tNaN\tNaN\tNaN\tNaN\n+38\t17.0\tNaN\tNaN\tNaN\tNaN\tNaN\n+39\t17.0\tNaN\tNaN\tNaN\tNaN\tNaN\n+40\t17.0\tNaN\tNaN\tNaN\tNaN\tNaN\n+41\t17.0\tNaN\tNaN\tNaN\tNaN\tNaN\n+42\t17.0\tNaN\tNaN\tNaN\tNaN\tNaN\n+43\t17.0\tNaN\tNaN\tNaN\tNaN\tNaN\n+44\t17.0\tNaN\tNaN\tNaN\tNaN\tNaN\n+45\t17.0\tNaN\tNaN\tNaN\tNaN\tNaN\n+46\t17.0\tNaN\tNaN\tNaN\tNaN\tNaN\n+47\t17.0\tNaN\tNaN\tNaN\tNaN\tNaN\n+48\t17.0\tNaN\tNaN\tNaN\tNaN\tNaN\n+49\t17.0\tNaN\tNaN\tNaN\tNaN\tNaN\n+50\t17.0\tNaN\tNaN\tNaN\tNaN\tNaN\n+51\t17.0\tNaN\tNaN\tNaN\tNaN\tNaN\n+52\t17.0\tNaN\tNaN\tNaN\tNaN\tNaN\n+53\t17.0\tNaN\tNaN\tNaN\tNaN\tNaN\n+54\t17.0\tNaN\tNaN\tNaN\tNaN\tNaN\n+55\t17.0\tNaN\tNaN\tNaN\tNaN\tNaN\n+56\t17.0\tNaN\tNaN\tNaN\tNaN\tNaN\n+57\t17.0\tNaN\tNaN\tNaN\tNaN\tNaN\n+58\t17.0\tNaN\tNaN\tNaN\tNaN\tNaN\n+59\t17.0\tNaN\tNaN\tNaN\tNaN\tNaN\n+60\t17.0\tNaN\tNaN\tNaN\tNaN\tNaN\n+61\t17.0\tNaN\tNaN\tNaN\tNaN\tNaN\n+62\t17.0\tNaN\tNaN\tNaN\tNaN\tNaN\n+63\t17.0\tNaN\tNaN\tNaN\tNaN\tNaN\n+64\t17.0\tNaN\tNaN\tNaN\tNaN\tNaN\n+65\t17.0\tNaN\tNaN\tNaN\tNaN\tNaN\n+66\t17.0\tNaN\tNaN\tNaN\tNaN\tNaN\n+67\t17.0\tNaN\tNaN\tNaN\tNaN\tNaN\n+68\t17.0\tNaN\tNaN\tNaN\tNaN\tNaN\n+69\t17.0\tNaN\tNaN\tNaN\tNaN\tNaN\n+70\t17.0\tNaN\tNaN\tNaN\tNaN\tNaN\n+>>END_MODULE\n+>>Per sequence quality scores\tfail\n+#Quality\tCount\n+17\t20.0\n+>>END_MODULE\n+>>Per base sequence content\tfail\n+#Base\tG\tA\tT\tC\n+1\t20.0\t5.0\t35.0\t40.0\n+2\t10.0\t10.0\t45.0\t35.0\n+3\t35.0\t20.0\t20.0\t25.0\n+4\t35.0\t30.0\t25.0\t10.0\n+5\t20.0\t20.0\t30.0\t30.0\n+6\t20.0\t35.0\t20.0\t25.0\n+7\t15.0\t40.0\t35.0\t10.0\n+8\t20.0\t15.0\t45.0\t20.0\n+9\t20.0\t25.0\t35.0\t20.0\n+10\t20.0\t20.0\t30.0\t30.0\n+11\t15.0\t20.0\t45.0\t20.0\n+12\t10.0\t40.0\t35.0\t15.0\n+13\t25.0\t35.0\t20.0\t20.0\n+14\t35.0\t20.0\t20.0\t25.0\n+15\t30.0\t35.0\t15.0\t20.0\n+16\t10.0\t45.0\t25.0\t20.0\n+17\t25.0\t25.0\t40.0\t10.0\n+18\t25.0\t35.0\t10.0\t30.0\n+19\t5.0\t30.0\t25.0\t40.0\n+20\t20.0\t15.0\t40.0\t25.0\n+21\t25.0\t25.0\t25.0\t25.0\n+22\t15.0\t30.0\t20.0\t35.0\n+23\t20.0\t5.0\t45.0\t30.0\n+24\t10.0\t30.0\t35.0\t25.0\n+25\t30.0\t40.0\t15.0\t15.0\n+26\t15.0\t35.0\t20.0\t30.0\n+27\t15.0\t35.0\t30.0\t20.0\n+28\t25.0\t25.0\t30.0\t20.0\n+29\t15.0\t30.0\t20.0\t35.0\n+30\t20.0\t35.0\t30.0\t15.0\n+31\t20.0\t35.0\t25.0\t20.0\n+32\t35.0\t15.0\t35.0\t15.0\n+33\t30.0\t35.0\t15.0\t20.0\n+34\t25.0\t25.0\t25.0\t25.0\n+35\t25.0\t20.0\t35.0\t20.0\n+36\t30.0\t25.0\t20.0\t25.0\n+37\t15.0\t45.0\t25.0\t15.0\n+38\t30.0\t25.0\t35.0\t10.0\n+39\t20.0\t45.0\t15.0\t20.0\n+40\t15.0\t35.0\t20.0\t30.0\n+41\t35.0\t25.0\t20.0\t20.0\n+42\t30.0\t30.0\t35.0\t5.0\n+43\t25.0\t15.0\t40.0\t20.0\n+44\t40.0\t20.0\t30.0\t10.0\n+45\t15.0\t35.0\t25.0\t25.0\n+46\t15.0\t30.0\t40.0\t15.0\n+47\t35.0\t15.0\t30.0\t20.0\n+48\t30.0\t35.0\t20.0\t15.0\n+49\t10.0\t55.00000000000001\t30.0\t5.0\n+50\t40.0\t25.0\t20.0\t15.0\n+51\t25.0\t35.0\t10.0\t30.0\n+52\t30.0\t25.0\t20.0\t25.0\n+53\t30.0\t10.0\t30.0\t30.0\n+54\t20.0\t40.0\t20.0\t20.0\n+55\t10.0\t35.0\t10.0\t45.0\n+56\t50.0\t10.0\t30.0\t10.0\n+57\t15.0\t45.0\t30.0\t10.0\n+58\t20.0\t35.0\t20.0\t25.0\n+59\t30.0\t35.0\t30.0\t5.0\n+60\t20.0\t35.0\t25.0\t'..b"6\t0.0\n+17\t0.0\n+18\t0.0\n+19\t0.0\n+20\t0.0\n+21\t0.0\n+22\t0.0\n+23\t0.0\n+24\t0.0\n+25\t0.0\n+26\t0.0\n+27\t0.0\n+28\t0.0\n+29\t0.0\n+30\t0.0\n+31\t0.0\n+32\t0.0\n+33\t0.0\n+34\t0.0\n+35\t0.0\n+36\t0.0\n+37\t0.0\n+38\t0.0\n+39\t0.0\n+40\t0.0\n+41\t0.0\n+42\t0.0\n+43\t0.0\n+44\t0.0\n+45\t0.0\n+46\t0.0\n+47\t0.0\n+48\t0.0\n+49\t0.0\n+50\t0.0\n+51\t0.0\n+52\t0.0\n+53\t0.0\n+54\t0.0\n+55\t0.0\n+56\t0.0\n+57\t0.0\n+58\t0.0\n+59\t0.0\n+60\t0.0\n+61\t0.0\n+62\t0.0\n+63\t0.0\n+64\t0.0\n+65\t0.0\n+66\t0.0\n+67\t0.0\n+68\t0.0\n+69\t0.0\n+70\t0.0\n+>>END_MODULE\n+>>Sequence Length Distribution\tpass\n+#Length\tCount\n+70\t20.0\n+>>END_MODULE\n+>>Sequence Duplication Levels\tpass\n+#Total Deduplicated Percentage\t100.0\n+#Duplication Level\tPercentage of total\n+1\t100.0\n+2\t0.0\n+3\t0.0\n+4\t0.0\n+5\t0.0\n+6\t0.0\n+7\t0.0\n+8\t0.0\n+9\t0.0\n+>10\t0.0\n+>50\t0.0\n+>100\t0.0\n+>500\t0.0\n+>1k\t0.0\n+>5k\t0.0\n+>10k+\t0.0\n+>>END_MODULE\n+>>Overrepresented sequences\tfail\n+#Sequence\tCount\tPercentage\tPossible Source\n+CCTTTCGCCATCAACTAACGATTCTGTCAAAAACTGACGCGTTGGATGAG\t1\t5.0\tNo Hit\n+TGGCGCTCTCCGTCTTTCTCCATTTCGTCGTGGCCTTGCTATTGACTCTA\t1\t5.0\tNo Hit\n+ACCATAAACGCAAGCCTCAACGCAGCGACGAGCACGAGAGCGGTCAGTAG\t1\t5.0\tNo Hit\n+TGTTTTCCGTAAATTCAGCGCCTTCCATGATGCGACAGGCCGTTTGAATG\t1\t5.0\tNo Hit\n+CTGGCACTTCTGCCGTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGT\t1\t5.0\tNo Hit\n+TCTGCGTTTGCTGATGAACTAAGTCAACCTCAGCACTAACCTTGCGAGTC\t1\t5.0\tNo Hit\n+CCATACAAAACAGGGTCGCCAGCAATATCGGTATAAGTCAAAGCACCTTT\t1\t5.0\tNo Hit\n+TAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACAACTATTTTCAAG\t1\t5.0\tNo Hit\n+CAAATTAGCATAAGCAGCTTGCAGACCCATAATGTCAATAGATGTGGTAG\t1\t5.0\tNo Hit\n+GCGTTAAGGTACTGAATCTCTTTAGTCGCAGTAGGCGGAAAACGAACAAG\t1\t5.0\tNo Hit\n+CTGAATGGAATTAAGAAAACCACCAATACCAGCATTAACCTTCAAACTAT\t1\t5.0\tNo Hit\n+GCGACCATTCAAAGGATAAACATCATAGGCAGTCGGGAGGGTAGTCGGAA\t1\t5.0\tNo Hit\n+GTGAAATTTCTAGGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAG\t1\t5.0\tNo Hit\n+CTCAAATCCGGCGTCAACCATACCAGCATAGGAAGCATCAGCACCAGCAC\t1\t5.0\tNo Hit\n+TTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGATTATGACC\t1\t5.0\tNo Hit\n+CTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATA\t1\t5.0\tNo Hit\n+TTAGGTGTGTGTAAAACAGGTGCCGAAGAAGCTGGATTAACAGAATTGAG\t1\t5.0\tNo Hit\n+GCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGA\t1\t5.0\tNo Hit\n+TTTCGGATATTTCTGATGAGTCGAAAAATTATCTTGATAAAGCAGTAATT\t1\t5.0\tNo Hit\n+CTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAA\t1\t5.0\tNo Hit\n+>>END_MODULE\n+>>Adapter Content\tpass\n+#Position\tIllumina Universal Adapter\tIllumina Small RNA 3' Adapter\tIllumina Small RNA 5' Adapter\tNextera Transposase Sequence\tPolyA\tPolyG\n+1\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+2\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+3\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+4\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+5\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+6\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+7\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+8\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+9\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+10\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+11\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+12\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+13\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+14\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+15\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+16\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+17\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+18\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+19\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+20\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+21\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+22\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+23\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+24\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+25\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+26\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+27\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+28\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+29\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+30\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+31\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+32\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+33\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+34\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+35\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+36\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+37\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+38\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+39\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+40\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+41\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+42\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+43\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+44\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+45\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+46\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+47\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+48\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+49\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+50\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+51\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+52\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+53\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+54\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+55\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+56\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+57\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+58\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+59\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+>>END_MODULE\n"

diff -r 000000000000 -r e462044ece67 test-data/fastqc_data_kmer.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fastqc_data_kmer.txt Tue Jun 04 14:14:49 2024 +0000

diff -r 000000000000 -r e462044ece67 test-data/fastqc_data_kmer_summary.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fastqc_data_kmer_summary.txt Tue Jun 04 14:14:49 2024 +0000

diff -r 000000000000 -r e462044ece67 test-data/fastqc_data_min_length.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fastqc_data_min_length.txt Tue Jun 04 14:14:49 2024 +0000

diff -r 000000000000 -r e462044ece67 test-data/fastqc_data_min_length_summary.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fastqc_data_min_length_summary.txt Tue Jun 04 14:14:49 2024 +0000

diff -r 000000000000 -r e462044ece67 test-data/fastqc_data_nogroup.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fastqc_data_nogroup.txt Tue Jun 04 14:14:49 2024 +0000

b'@@ -0,0 +1,1857 @@\n+##Falco\t1.2.2\n+>>Basic Statistics\tpass\n+#Measure\tValue\n+Filename\t1000trimmed_fastq\n+File type\tConventional base calls\n+Encoding\tSanger / Illumina 1.9\n+Total Sequences\t4905\n+Sequences flagged as poor quality\t0\n+Sequence length\t1-108\n+%GC\t41\n+>>END_MODULE\n+>>Per base sequence quality\tpass\n+#Base\tMean\tMedian\tLower Quartile\tUpper Quartile\t10th Percentile\t90th Percentile\n+1\t29.2828\t31\t27\t33\t23\t34\n+2\t28.8329\t30\t27\t32\t22\t33\n+3\t28.897\t30\t27\t32\t23\t34\n+4\t29.0068\t30\t27\t32\t23\t34\n+5\t28.9378\t30\t27\t32\t22\t34\n+6\t29.0029\t30\t27\t32\t23\t34\n+7\t28.8998\t30\t27\t32\t22\t34\n+8\t28.9007\t30\t27\t32\t22\t33\n+9\t28.7546\t30\t27\t32\t22\t34\n+10\t28.7413\t30\t27\t32\t22\t33\n+11\t28.9029\t30\t27\t32\t23\t33\n+12\t28.8793\t30\t27\t32\t22\t33\n+13\t28.6187\t30\t26\t32\t22\t33\n+14\t28.6381\t30\t26\t32\t22\t34\n+15\t28.4293\t30\t26\t32\t22\t33\n+16\t28.5692\t30\t26\t32\t22\t33\n+17\t28.484\t30\t26\t32\t22\t33\n+18\t28.6611\t30\t26\t32\t22\t33\n+19\t28.7058\t30\t26\t32\t23\t33\n+20\t28.3636\t30\t26\t32\t22\t33\n+21\t28.3767\t29\t26\t32\t22\t33\n+22\t28.165\t29\t26\t32\t22\t33\n+23\t28.2069\t29\t26\t32\t22\t33\n+24\t28.2375\t29\t26\t32\t22\t33\n+25\t28.0227\t29\t26\t32\t21\t33\n+26\t28.1444\t29\t26\t32\t22\t33\n+27\t28.0071\t29\t26\t32\t21\t33\n+28\t27.8097\t29\t25\t32\t21\t33\n+29\t27.8464\t29\t25\t32\t21\t33\n+30\t27.8357\t29\t25\t32\t21\t33\n+31\t27.75\t29\t25\t31\t21\t33\n+32\t27.618\t28\t25\t31\t21\t33\n+33\t27.364\t28\t25\t31\t21\t33\n+34\t27.4264\t28\t25\t31\t21\t33\n+35\t27.288\t28\t24\t31\t21\t33\n+36\t27.099\t28\t24\t31\t20\t33\n+37\t27.0253\t28\t24\t31\t21\t33\n+38\t27.2932\t28\t24\t31\t21\t33\n+39\t27.1829\t28\t24\t31\t21\t33\n+40\t26.9911\t28\t24\t31\t20\t33\n+41\t27.0668\t28\t24\t31\t21\t33\n+42\t27.0341\t27\t24\t31\t21\t33\n+43\t26.7831\t27\t24\t31\t20\t33\n+44\t26.6236\t27\t24\t30\t20\t32\n+45\t26.6404\t27\t24\t30\t20\t32\n+46\t26.9469\t28\t24\t31\t21\t32\n+47\t26.714\t27\t24\t31\t20\t32\n+48\t26.4617\t27\t24\t30\t20\t32\n+49\t26.4017\t27\t23\t30\t20\t32\n+50\t26.2447\t27\t23\t30\t20\t32\n+51\t26.1933\t27\t23\t30\t20\t32\n+52\t26.4316\t27\t23\t30\t20\t32\n+53\t25.4198\t26\t22\t29\t19\t31\n+54\t25.7478\t27\t22\t30\t17\t32\n+55\t30.2427\t32\t29\t33\t24\t34\n+56\t30.2882\t31\t28\t33\t25\t34\n+57\t30.5335\t32\t29\t33\t26\t34\n+58\t30.4879\t32\t29\t33\t26\t34\n+59\t30.3289\t31\t28\t33\t26\t34\n+60\t30.4893\t32\t29\t33\t26\t34\n+61\t30.4003\t31\t29\t33\t26\t34\n+62\t30.4621\t31\t29\t33\t26\t34\n+63\t30.4187\t32\t29\t33\t25\t34\n+64\t30.3083\t31\t29\t33\t25\t34\n+65\t30.5751\t32\t29\t33\t26\t34\n+66\t30.5405\t32\t29\t33\t26\t34\n+67\t30.4823\t32\t29\t33\t25\t34\n+68\t30.2761\t31\t28\t33\t25\t34\n+69\t29.8262\t31\t28\t33\t24\t34\n+70\t30.3446\t31\t29\t33\t25\t34\n+71\t30.2077\t31\t29\t33\t25\t34\n+72\t30.4043\t32\t29\t33\t25\t34\n+73\t30.3667\t31\t29\t33\t26\t34\n+74\t30.3122\t31\t29\t33\t26\t34\n+75\t30.1149\t31\t28\t33\t25\t34\n+76\t30.011\t31\t28\t33\t25\t34\n+77\t29.3468\t31\t28\t33\t24\t34\n+78\t30.0795\t31\t28\t33\t25\t34\n+79\t29.9588\t31\t28\t33\t24\t34\n+80\t29.6797\t31\t28\t33\t24\t34\n+81\t29.6487\t31\t27\t33\t24\t34\n+82\t29.6591\t31\t28\t33\t24\t34\n+83\t29.648\t31\t28\t32\t25\t34\n+84\t29.5434\t31\t27\t32\t24\t34\n+85\t29.3078\t30\t27\t32\t24\t34\n+86\t29.3807\t30\t27\t33\t24\t34\n+87\t29.3004\t30\t27\t32\t24\t34\n+88\t28.9146\t30\t27\t32\t23\t34\n+89\t28.6568\t30\t27\t32\t22\t33\n+90\t28.7378\t30\t26\t32\t23\t33\n+91\t28.5972\t29\t26\t32\t23\t33\n+92\t28.6267\t29\t26\t32\t23\t33\n+93\t28.5052\t29\t26\t32\t23\t33\n+94\t28.4124\t29\t26\t32\t23\t33\n+95\t28.1311\t29\t26\t32\t22\t33\n+96\t27.9249\t29\t25\t31\t22\t33\n+97\t27.9742\t29\t26\t31\t22\t33\n+98\t26.9919\t28\t25\t31\t21\t33\n+99\t27.6385\t28\t25\t31\t22\t33\n+100\t27.7238\t28\t25\t31\t22\t33\n+101\t27.5057\t28\t25\t31\t21\t33\n+102\t27.3208\t28\t25\t31\t21\t33\n+103\t27.0717\t28\t24\t31\t21\t33\n+104\t26.84\t27\t24\t31\t20\t32\n+105\t26.9019\t28\t24\t31\t20\t33\n+106\t27.0257\t28\t24\t31\t21\t33\n+107\t25.7095\t26\t23\t29\t20\t31\n+108\t27.5651\t28\t24\t31\t22\t33\n+>>END_MODULE\n+>>Per tile sequence quality\tfail\n+#Tile\tBase\tMean\n+0\t1\t-29.4857\n+0\t2\t-28.7721\n+0\t3\t-28.5832\n+0\t4\t-28.7282\n+0\t5\t-28.9662\n+0\t6\t-28.9765\n+0\t7\t-29.0324\n+0\t8\t-28.9563\n+0\t9\t-28.4479\n+0\t10\t-28.2935\n+0\t11\t-28.6264\n+0\t12\t-28.711\n+0\t13\t-28.5163\n+0\t14\t-28.3915\n+0\t15\t-28.2392\n+0\t16\t-28.5304\n+0\t17\t-28.3975\n+0\t18\t-28.5859\n+0\t19\t-28.6272\n+0\t20\t-28.1273\n+0\t21\t-28.2058\n+0\t22\t-28.1046\n+0\t23\t-28.3908\n+0\t24\t-28.0801\n+0\t25\t-28.0111\n+0\t26\t-27.9571\n+0\t27\t-28.1062\n+0\t28\t-27.7915\n+0\t29\t-27.6043\n+0\t30\t-27.7709\n+0\t31\t-27.5781\n+0\t32\t-27.8211\n+0\t33\t-27.6197\n+0\t34\t-27.447\n+0\t35\t-27.3368\n+0\t36\t-27.2226\n+0\t37\t-27.2582\n+0\t38\t-27.2825\n+0\t39\t-26.7901\n+0\t40\t-26.9377\n+0\t41\t-27.17\n+0\t42\t-27.1488\n+0\t43\t-26.1931\n+0\t44\t-26.6'..b'\n+25\t0\n+26\t0\n+27\t0\n+28\t0\n+29\t0\n+30\t0\n+31\t0\n+32\t0\n+33\t0\n+34\t0\n+35\t0\n+36\t0\n+37\t0\n+38\t0\n+39\t0\n+40\t0\n+41\t0\n+42\t0\n+43\t0\n+44\t0\n+45\t0\n+46\t0\n+47\t0\n+48\t0\n+49\t0\n+50\t0\n+51\t0\n+52\t0\n+53\t0\n+54\t0\n+55\t0\n+56\t0\n+57\t0\n+58\t0\n+59\t0\n+60\t0\n+61\t0\n+62\t0\n+63\t0\n+64\t0\n+65\t0\n+66\t0\n+67\t0\n+68\t0\n+69\t0\n+70\t0\n+71\t0\n+72\t0\n+73\t0\n+74\t0\n+75\t0\n+76\t0\n+77\t0\n+78\t0\n+79\t0\n+80\t0\n+81\t0\n+82\t0\n+83\t0\n+84\t0\n+85\t0\n+86\t0\n+87\t0\n+88\t0\n+89\t0\n+90\t0\n+91\t0\n+92\t0\n+93\t0\n+94\t0\n+95\t0\n+96\t0\n+97\t0\n+98\t0\n+99\t0\n+100\t0\n+101\t0\n+102\t0\n+103\t0\n+104\t0\n+105\t0\n+106\t0\n+107\t0\n+108\t0\n+>>END_MODULE\n+>>Sequence Length Distribution\twarn\n+#Length\tCount\n+1\t3.0\n+2\t11.0\n+3\t28.0\n+4\t56.0\n+5\t43.0\n+6\t52.0\n+7\t39.0\n+8\t56.0\n+9\t60.0\n+10\t57.0\n+11\t43.0\n+12\t46.0\n+13\t45.0\n+14\t66.0\n+15\t59.0\n+16\t49.0\n+17\t73.0\n+18\t54.0\n+19\t44.0\n+20\t52.0\n+21\t73.0\n+22\t72.0\n+23\t68.0\n+24\t56.0\n+25\t86.0\n+26\t92.0\n+27\t75.0\n+28\t69.0\n+29\t74.0\n+30\t96.0\n+31\t72.0\n+32\t81.0\n+33\t65.0\n+34\t87.0\n+35\t86.0\n+36\t87.0\n+37\t100.0\n+38\t82.0\n+39\t78.0\n+40\t76.0\n+41\t79.0\n+42\t88.0\n+43\t83.0\n+44\t75.0\n+45\t74.0\n+46\t72.0\n+47\t84.0\n+48\t74.0\n+49\t81.0\n+50\t91.0\n+51\t80.0\n+52\t98.0\n+53\t43.0\n+54\t8.0\n+55\t4.0\n+56\t1.0\n+64\t1.0\n+97\t1.0\n+98\t32.0\n+106\t34.0\n+107\t169.0\n+108\t1122.0\n+>>END_MODULE\n+>>Sequence Duplication Levels\tpass\n+#Total Deduplicated Percentage\t98.736\n+#Duplication Level\tPercentage of deduplicated\tPercentage of total\n+1\t99.4425\t98.1855\n+2\t0.474912\t0.937819\n+3\t0.0412967\t0.122324\n+4\t0.0206484\t0.0815494\n+5\t0\t0\n+6\t0\t0\n+7\t0\t0\n+8\t0\t0\n+9\t0\t0\n+>10\t0.0206484\t0.672783\n+>50\t0\t0\n+>100\t0\t0\n+>500\t0\t0\n+>1k\t0\t0\n+>5k\t0\t0\n+>10k+\t0\t0\n+>>END_MODULE\n+>>Overrepresented sequences\twarn\n+#Sequence\tCount\tPercentage\tPossible Source\n+ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT\t33\t0.672783\tNo Hit\n+>>END_MODULE\n+>>Adapter Content\tpass\n+#Position\tIllumina Universal Adapter\tIllumina Small RNA 3 prime Adapter\tIllumina Small RNA 5 prime Adapter\tNextera Transposase Sequence\tSOLID Small RNA Adapter\n+1\t0\t0\t0\t0\t0\n+2\t0\t0\t0\t0\t0\n+3\t0\t0\t0\t0\t0\n+4\t0\t0\t0\t0\t0\n+5\t0\t0\t0\t0\t0\n+6\t0\t0\t0\t0\t0\n+7\t0\t0\t0\t0\t0\n+8\t0\t0\t0\t0\t0\n+9\t0\t0\t0\t0\t0\n+10\t0\t0\t0\t0\t0\n+11\t0\t0\t0\t0\t0\n+12\t0\t0\t0\t0\t0\n+13\t0\t0\t0\t0\t0\n+14\t0\t0\t0\t0\t0\n+15\t0\t0\t0\t0\t0\n+16\t0\t0\t0\t0\t0\n+17\t0\t0\t0\t0\t0\n+18\t0\t0\t0\t0\t0\n+19\t0\t0\t0\t0\t0\n+20\t0.122324\t0\t0\t0\t0\n+21\t0.122324\t0\t0\t0\t0\n+22\t0.122324\t0\t0\t0\t0\n+23\t0.122324\t0\t0\t0\t0\n+24\t0.122324\t0\t0\t0\t0\n+25\t0.122324\t0\t0\t0\t0\n+26\t0.122324\t0\t0\t0\t0\n+27\t0.142712\t0\t0\t0\t0\n+28\t0.183486\t0\t0\t0\t0\n+29\t0.224261\t0\t0\t0\t0\n+30\t0.224261\t0\t0\t0\t0\n+31\t0.224261\t0\t0\t0\t0\n+32\t0.224261\t0\t0\t0\t0\n+33\t0.224261\t0\t0\t0\t0\n+34\t0.224261\t0\t0\t0\t0\n+35\t0.265036\t0\t0\t0\t0\n+36\t0.285423\t0\t0\t0\t0\n+37\t0.326198\t0\t0\t0\t0\n+38\t0.407747\t0\t0\t0\t0\n+39\t0.468909\t0\t0\t0\t0\n+40\t0.468909\t0\t0\t0\t0\n+41\t0.468909\t0\t0\t0\t0\n+42\t0.468909\t0\t0\t0\t0\n+43\t0.468909\t0\t0\t0\t0\n+44\t0.468909\t0\t0\t0\t0\n+45\t0.468909\t0\t0\t0\t0\n+46\t0.468909\t0\t0\t0\t0\n+47\t0.468909\t0\t0\t0\t0\n+48\t0.468909\t0\t0\t0\t0\n+49\t0.468909\t0\t0\t0\t0\n+50\t0.468909\t0\t0\t0\t0\n+51\t0.468909\t0\t0\t0\t0\n+52\t0.468909\t0\t0\t0\t0\n+53\t0.468909\t0\t0\t0\t0\n+54\t0.468909\t0\t0\t0\t0\n+55\t0.468909\t0\t0\t0\t0\n+56\t0.468909\t0\t0\t0\t0\n+57\t0.468909\t0\t0\t0\t0\n+58\t0.468909\t0\t0\t0\t0\n+59\t0.468909\t0\t0\t0\t0\n+60\t0.468909\t0\t0\t0\t0\n+61\t0.468909\t0\t0\t0\t0\n+62\t0.468909\t0\t0\t0\t0\n+63\t0.468909\t0\t0\t0\t0\n+64\t0.468909\t0\t0\t0\t0\n+65\t0.468909\t0\t0\t0\t0\n+66\t0.468909\t0\t0\t0\t0\n+67\t0.468909\t0\t0\t0\t0\n+68\t0.468909\t0\t0\t0\t0\n+69\t0.468909\t0\t0\t0\t0\n+70\t0.468909\t0\t0\t0\t0\n+71\t0.468909\t0\t0\t0\t0\n+72\t0.468909\t0\t0\t0\t0\n+73\t0.468909\t0\t0\t0\t0\n+74\t0.489297\t0\t0\t0\t0\n+75\t0.489297\t0\t0\t0\t0\n+76\t0.489297\t0\t0\t0\t0\n+77\t0.489297\t0\t0\t0\t0\n+78\t0.489297\t0\t0\t0\t0\n+79\t0.489297\t0\t0\t0\t0\n+80\t0.489297\t0\t0\t0\t0\n+81\t0.489297\t0\t0\t0\t0\n+82\t0.489297\t0\t0\t0\t0\n+83\t0.509684\t0\t0\t0\t0\n+84\t0.509684\t0\t0\t0\t0\n+85\t0.509684\t0\t0\t0\t0\n+86\t0.509684\t0\t0\t0\t0\n+87\t0.509684\t0\t0\t0\t0\n+88\t0.509684\t0\t0\t0\t0\n+89\t0.509684\t0\t0\t0\t0\n+90\t0.509684\t0\t0\t0\t0\n+91\t0.509684\t0\t0\t0\t0\n+92\t0.570846\t0\t0\t0\t0\n+93\t0.632008\t0\t0\t0\t0\n+94\t0.632008\t0\t0\t0\t0\n+95\t0.632008\t0\t0\t0\t0\n+96\t0.632008\t0\t0\t0\t0\n+97\t0.632008\t0\t0\t0\t0\n+98\t0.632008\t0\t0\t0\t0\n+99\t0.632008\t0\t0\t0\t0\n+100\t0.632008\t0\t0\t0\t0\n+101\t0.632008\t0\t0\t0\t0\n+102\t0.632008\t0\t0\t0\t0\n+103\t0.632008\t0\t0\t0\t0\n+104\t0.632008\t0\t0\t0\t0\n+105\t0.632008\t0\t0\t0\t0\n+106\t0.632008\t0\t0\t0\t0\n+107\t0.632008\t0\t0\t0\t0\n+108\t0.632008\t0\t0\t0\t0\n+>>END_MODULE\n'

diff -r 000000000000 -r e462044ece67 test-data/fastqc_data_nogroup_summary.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fastqc_data_nogroup_summary.txt Tue Jun 04 14:14:49 2024 +0000

diff -r 000000000000 -r e462044ece67 test-data/fastqc_report.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fastqc_report.html Tue Jun 04 14:14:49 2024 +0000

[

b'@@ -0,0 +1,2 @@\n+<html><head> <meta charset="utf-8"> <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">\t<title> 1000trimmed_fastq - report\t</title><link rel="stylesheet" href="https://stackpath.bootstrapcdn.com/bootstrap/4.3.1/css/bootstrap.min.css" integrity="sha384-ggOyR0iXCbMQv3Xipma34MD+dH/1fQ784/j6cY/iJTQUOhcWr7x9JvoRxT2MZw1T" crossorigin="anonymous"><link href="https://stackpath.bootstrapcdn.com/font-awesome/4.7.0/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-wvfXpqpZZVQGK6TAh5PVlGOfQNHSoD2xbE+QkPxCAFlNEevoEH3Sl0sibVcOQVnN" crossorigin="anonymous"><style type="text/css"> @media screen { div.summary { width: 18em; position:fixed; top: 4em; margin:1em 0 0 1em; } div.main { display:block; position:absolute; overflow:auto; height:auto; width:auto; top:4.5em; bottom:2.3em; left:18em; right:0; border-left: 1px solid #CCC; padding:0 0 0 1em; background-color: white; z-index:1; } div.header { background-color: #EEE; border:0; margin:0; padding: 0.2em; font-size: 200%; position:fixed; width:100%; top:0; left:0; z-index:2; } div.footer { background-color: #EEE; border:0; margin:0;\tpadding:0.5em; height: 2.5em;\toverflow:hidden; font-size: 100%; position:fixed; bottom:0; width:100%; z-index:2; } img.indented { margin-left: 3em; } } @media print {\timg {\t\tmax-width:100% !important;\t\tpage-break-inside: avoid;\t}\th2, h3 {\t\tpage-break-after: avoid;\t}\tdiv.header { background-color: #FFF; }\t } body { color: #000; background-color: #FFF; border: 0; margin: 0; padding: 0; } div.header { border:0; margin:0; padding: 0.5em; font-size: 200%; width:100%; } #header_title { display:inline-block; float:left; clear:left; } #header_filename { display:inline-block; float:right; clear:right; font-size: 50%; margin-right:2em; text-align: right; } div.header h3 { font-size: 50%; margin-bottom: 0; } div.summary ul { padding-left:0; list-style-type:none; } div.summary ul li img { margin-bottom:-0.5em; margin-top:0.5em; }\t div.main { background-color: white; } div.module { padding-bottom:3em; padding-top:3em; border-bottom: 1px solid #990000 }\t div.footer { background-color: #EEE; border:0; margin:0; padding: 0.5em; font-size: 100%; width:100%; } h2 { color: #2a5e8c; padding-bottom: 0; margin-bottom: 0; clear:left; }table { margin-left: 3em; text-align: center; } th { text-align: center; background-color: #000080; color: #FFF; padding: 0.4em;} td { font-family: monospace; text-align: left; background-color: #EEE; color: #000; padding: 0.4em;}img { padding-top: 0; margin-top: 0; border-top: 0;} p { padding-top: 0; margin-top: 0;}.pass { color : #009900;}.warn { color : #999900;}.fail { color : #990000;}</style><script src="https://cdn.plot.ly/plotly-latest.min.js"></script></head><body><div class="header">\t<div id="header_title">Report</div> <div id="header_filename">Mon May 27 16:50:45 2024\n+<br/> 1000trimmed_fastq\t</div></div><div class="summary"><h2>Summary</h2><ul> <li><a class="pass" href="#basicstatistics"> Basic Statistics </a></li> \t<li><a class="pass" href="#perbasesequencequality"> Per base sequence quality</a></li> \t<li><a class="fail" href="#pertilesequencequality">Per tile sequence quality</a></li> \t<li><a class="pass" href="#persequencequalityscores">Per sequence quality scores</a></li> \t<li><a class="fail" href="#perbasesequencecontent">Per base sequence content</a></li> \t<li><a class="warn" href="#persequencegccontent">Per sequence GC content</a></li> \t<li><a class="pass" href="#perbasencontent">Per base N content</a></li> \t<li><a class="warn" href="#sequencelengthdistribution">Sequence Length Distribution</a></li> \t<li><a class="pass" href="#sequenceduplicationlevels">Sequence Duplication Levels</a></li'..b',37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108], y : 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[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108], y : [0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0], type : \'line\', name : "Illumina Small RNA 3 prime Adapter"},{x : [1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108], y : 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[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108], y : [0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0], type : \'line\', name : "SOLID Small RNA Adapter"} ], { margin: { t: 0 }, showlegend: true, xaxis : {title : \'Base position\'}, yaxis : {title : \'% sequences with adapter before position\'} } );}if (document.getElementById(\'kmerlineplot\') !== null) { Plotly.newPlot(\'kmerlineplot\', [ ], { margin: { t: 0 }, showlegend: true, xaxis : {title : \'Base position\'}, yaxis : {title : \'log2(obs/ exp max)\'} } );}</script></html>\n\\ No newline at end of file\n'

diff -r 000000000000 -r e462044ece67 test-data/fastqc_report_adapters.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fastqc_report_adapters.html Tue Jun 04 14:14:49 2024 +0000

[

b'@@ -0,0 +1,2 @@\n+<html><head> <meta charset="utf-8"> <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">\t<title> 1000trimmed_fastq - report\t</title><link rel="stylesheet" href="https://stackpath.bootstrapcdn.com/bootstrap/4.3.1/css/bootstrap.min.css" integrity="sha384-ggOyR0iXCbMQv3Xipma34MD+dH/1fQ784/j6cY/iJTQUOhcWr7x9JvoRxT2MZw1T" crossorigin="anonymous"><link href="https://stackpath.bootstrapcdn.com/font-awesome/4.7.0/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-wvfXpqpZZVQGK6TAh5PVlGOfQNHSoD2xbE+QkPxCAFlNEevoEH3Sl0sibVcOQVnN" crossorigin="anonymous"><style type="text/css"> @media screen { div.summary { width: 18em; position:fixed; top: 4em; margin:1em 0 0 1em; } div.main { display:block; position:absolute; overflow:auto; height:auto; width:auto; top:4.5em; bottom:2.3em; left:18em; right:0; border-left: 1px solid #CCC; padding:0 0 0 1em; background-color: white; z-index:1; } div.header { background-color: #EEE; border:0; margin:0; padding: 0.2em; font-size: 200%; position:fixed; width:100%; top:0; left:0; z-index:2; } div.footer { background-color: #EEE; border:0; margin:0;\tpadding:0.5em; height: 2.5em;\toverflow:hidden; font-size: 100%; position:fixed; bottom:0; width:100%; z-index:2; } img.indented { margin-left: 3em; } } @media print {\timg {\t\tmax-width:100% !important;\t\tpage-break-inside: avoid;\t}\th2, h3 {\t\tpage-break-after: avoid;\t}\tdiv.header { background-color: #FFF; }\t } body { color: #000; background-color: #FFF; border: 0; margin: 0; padding: 0; } div.header { border:0; margin:0; padding: 0.5em; font-size: 200%; width:100%; } #header_title { display:inline-block; float:left; clear:left; } #header_filename { display:inline-block; float:right; clear:right; font-size: 50%; margin-right:2em; text-align: right; } div.header h3 { font-size: 50%; margin-bottom: 0; } div.summary ul { padding-left:0; list-style-type:none; } div.summary ul li img { margin-bottom:-0.5em; margin-top:0.5em; }\t div.main { background-color: white; } div.module { padding-bottom:3em; padding-top:3em; border-bottom: 1px solid #990000 }\t div.footer { background-color: #EEE; border:0; margin:0; padding: 0.5em; font-size: 100%; width:100%; } h2 { color: #2a5e8c; padding-bottom: 0; margin-bottom: 0; clear:left; }table { margin-left: 3em; text-align: center; } th { text-align: center; background-color: #000080; color: #FFF; padding: 0.4em;} td { font-family: monospace; text-align: left; background-color: #EEE; color: #000; padding: 0.4em;}img { padding-top: 0; margin-top: 0; border-top: 0;} p { padding-top: 0; margin-top: 0;}.pass { color : #009900;}.warn { color : #999900;}.fail { color : #990000;}</style><script src="https://cdn.plot.ly/plotly-latest.min.js"></script></head><body><div class="header">\t<div id="header_title">Report</div> <div id="header_filename">Mon May 27 16:55:06 2024\n+<br/> 1000trimmed_fastq\t</div></div><div class="summary"><h2>Summary</h2><ul> <li><a class="pass" href="#basicstatistics"> Basic Statistics </a></li> \t<li><a class="pass" href="#perbasesequencequality"> Per base sequence quality</a></li> \t<li><a class="fail" href="#pertilesequencequality">Per tile sequence quality</a></li> \t<li><a class="pass" href="#persequencequalityscores">Per sequence quality scores</a></li> \t<li><a class="fail" href="#perbasesequencecontent">Per base sequence content</a></li> \t<li><a class="warn" href="#persequencegccontent">Per sequence GC content</a></li> \t<li><a class="pass" href="#perbasencontent">Per base N content</a></li> \t<li><a class="warn" href="#sequencelengthdistribution">Sequence Length Distribution</a></li> \t<li><a class="pass" href="#sequenceduplicationlevels">Sequence Duplication Levels</a></li'..b',37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108], y : 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[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108], y : [0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0], type : \'line\', name : "Illumina Small RNA 3 prime Adapter"},{x : [1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108], y : 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end of file\n'

diff -r 000000000000 -r e462044ece67 test-data/fastqc_report_bisulfite.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fastqc_report_bisulfite.html Tue Jun 04 14:14:49 2024 +0000

[

b'@@ -0,0 +1,2 @@\n+<html><head> <meta charset="utf-8"> <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">\t<title> 1000trimmed_fastq - report\t</title><link rel="stylesheet" href="https://stackpath.bootstrapcdn.com/bootstrap/4.3.1/css/bootstrap.min.css" integrity="sha384-ggOyR0iXCbMQv3Xipma34MD+dH/1fQ784/j6cY/iJTQUOhcWr7x9JvoRxT2MZw1T" crossorigin="anonymous"><link href="https://stackpath.bootstrapcdn.com/font-awesome/4.7.0/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-wvfXpqpZZVQGK6TAh5PVlGOfQNHSoD2xbE+QkPxCAFlNEevoEH3Sl0sibVcOQVnN" crossorigin="anonymous"><style type="text/css"> @media screen { div.summary { width: 18em; position:fixed; top: 4em; margin:1em 0 0 1em; } div.main { display:block; position:absolute; overflow:auto; height:auto; width:auto; top:4.5em; bottom:2.3em; left:18em; right:0; border-left: 1px solid #CCC; padding:0 0 0 1em; background-color: white; z-index:1; } div.header { background-color: #EEE; border:0; margin:0; padding: 0.2em; font-size: 200%; position:fixed; width:100%; top:0; left:0; z-index:2; } div.footer { background-color: #EEE; border:0; margin:0;\tpadding:0.5em; height: 2.5em;\toverflow:hidden; font-size: 100%; position:fixed; bottom:0; width:100%; z-index:2; } img.indented { margin-left: 3em; } } @media print {\timg {\t\tmax-width:100% !important;\t\tpage-break-inside: avoid;\t}\th2, h3 {\t\tpage-break-after: avoid;\t}\tdiv.header { background-color: #FFF; }\t } body { color: #000; background-color: #FFF; border: 0; margin: 0; padding: 0; } div.header { border:0; margin:0; padding: 0.5em; font-size: 200%; width:100%; } #header_title { display:inline-block; float:left; clear:left; } #header_filename { display:inline-block; float:right; clear:right; font-size: 50%; margin-right:2em; text-align: right; } div.header h3 { font-size: 50%; margin-bottom: 0; } div.summary ul { padding-left:0; list-style-type:none; } div.summary ul li img { margin-bottom:-0.5em; margin-top:0.5em; }\t div.main { background-color: white; } div.module { padding-bottom:3em; padding-top:3em; border-bottom: 1px solid #990000 }\t div.footer { background-color: #EEE; border:0; margin:0; padding: 0.5em; font-size: 100%; width:100%; } h2 { color: #2a5e8c; padding-bottom: 0; margin-bottom: 0; clear:left; }table { margin-left: 3em; text-align: center; } th { text-align: center; background-color: #000080; color: #FFF; padding: 0.4em;} td { font-family: monospace; text-align: left; background-color: #EEE; color: #000; padding: 0.4em;}img { padding-top: 0; margin-top: 0; border-top: 0;} p { padding-top: 0; margin-top: 0;}.pass { color : #009900;}.warn { color : #999900;}.fail { color : #990000;}</style><script src="https://cdn.plot.ly/plotly-latest.min.js"></script></head><body><div class="header">\t<div id="header_title">Report</div> <div id="header_filename">Mon May 27 17:08:30 2024\n+<br/> 1000trimmed_fastq\t</div></div><div class="summary"><h2>Summary</h2><ul> <li><a class="pass" href="#basicstatistics"> Basic Statistics </a></li> \t<li><a class="pass" href="#perbasesequencequality"> Per base sequence quality</a></li> \t<li><a class="fail" href="#pertilesequencequality">Per tile sequence quality</a></li> \t<li><a class="pass" href="#persequencequalityscores">Per sequence quality scores</a></li> \t<li><a class="warn" href="#perbasesequencecontent">Per base sequence content</a></li> \t<li><a class="warn" href="#persequencegccontent">Per sequence GC content</a></li> \t<li><a class="pass" href="#perbasencontent">Per base N content</a></li> \t<li><a class="warn" href="#sequencelengthdistribution">Sequence Length Distribution</a></li> \t<li><a class="pass" href="#sequenceduplicationlevels">Sequence Duplication Levels</a></li'..b',37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108], y : [0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.122324,0.122324,0.122324,0.122324,0.122324,0.122324,0.122324,0.142712,0.183486,0.224261,0.224261,0.224261,0.224261,0.224261,0.224261,0.265036,0.285423,0.326198,0.407747,0.468909,0.468909,0.468909,0.468909,0.468909,0.468909,0.468909,0.468909,0.468909,0.468909,0.468909,0.468909,0.468909,0.468909,0.468909,0.468909,0.468909,0.468909,0.468909,0.468909,0.468909,0.468909,0.468909,0.468909,0.468909,0.468909,0.468909,0.468909,0.468909,0.468909,0.468909,0.468909,0.468909,0.468909,0.468909,0.489297,0.489297,0.489297,0.489297,0.489297,0.489297,0.489297,0.489297,0.489297,0.509684,0.509684,0.509684,0.509684,0.509684,0.509684,0.509684,0.509684,0.509684,0.570846,0.632008,0.632008,0.632008,0.632008,0.632008,0.632008,0.632008,0.632008,0.632008,0.632008,0.632008,0.632008,0.632008,0.632008,0.632008,0.632008], type : \'line\', name : "Illumina Universal Adapter"},{x : [1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108], y : [0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0], type : \'line\', name : "Illumina Small RNA 3 prime Adapter"},{x : [1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108], y : [0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0], type : \'line\', name : "Illumina Small RNA 5 prime Adapter"},{x : [1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108], y : [0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0], type : \'line\', name : "Nextera Transposase Sequence"},{x : [1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108], y : [0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0], type : \'line\', name : "SOLID Small RNA Adapter"} ], { margin: { t: 0 }, showlegend: true, xaxis : {title : \'Base position\'}, yaxis : {title : \'% sequences with adapter before position\'} } );}if (document.getElementById(\'kmerlineplot\') !== null) { Plotly.newPlot(\'kmerlineplot\', [ ], { margin: { t: 0 }, showlegend: true, xaxis : {title : \'Base position\'}, yaxis : {title : \'log2(obs/ exp max)\'} } );}</script></html>\n\\ No newline at end of file\n'

diff -r 000000000000 -r e462044ece67 test-data/fastqc_report_bisulfite.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fastqc_report_bisulfite.txt Tue Jun 04 14:14:49 2024 +0000

diff -r 000000000000 -r e462044ece67 test-data/fastqc_report_bisulfite_summary.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fastqc_report_bisulfite_summary.txt Tue Jun 04 14:14:49 2024 +0000

@@ -0,0 +1,11 @@
+PASS Basic Statistics 1000trimmed_fastq
+PASS Per base sequence quality 1000trimmed_fastq
+FAIL Per tile sequence quality 1000trimmed_fastq
+PASS Per sequence quality scores 1000trimmed_fastq
+WARN Per base sequence content 1000trimmed_fastq
+WARN Per sequence GC content 1000trimmed_fastq
+PASS Per base N content 1000trimmed_fastq
+WARN Sequence Length Distribution 1000trimmed_fastq
+PASS Sequence Duplication Levels 1000trimmed_fastq
+WARN Overrepresented sequences 1000trimmed_fastq
+PASS Adapter Content 1000trimmed_fastq

diff -r 000000000000 -r e462044ece67 test-data/fastqc_report_contaminants.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fastqc_report_contaminants.html Tue Jun 04 14:14:49 2024 +0000

[

b'@@ -0,0 +1,2 @@\n+<html><head> <meta charset="utf-8"> <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">\t<title> 1000trimmed_fastq - report\t</title><link rel="stylesheet" href="https://stackpath.bootstrapcdn.com/bootstrap/4.3.1/css/bootstrap.min.css" integrity="sha384-ggOyR0iXCbMQv3Xipma34MD+dH/1fQ784/j6cY/iJTQUOhcWr7x9JvoRxT2MZw1T" crossorigin="anonymous"><link href="https://stackpath.bootstrapcdn.com/font-awesome/4.7.0/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-wvfXpqpZZVQGK6TAh5PVlGOfQNHSoD2xbE+QkPxCAFlNEevoEH3Sl0sibVcOQVnN" crossorigin="anonymous"><style type="text/css"> @media screen { div.summary { width: 18em; position:fixed; top: 4em; margin:1em 0 0 1em; } div.main { display:block; position:absolute; overflow:auto; height:auto; width:auto; top:4.5em; bottom:2.3em; left:18em; right:0; border-left: 1px solid #CCC; padding:0 0 0 1em; background-color: white; z-index:1; } div.header { background-color: #EEE; border:0; margin:0; padding: 0.2em; font-size: 200%; position:fixed; width:100%; top:0; left:0; z-index:2; } div.footer { background-color: #EEE; border:0; margin:0;\tpadding:0.5em; height: 2.5em;\toverflow:hidden; font-size: 100%; position:fixed; bottom:0; width:100%; z-index:2; } img.indented { margin-left: 3em; } } @media print {\timg {\t\tmax-width:100% !important;\t\tpage-break-inside: avoid;\t}\th2, h3 {\t\tpage-break-after: avoid;\t}\tdiv.header { background-color: #FFF; }\t } body { color: #000; background-color: #FFF; border: 0; margin: 0; padding: 0; } div.header { border:0; margin:0; padding: 0.5em; font-size: 200%; width:100%; } #header_title { display:inline-block; float:left; clear:left; } #header_filename { display:inline-block; float:right; clear:right; font-size: 50%; margin-right:2em; text-align: right; } div.header h3 { font-size: 50%; margin-bottom: 0; } div.summary ul { padding-left:0; list-style-type:none; } div.summary ul li img { margin-bottom:-0.5em; margin-top:0.5em; }\t div.main { background-color: white; } div.module { padding-bottom:3em; padding-top:3em; border-bottom: 1px solid #990000 }\t div.footer { background-color: #EEE; border:0; margin:0; padding: 0.5em; font-size: 100%; width:100%; } h2 { color: #2a5e8c; padding-bottom: 0; margin-bottom: 0; clear:left; }table { margin-left: 3em; text-align: center; } th { text-align: center; background-color: #000080; color: #FFF; padding: 0.4em;} td { font-family: monospace; text-align: left; background-color: #EEE; color: #000; padding: 0.4em;}img { padding-top: 0; margin-top: 0; border-top: 0;} p { padding-top: 0; margin-top: 0;}.pass { color : #009900;}.warn { color : #999900;}.fail { color : #990000;}</style><script src="https://cdn.plot.ly/plotly-latest.min.js"></script></head><body><div class="header">\t<div id="header_title">Report</div> <div id="header_filename">Mon May 27 16:52:55 2024\n+<br/> 1000trimmed_fastq\t</div></div><div class="summary"><h2>Summary</h2><ul> <li><a class="pass" href="#basicstatistics"> Basic Statistics </a></li> \t<li><a class="pass" href="#perbasesequencequality"> Per base sequence quality</a></li> \t<li><a class="fail" href="#pertilesequencequality">Per tile sequence quality</a></li> \t<li><a class="pass" href="#persequencequalityscores">Per sequence quality scores</a></li> \t<li><a class="fail" href="#perbasesequencecontent">Per base sequence content</a></li> \t<li><a class="warn" href="#persequencegccontent">Per sequence GC content</a></li> \t<li><a class="pass" href="#perbasencontent">Per base N content</a></li> \t<li><a class="warn" href="#sequencelengthdistribution">Sequence Length Distribution</a></li> \t<li><a class="pass" href="#sequenceduplicationlevels">Sequence Duplication Levels</a></li'..b',37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108], y : [0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.122324,0.122324,0.122324,0.122324,0.122324,0.122324,0.122324,0.142712,0.183486,0.224261,0.224261,0.224261,0.224261,0.224261,0.224261,0.265036,0.285423,0.326198,0.407747,0.468909,0.468909,0.468909,0.468909,0.468909,0.468909,0.468909,0.468909,0.468909,0.468909,0.468909,0.468909,0.468909,0.468909,0.468909,0.468909,0.468909,0.468909,0.468909,0.468909,0.468909,0.468909,0.468909,0.468909,0.468909,0.468909,0.468909,0.468909,0.468909,0.468909,0.468909,0.468909,0.468909,0.468909,0.468909,0.489297,0.489297,0.489297,0.489297,0.489297,0.489297,0.489297,0.489297,0.489297,0.509684,0.509684,0.509684,0.509684,0.509684,0.509684,0.509684,0.509684,0.509684,0.570846,0.632008,0.632008,0.632008,0.632008,0.632008,0.632008,0.632008,0.632008,0.632008,0.632008,0.632008,0.632008,0.632008,0.632008,0.632008,0.632008], type : \'line\', name : "Illumina Universal Adapter"},{x : 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diff -r 000000000000 -r e462044ece67 test-data/fastqc_report_customlimits.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fastqc_report_customlimits.html Tue Jun 04 14:14:49 2024 +0000

[

b'@@ -0,0 +1,2 @@\n+<html><head> <meta charset="utf-8"> <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">\t<title> 1000trimmed_fastq - report\t</title><link rel="stylesheet" href="https://stackpath.bootstrapcdn.com/bootstrap/4.3.1/css/bootstrap.min.css" integrity="sha384-ggOyR0iXCbMQv3Xipma34MD+dH/1fQ784/j6cY/iJTQUOhcWr7x9JvoRxT2MZw1T" crossorigin="anonymous"><link href="https://stackpath.bootstrapcdn.com/font-awesome/4.7.0/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-wvfXpqpZZVQGK6TAh5PVlGOfQNHSoD2xbE+QkPxCAFlNEevoEH3Sl0sibVcOQVnN" crossorigin="anonymous"><style type="text/css"> @media screen { div.summary { width: 18em; position:fixed; top: 4em; margin:1em 0 0 1em; } div.main { display:block; position:absolute; overflow:auto; height:auto; width:auto; top:4.5em; bottom:2.3em; left:18em; right:0; border-left: 1px solid #CCC; padding:0 0 0 1em; background-color: white; z-index:1; } div.header { background-color: #EEE; border:0; margin:0; padding: 0.2em; font-size: 200%; position:fixed; width:100%; top:0; left:0; z-index:2; } div.footer { background-color: #EEE; border:0; margin:0;\tpadding:0.5em; height: 2.5em;\toverflow:hidden; font-size: 100%; position:fixed; bottom:0; width:100%; z-index:2; } img.indented { margin-left: 3em; } } @media print {\timg {\t\tmax-width:100% !important;\t\tpage-break-inside: avoid;\t}\th2, h3 {\t\tpage-break-after: avoid;\t}\tdiv.header { background-color: #FFF; }\t } body { color: #000; background-color: #FFF; border: 0; margin: 0; padding: 0; } div.header { border:0; margin:0; padding: 0.5em; font-size: 200%; width:100%; } #header_title { display:inline-block; float:left; clear:left; } #header_filename { display:inline-block; float:right; clear:right; font-size: 50%; margin-right:2em; text-align: right; } div.header h3 { font-size: 50%; margin-bottom: 0; } div.summary ul { padding-left:0; list-style-type:none; } div.summary ul li img { margin-bottom:-0.5em; margin-top:0.5em; }\t div.main { background-color: white; } div.module { padding-bottom:3em; padding-top:3em; border-bottom: 1px solid #990000 }\t div.footer { background-color: #EEE; border:0; margin:0; padding: 0.5em; font-size: 100%; width:100%; } h2 { color: #2a5e8c; padding-bottom: 0; margin-bottom: 0; clear:left; }table { margin-left: 3em; text-align: center; } th { text-align: center; background-color: #000080; color: #FFF; padding: 0.4em;} td { font-family: monospace; text-align: left; background-color: #EEE; color: #000; padding: 0.4em;}img { padding-top: 0; margin-top: 0; border-top: 0;} p { padding-top: 0; margin-top: 0;}.pass { color : #009900;}.warn { color : #999900;}.fail { color : #990000;}</style><script src="https://cdn.plot.ly/plotly-latest.min.js"></script></head><body><div class="header">\t<div id="header_title">Report</div> <div id="header_filename">Mon May 27 16:57:19 2024\n+<br/> 1000trimmed_fastq\t</div></div><div class="summary"><h2>Summary</h2><ul> <li><a class="pass" href="#basicstatistics"> Basic Statistics </a></li> \t<li><a class="pass" href="#perbasesequencequality"> Per base sequence quality</a></li> \t<li><a class="fail" href="#pertilesequencequality">Per tile sequence quality</a></li> \t<li><a class="pass" href="#persequencequalityscores">Per sequence quality scores</a></li> \t<li><a class="fail" href="#perbasesequencecontent">Per base sequence content</a></li> \t<li><a class="warn" href="#persequencegccontent">Per sequence GC content</a></li> \t<li><a class="pass" href="#perbasencontent">Per base N content</a></li> \t<li><a class="warn" href="#sequencelengthdistribution">Sequence Length Distribution</a></li> \t<li><a class="pass" href="#sequenceduplicationlevels">Sequence Duplication Levels</a></li'..b',37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108], y : 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diff -r 000000000000 -r e462044ece67 test-data/fastqc_report_hisat.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fastqc_report_hisat.html Tue Jun 04 14:14:49 2024 +0000

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alt="Adapter graph"/></p></div></div><div class="footer">Produced by <a href="http://www.bioinformatics.babraham.ac.uk/projects/fastqc/">FastQC</a> (version 0.12.1)</div></body></html>\n\\ No newline at end of file\n'

diff -r 000000000000 -r e462044ece67 test-data/fastqc_report_kmer.html
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+++ b/test-data/fastqc_report_kmer.html Tue Jun 04 14:14:49 2024 +0000

[

b'@@ -0,0 +1,2 @@\n+<html><head> <meta charset="utf-8"> <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">\t<title> 1000trimmed_fastq - report\t</title><link rel="stylesheet" href="https://stackpath.bootstrapcdn.com/bootstrap/4.3.1/css/bootstrap.min.css" integrity="sha384-ggOyR0iXCbMQv3Xipma34MD+dH/1fQ784/j6cY/iJTQUOhcWr7x9JvoRxT2MZw1T" crossorigin="anonymous"><link href="https://stackpath.bootstrapcdn.com/font-awesome/4.7.0/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-wvfXpqpZZVQGK6TAh5PVlGOfQNHSoD2xbE+QkPxCAFlNEevoEH3Sl0sibVcOQVnN" crossorigin="anonymous"><style type="text/css"> @media screen { div.summary { width: 18em; position:fixed; top: 4em; margin:1em 0 0 1em; } div.main { display:block; position:absolute; overflow:auto; height:auto; width:auto; top:4.5em; bottom:2.3em; left:18em; right:0; border-left: 1px solid #CCC; padding:0 0 0 1em; background-color: white; z-index:1; } div.header { background-color: #EEE; border:0; margin:0; padding: 0.2em; font-size: 200%; position:fixed; width:100%; top:0; left:0; z-index:2; } div.footer { background-color: #EEE; border:0; margin:0;\tpadding:0.5em; height: 2.5em;\toverflow:hidden; font-size: 100%; position:fixed; bottom:0; width:100%; z-index:2; } img.indented { margin-left: 3em; } } @media print {\timg {\t\tmax-width:100% !important;\t\tpage-break-inside: avoid;\t}\th2, h3 {\t\tpage-break-after: avoid;\t}\tdiv.header { background-color: #FFF; }\t } body { color: #000; background-color: #FFF; border: 0; margin: 0; padding: 0; } div.header { border:0; margin:0; padding: 0.5em; font-size: 200%; width:100%; } #header_title { display:inline-block; float:left; clear:left; } #header_filename { display:inline-block; float:right; clear:right; font-size: 50%; margin-right:2em; text-align: right; } div.header h3 { font-size: 50%; margin-bottom: 0; } div.summary ul { padding-left:0; list-style-type:none; } div.summary ul li img { margin-bottom:-0.5em; margin-top:0.5em; }\t div.main { background-color: white; } div.module { padding-bottom:3em; padding-top:3em; border-bottom: 1px solid #990000 }\t div.footer { background-color: #EEE; border:0; margin:0; padding: 0.5em; font-size: 100%; width:100%; } h2 { color: #2a5e8c; padding-bottom: 0; margin-bottom: 0; clear:left; }table { margin-left: 3em; text-align: center; } th { text-align: center; background-color: #000080; color: #FFF; padding: 0.4em;} td { font-family: monospace; text-align: left; background-color: #EEE; color: #000; padding: 0.4em;}img { padding-top: 0; margin-top: 0; border-top: 0;} p { padding-top: 0; margin-top: 0;}.pass { color : #009900;}.warn { color : #999900;}.fail { color : #990000;}</style><script src="https://cdn.plot.ly/plotly-latest.min.js"></script></head><body><div class="header">\t<div id="header_title">Report</div> <div id="header_filename">Mon May 27 16:59:30 2024\n+<br/> 1000trimmed_fastq\t</div></div><div class="summary"><h2>Summary</h2><ul> <li><a class="pass" href="#basicstatistics"> Basic Statistics </a></li> \t<li><a class="pass" href="#perbasesequencequality"> Per base sequence quality</a></li> \t<li><a class="fail" href="#pertilesequencequality">Per tile sequence quality</a></li> \t<li><a class="pass" href="#persequencequalityscores">Per sequence quality scores</a></li> \t<li><a class="fail" href="#perbasesequencecontent">Per base sequence content</a></li> \t<li><a class="warn" href="#persequencegccontent">Per sequence GC content</a></li> \t<li><a class="pass" href="#perbasencontent">Per base N content</a></li> \t<li><a class="warn" href="#sequencelengthdistribution">Sequence Length Distribution</a></li> \t<li><a class="pass" href="#sequenceduplicationlevels">Sequence Duplication Levels</a></li'..b',37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108], y : 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[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108], y : [0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0], type : \'line\', name : "SOLID Small RNA Adapter"} ], { margin: { t: 0 }, showlegend: true, xaxis : {title : \'Base position\'}, yaxis : {title : \'% sequences with adapter before position\'} } );}if (document.getElementById(\'kmerlineplot\') !== null) { Plotly.newPlot(\'kmerlineplot\', [ ], { margin: { t: 0 }, showlegend: true, xaxis : {title : \'Base position\'}, yaxis : {title : \'log2(obs/ exp max)\'} } );}</script></html>\n\\ No newline at end of file\n'

diff -r 000000000000 -r e462044ece67 test-data/fastqc_report_min_length.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fastqc_report_min_length.html Tue Jun 04 14:14:49 2024 +0000

[

b'@@ -0,0 +1,2 @@\n+<html><head> <meta charset="utf-8"> <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">\t<title> 1000trimmed_fastq - report\t</title><link rel="stylesheet" href="https://stackpath.bootstrapcdn.com/bootstrap/4.3.1/css/bootstrap.min.css" integrity="sha384-ggOyR0iXCbMQv3Xipma34MD+dH/1fQ784/j6cY/iJTQUOhcWr7x9JvoRxT2MZw1T" crossorigin="anonymous"><link href="https://stackpath.bootstrapcdn.com/font-awesome/4.7.0/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-wvfXpqpZZVQGK6TAh5PVlGOfQNHSoD2xbE+QkPxCAFlNEevoEH3Sl0sibVcOQVnN" crossorigin="anonymous"><style type="text/css"> @media screen { div.summary { width: 18em; position:fixed; top: 4em; margin:1em 0 0 1em; } div.main { display:block; position:absolute; overflow:auto; height:auto; width:auto; top:4.5em; bottom:2.3em; left:18em; right:0; border-left: 1px solid #CCC; padding:0 0 0 1em; background-color: white; z-index:1; } div.header { background-color: #EEE; border:0; margin:0; padding: 0.2em; font-size: 200%; position:fixed; width:100%; top:0; left:0; z-index:2; } div.footer { background-color: #EEE; border:0; margin:0;\tpadding:0.5em; height: 2.5em;\toverflow:hidden; font-size: 100%; position:fixed; bottom:0; width:100%; z-index:2; } img.indented { margin-left: 3em; } } @media print {\timg {\t\tmax-width:100% !important;\t\tpage-break-inside: avoid;\t}\th2, h3 {\t\tpage-break-after: avoid;\t}\tdiv.header { background-color: #FFF; }\t } body { color: #000; background-color: #FFF; border: 0; margin: 0; padding: 0; } div.header { border:0; margin:0; padding: 0.5em; font-size: 200%; width:100%; } #header_title { display:inline-block; float:left; clear:left; } #header_filename { display:inline-block; float:right; clear:right; font-size: 50%; margin-right:2em; text-align: right; } div.header h3 { font-size: 50%; margin-bottom: 0; } div.summary ul { padding-left:0; list-style-type:none; } div.summary ul li img { margin-bottom:-0.5em; margin-top:0.5em; }\t div.main { background-color: white; } div.module { padding-bottom:3em; padding-top:3em; border-bottom: 1px solid #990000 }\t div.footer { background-color: #EEE; border:0; margin:0; padding: 0.5em; font-size: 100%; width:100%; } h2 { color: #2a5e8c; padding-bottom: 0; margin-bottom: 0; clear:left; }table { margin-left: 3em; text-align: center; } th { text-align: center; background-color: #000080; color: #FFF; padding: 0.4em;} td { font-family: monospace; text-align: left; background-color: #EEE; color: #000; padding: 0.4em;}img { padding-top: 0; margin-top: 0; border-top: 0;} p { padding-top: 0; margin-top: 0;}.pass { color : #009900;}.warn { color : #999900;}.fail { color : #990000;}</style><script src="https://cdn.plot.ly/plotly-latest.min.js"></script></head><body><div class="header">\t<div id="header_title">Report</div> <div id="header_filename">Mon May 27 17:01:42 2024\n+<br/> 1000trimmed_fastq\t</div></div><div class="summary"><h2>Summary</h2><ul> <li><a class="pass" href="#basicstatistics"> Basic Statistics </a></li> \t<li><a class="pass" href="#perbasesequencequality"> Per base sequence quality</a></li> \t<li><a class="fail" href="#pertilesequencequality">Per tile sequence quality</a></li> \t<li><a class="pass" href="#persequencequalityscores">Per sequence quality scores</a></li> \t<li><a class="fail" href="#perbasesequencecontent">Per base sequence content</a></li> \t<li><a class="warn" href="#persequencegccontent">Per sequence GC content</a></li> \t<li><a class="pass" href="#perbasencontent">Per base N content</a></li> \t<li><a class="warn" href="#sequencelengthdistribution">Sequence Length Distribution</a></li> \t<li><a class="pass" href="#sequenceduplicationlevels">Sequence Duplication Levels</a></li'..b',37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108], y : 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[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108], y : [0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0], type : \'line\', name : "Illumina Small RNA 3 prime Adapter"},{x : [1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108], y : 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[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108], y : [0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0], type : \'line\', name : "SOLID Small RNA Adapter"} ], { margin: { t: 0 }, showlegend: true, xaxis : {title : \'Base position\'}, yaxis : {title : \'% sequences with adapter before position\'} } );}if (document.getElementById(\'kmerlineplot\') !== null) { Plotly.newPlot(\'kmerlineplot\', [ ], { margin: { t: 0 }, showlegend: true, xaxis : {title : \'Base position\'}, yaxis : {title : \'log2(obs/ exp max)\'} } );}</script></html>\n\\ No newline at end of file\n'

diff -r 000000000000 -r e462044ece67 test-data/fastqc_report_nogroup.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fastqc_report_nogroup.html Tue Jun 04 14:14:49 2024 +0000

[

b'@@ -0,0 +1,2 @@\n+<html><head> <meta charset="utf-8"> <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">\t<title> 1000trimmed_fastq - report\t</title><link rel="stylesheet" href="https://stackpath.bootstrapcdn.com/bootstrap/4.3.1/css/bootstrap.min.css" integrity="sha384-ggOyR0iXCbMQv3Xipma34MD+dH/1fQ784/j6cY/iJTQUOhcWr7x9JvoRxT2MZw1T" crossorigin="anonymous"><link href="https://stackpath.bootstrapcdn.com/font-awesome/4.7.0/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-wvfXpqpZZVQGK6TAh5PVlGOfQNHSoD2xbE+QkPxCAFlNEevoEH3Sl0sibVcOQVnN" crossorigin="anonymous"><style type="text/css"> @media screen { div.summary { width: 18em; position:fixed; top: 4em; margin:1em 0 0 1em; } div.main { display:block; position:absolute; overflow:auto; height:auto; width:auto; top:4.5em; bottom:2.3em; left:18em; right:0; border-left: 1px solid #CCC; padding:0 0 0 1em; background-color: white; z-index:1; } div.header { background-color: #EEE; border:0; margin:0; padding: 0.2em; font-size: 200%; position:fixed; width:100%; top:0; left:0; z-index:2; } div.footer { background-color: #EEE; border:0; margin:0;\tpadding:0.5em; height: 2.5em;\toverflow:hidden; font-size: 100%; position:fixed; bottom:0; width:100%; z-index:2; } img.indented { margin-left: 3em; } } @media print {\timg {\t\tmax-width:100% !important;\t\tpage-break-inside: avoid;\t}\th2, h3 {\t\tpage-break-after: avoid;\t}\tdiv.header { background-color: #FFF; }\t } body { color: #000; background-color: #FFF; border: 0; margin: 0; padding: 0; } div.header { border:0; margin:0; padding: 0.5em; font-size: 200%; width:100%; } #header_title { display:inline-block; float:left; clear:left; } #header_filename { display:inline-block; float:right; clear:right; font-size: 50%; margin-right:2em; text-align: right; } div.header h3 { font-size: 50%; margin-bottom: 0; } div.summary ul { padding-left:0; list-style-type:none; } div.summary ul li img { margin-bottom:-0.5em; margin-top:0.5em; }\t div.main { background-color: white; } div.module { padding-bottom:3em; padding-top:3em; border-bottom: 1px solid #990000 }\t div.footer { background-color: #EEE; border:0; margin:0; padding: 0.5em; font-size: 100%; width:100%; } h2 { color: #2a5e8c; padding-bottom: 0; margin-bottom: 0; clear:left; }table { margin-left: 3em; text-align: center; } th { text-align: center; background-color: #000080; color: #FFF; padding: 0.4em;} td { font-family: monospace; text-align: left; background-color: #EEE; color: #000; padding: 0.4em;}img { padding-top: 0; margin-top: 0; border-top: 0;} p { padding-top: 0; margin-top: 0;}.pass { color : #009900;}.warn { color : #999900;}.fail { color : #990000;}</style><script src="https://cdn.plot.ly/plotly-latest.min.js"></script></head><body><div class="header">\t<div id="header_title">Report</div> <div id="header_filename">Mon May 27 17:04:08 2024\n+<br/> 1000trimmed_fastq\t</div></div><div class="summary"><h2>Summary</h2><ul> <li><a class="pass" href="#basicstatistics"> Basic Statistics </a></li> \t<li><a class="pass" href="#perbasesequencequality"> Per base sequence quality</a></li> \t<li><a class="fail" href="#pertilesequencequality">Per tile sequence quality</a></li> \t<li><a class="pass" href="#persequencequalityscores">Per sequence quality scores</a></li> \t<li><a class="fail" href="#perbasesequencecontent">Per base sequence content</a></li> \t<li><a class="warn" href="#persequencegccontent">Per sequence GC content</a></li> \t<li><a class="pass" href="#perbasencontent">Per base N content</a></li> \t<li><a class="warn" href="#sequencelengthdistribution">Sequence Length Distribution</a></li> \t<li><a class="pass" href="#sequenceduplicationlevels">Sequence Duplication Levels</a></li'..b',37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108], y : 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end of file\n'

diff -r 000000000000 -r e462044ece67 test-data/fastqc_report_reverse_complement.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fastqc_report_reverse_complement.html Tue Jun 04 14:14:49 2024 +0000

[

b'@@ -0,0 +1,2 @@\n+<html><head> <meta charset="utf-8"> <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">\t<title> 1000trimmed_fastq - report\t</title><link rel="stylesheet" href="https://stackpath.bootstrapcdn.com/bootstrap/4.3.1/css/bootstrap.min.css" integrity="sha384-ggOyR0iXCbMQv3Xipma34MD+dH/1fQ784/j6cY/iJTQUOhcWr7x9JvoRxT2MZw1T" crossorigin="anonymous"><link href="https://stackpath.bootstrapcdn.com/font-awesome/4.7.0/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-wvfXpqpZZVQGK6TAh5PVlGOfQNHSoD2xbE+QkPxCAFlNEevoEH3Sl0sibVcOQVnN" crossorigin="anonymous"><style type="text/css"> @media screen { div.summary { width: 18em; position:fixed; top: 4em; margin:1em 0 0 1em; } div.main { display:block; position:absolute; overflow:auto; height:auto; width:auto; top:4.5em; bottom:2.3em; left:18em; right:0; border-left: 1px solid #CCC; padding:0 0 0 1em; background-color: white; z-index:1; } div.header { background-color: #EEE; border:0; margin:0; padding: 0.2em; font-size: 200%; position:fixed; width:100%; top:0; left:0; z-index:2; } div.footer { background-color: #EEE; border:0; margin:0;\tpadding:0.5em; height: 2.5em;\toverflow:hidden; font-size: 100%; position:fixed; bottom:0; width:100%; z-index:2; } img.indented { margin-left: 3em; } } @media print {\timg {\t\tmax-width:100% !important;\t\tpage-break-inside: avoid;\t}\th2, h3 {\t\tpage-break-after: avoid;\t}\tdiv.header { background-color: #FFF; }\t } body { color: #000; background-color: #FFF; border: 0; margin: 0; padding: 0; } div.header { border:0; margin:0; padding: 0.5em; font-size: 200%; width:100%; } #header_title { display:inline-block; float:left; clear:left; } #header_filename { display:inline-block; float:right; clear:right; font-size: 50%; margin-right:2em; text-align: right; } div.header h3 { font-size: 50%; margin-bottom: 0; } div.summary ul { padding-left:0; list-style-type:none; } div.summary ul li img { margin-bottom:-0.5em; margin-top:0.5em; }\t div.main { background-color: white; } div.module { padding-bottom:3em; padding-top:3em; border-bottom: 1px solid #990000 }\t div.footer { background-color: #EEE; border:0; margin:0; padding: 0.5em; font-size: 100%; width:100%; } h2 { color: #2a5e8c; padding-bottom: 0; margin-bottom: 0; clear:left; }table { margin-left: 3em; text-align: center; } th { text-align: center; background-color: #000080; color: #FFF; padding: 0.4em;} td { font-family: monospace; text-align: left; background-color: #EEE; color: #000; padding: 0.4em;}img { padding-top: 0; margin-top: 0; border-top: 0;} p { padding-top: 0; margin-top: 0;}.pass { color : #009900;}.warn { color : #999900;}.fail { color : #990000;}</style><script src="https://cdn.plot.ly/plotly-latest.min.js"></script></head><body><div class="header">\t<div id="header_title">Report</div> <div id="header_filename">Mon May 27 17:10:44 2024\n+<br/> 1000trimmed_fastq\t</div></div><div class="summary"><h2>Summary</h2><ul> <li><a class="pass" href="#basicstatistics"> Basic Statistics </a></li> \t<li><a class="pass" href="#perbasesequencequality"> Per base sequence quality</a></li> \t<li><a class="fail" href="#pertilesequencequality">Per tile sequence quality</a></li> \t<li><a class="pass" href="#persequencequalityscores">Per sequence quality scores</a></li> \t<li><a class="fail" href="#perbasesequencecontent">Per base sequence content</a></li> \t<li><a class="warn" href="#persequencegccontent">Per sequence GC content</a></li> \t<li><a class="pass" href="#perbasencontent">Per base N content</a></li> \t<li><a class="warn" href="#sequencelengthdistribution">Sequence Length Distribution</a></li> \t<li><a class="pass" href="#sequenceduplicationlevels">Sequence Duplication Levels</a></li'..b',37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108], y : 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[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108], y : [0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0], type : \'line\', name : "Illumina Small RNA 3 prime Adapter"},{x : [1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108], y : 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[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108], y : [0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0], type : \'line\', name : "SOLID Small RNA Adapter"} ], { margin: { t: 0 }, showlegend: true, xaxis : {title : \'Base position\'}, yaxis : {title : \'% sequences with adapter before position\'} } );}if (document.getElementById(\'kmerlineplot\') !== null) { Plotly.newPlot(\'kmerlineplot\', [ ], { margin: { t: 0 }, showlegend: true, xaxis : {title : \'Base position\'}, yaxis : {title : \'log2(obs/ exp max)\'} } );}</script></html>\n\\ No newline at end of file\n'

diff -r 000000000000 -r e462044ece67 test-data/fastqc_report_reverse_complement.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fastqc_report_reverse_complement.txt Tue Jun 04 14:14:49 2024 +0000

diff -r 000000000000 -r e462044ece67 test-data/fastqc_report_reverse_complement_summary.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fastqc_report_reverse_complement_summary.txt Tue Jun 04 14:14:49 2024 +0000

diff -r 000000000000 -r e462044ece67 test-data/fastqc_report_subsample.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fastqc_report_subsample.html Tue Jun 04 14:14:49 2024 +0000

[

b'@@ -0,0 +1,2 @@\n+<html><head> <meta charset="utf-8"> <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">\t<title> 1000trimmed_fastq - report\t</title><link rel="stylesheet" href="https://stackpath.bootstrapcdn.com/bootstrap/4.3.1/css/bootstrap.min.css" integrity="sha384-ggOyR0iXCbMQv3Xipma34MD+dH/1fQ784/j6cY/iJTQUOhcWr7x9JvoRxT2MZw1T" crossorigin="anonymous"><link href="https://stackpath.bootstrapcdn.com/font-awesome/4.7.0/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-wvfXpqpZZVQGK6TAh5PVlGOfQNHSoD2xbE+QkPxCAFlNEevoEH3Sl0sibVcOQVnN" crossorigin="anonymous"><style type="text/css"> @media screen { div.summary { width: 18em; position:fixed; top: 4em; margin:1em 0 0 1em; } div.main { display:block; position:absolute; overflow:auto; height:auto; width:auto; top:4.5em; bottom:2.3em; left:18em; right:0; border-left: 1px solid #CCC; padding:0 0 0 1em; background-color: white; z-index:1; } div.header { background-color: #EEE; border:0; margin:0; padding: 0.2em; font-size: 200%; position:fixed; width:100%; top:0; left:0; z-index:2; } div.footer { background-color: #EEE; border:0; margin:0;\tpadding:0.5em; height: 2.5em;\toverflow:hidden; font-size: 100%; position:fixed; bottom:0; width:100%; z-index:2; } img.indented { margin-left: 3em; } } @media print {\timg {\t\tmax-width:100% !important;\t\tpage-break-inside: avoid;\t}\th2, h3 {\t\tpage-break-after: avoid;\t}\tdiv.header { background-color: #FFF; }\t } body { color: #000; background-color: #FFF; border: 0; margin: 0; padding: 0; } div.header { border:0; margin:0; padding: 0.5em; font-size: 200%; width:100%; } #header_title { display:inline-block; float:left; clear:left; } #header_filename { display:inline-block; float:right; clear:right; font-size: 50%; margin-right:2em; text-align: right; } div.header h3 { font-size: 50%; margin-bottom: 0; } div.summary ul { padding-left:0; list-style-type:none; } div.summary ul li img { margin-bottom:-0.5em; margin-top:0.5em; }\t div.main { background-color: white; } div.module { padding-bottom:3em; padding-top:3em; border-bottom: 1px solid #990000 }\t div.footer { background-color: #EEE; border:0; margin:0; padding: 0.5em; font-size: 100%; width:100%; } h2 { color: #2a5e8c; padding-bottom: 0; margin-bottom: 0; clear:left; }table { margin-left: 3em; text-align: center; } th { text-align: center; background-color: #000080; color: #FFF; padding: 0.4em;} td { font-family: monospace; text-align: left; background-color: #EEE; color: #000; padding: 0.4em;}img { padding-top: 0; margin-top: 0; border-top: 0;} p { padding-top: 0; margin-top: 0;}.pass { color : #009900;}.warn { color : #999900;}.fail { color : #990000;}</style><script src="https://cdn.plot.ly/plotly-latest.min.js"></script></head><body><div class="header">\t<div id="header_title">Report</div> <div id="header_filename">Mon May 27 17:06:18 2024\n+<br/> 1000trimmed_fastq\t</div></div><div class="summary"><h2>Summary</h2><ul> <li><a class="pass" href="#basicstatistics"> Basic Statistics </a></li> \t<li><a class="pass" href="#perbasesequencequality"> Per base sequence quality</a></li> \t<li><a class="fail" href="#pertilesequencequality">Per tile sequence quality</a></li> \t<li><a class="pass" href="#persequencequalityscores">Per sequence quality scores</a></li> \t<li><a class="fail" href="#perbasesequencecontent">Per base sequence content</a></li> \t<li><a class="warn" href="#persequencegccontent">Per sequence GC content</a></li> \t<li><a class="pass" href="#perbasencontent">Per base N content</a></li> \t<li><a class="warn" href="#sequencelengthdistribution">Sequence Length Distribution</a></li> \t<li><a class="pass" href="#sequenceduplicationlevels">Sequence Duplication Levels</a></li'..b',61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108], y : [0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0203874,0.0203874,0.0203874,0.0203874,0.0203874,0.0203874,0.0203874,0.0203874,0.0203874,0.0203874,0.0203874,0.0203874,0.0203874,0.0203874,0.0203874,0.0203874,0.0203874,0.0203874,0.0407747,0.0611621,0.0611621,0.0611621,0.0611621,0.0611621,0.0611621,0.0611621,0.0611621,0.0611621,0.0611621,0.0611621,0.0611621,0.0611621,0.0611621,0.0611621,0.0611621,0.0611621,0.0611621,0.0611621,0.0611621,0.0611621,0.0611621,0.0611621,0.0611621,0.0611621,0.0611621,0.0611621,0.0611621,0.0611621,0.0611621,0.0611621,0.0611621,0.0611621,0.0611621,0.0611621,0.0815494,0.0815494,0.0815494,0.0815494,0.0815494,0.0815494,0.0815494,0.0815494,0.0815494,0.0815494,0.0815494,0.0815494,0.0815494,0.0815494,0.0815494,0.0815494,0.0815494,0.0815494,0.101937,0.122324,0.122324,0.122324,0.122324,0.122324,0.122324,0.122324,0.122324,0.122324,0.122324,0.122324,0.122324,0.122324,0.122324,0.122324,0.122324], type : \'line\', name : "Illumina Universal Adapter"},{x : [1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108], y : [0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0], type : \'line\', name : "Illumina Small RNA 3 prime Adapter"},{x : [1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108], y : [0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0], type : \'line\', name : "Illumina Small RNA 5 prime Adapter"},{x : [1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108], y : [0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0], type : \'line\', name : "Nextera Transposase Sequence"},{x : [1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108], y : [0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0], type : \'line\', name : "SOLID Small RNA Adapter"} ], { margin: { t: 0 }, showlegend: true, xaxis : {title : \'Base position\'}, yaxis : {title : \'% sequences with adapter before position\'} } );}if (document.getElementById(\'kmerlineplot\') !== null) { Plotly.newPlot(\'kmerlineplot\', [ ], { margin: { t: 0 }, showlegend: true, xaxis : {title : \'Base position\'}, yaxis : {title : \'log2(obs/ exp max)\'} } );}</script></html>\n\\ No newline at end of file\n'

diff -r 000000000000 -r e462044ece67 test-data/fastqc_report_subsample.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fastqc_report_subsample.txt Tue Jun 04 14:14:49 2024 +0000

b'@@ -0,0 +1,1702 @@\n+##Falco\t1.2.2\n+>>Basic Statistics\tpass\n+#Measure\tValue\n+Filename\t1000trimmed_fastq\n+File type\tConventional base calls\n+Encoding\tSanger / Illumina 1.9\n+Total Sequences\t4905\n+Sequences flagged as poor quality\t0\n+Sequence length\t1-108\n+%GC\t41\n+>>END_MODULE\n+>>Per base sequence quality\tpass\n+#Base\tMean\tMedian\tLower Quartile\tUpper Quartile\t10th Percentile\t90th Percentile\n+1\t29.4827\t31\t28\t33\t24\t34\n+2\t28.7857\t30\t27\t32\t23\t33\n+3\t28.5673\t30\t26\t32\t22\t34\n+4\t28.7113\t30\t27\t32\t22\t33\n+5\t28.9727\t30\t27\t32\t22\t33\n+6\t28.9958\t30\t27\t32\t23\t33\n+7\t29.0064\t30\t27\t32\t23\t33\n+8\t28.9111\t30\t26\t32\t22\t34\n+9\t28.4449\t30\t26\t32\t22\t33\n+10-11\t28.4839\t30\t26\t32\t22.5\t33\n+12-13\t28.6404\t30\t26.5\t32\t22.5\t33.5\n+14-15\t28.3061\t30\t26\t32\t22\t33.5\n+16-17\t28.475\t30\t26\t32\t21.5\t33.5\n+18-19\t28.6173\t30\t26.5\t32\t22\t33.5\n+20-21\t28.2003\t29\t25.5\t32\t21.5\t33\n+22-23\t28.2737\t29.5\t26\t32\t22\t33\n+24-25\t27.9832\t29\t25\t32\t21\t33\n+26-27\t28.0618\t29\t25.5\t32\t22\t33\n+28-29\t27.7414\t28.5\t25.5\t31.5\t21.5\t33\n+30-31\t27.7052\t29\t24.5\t31.5\t21.5\t33\n+32-33\t27.6112\t29\t25\t31\t21\t33\n+34-35\t27.4184\t28\t24\t31\t21\t33\n+36-37\t27.1797\t28\t24.5\t31\t20.5\t33\n+38-39\t27.0806\t28\t24\t31\t21\t32\n+40-41\t27.1123\t28\t24.5\t31\t20.5\t32.5\n+42-43\t26.7373\t27.5\t24\t30.5\t21\t32.5\n+44-45\t26.64\t27\t24\t30\t20.5\t32\n+46-47\t26.5893\t27\t23.5\t30.5\t20.5\t32\n+48-49\t26.033\t26.5\t22.5\t30\t20\t32\n+50-51\t26.26\t26.5\t23\t30\t20.5\t32\n+52-53\t25.3328\t26\t22\t29\t18.5\t31.5\n+54-55\t28.2884\t29.5\t25.5\t31.5\t21.5\t33\n+56-57\t30.3321\t31.5\t28.5\t33\t25\t34\n+58-59\t29.8107\t31\t27.5\t33\t24\t34\n+60-61\t30.3107\t31\t29\t33\t26\t34\n+62-63\t30.475\t31.5\t29\t33\t25.5\t34\n+64-65\t29.8684\t30.5\t28\t33\t23.5\t34\n+66-67\t30.2842\t31.5\t28.5\t33\t25.5\t34\n+68-69\t29.8453\t31\t28\t33\t24\t34\n+70-71\t30.2878\t31.5\t28.5\t33\t25.5\t34\n+72-73\t30.2662\t31.5\t28\t33\t25\t34\n+74-75\t29.2986\t30.5\t27.5\t32.5\t23.5\t34\n+76-77\t29.4748\t30\t27.5\t32\t24.5\t34\n+78-79\t29.7374\t31\t28\t33\t24\t34\n+80-81\t29.3453\t30.5\t27.5\t33\t23.5\t34\n+82-83\t29.4137\t30\t27\t32.5\t23.5\t34\n+84-85\t29.4424\t30.5\t27\t32.5\t24.5\t34\n+86-87\t29.1691\t30\t28\t32.5\t23.5\t33\n+88-89\t28.6295\t29.5\t26.5\t32\t22\t33\n+90-91\t28.4568\t29\t26\t32\t22\t33.5\n+92-93\t28.3669\t29\t26\t31.5\t22.5\t33\n+94-95\t27.9604\t29\t25.5\t31.5\t22\t33\n+96-97\t27.8345\t28.5\t25\t31\t21.5\t33\n+98-99\t27.2099\t28\t25\t31\t21.5\t33\n+100-101\t27.1654\t27.5\t24\t31\t20.5\t32.5\n+102-103\t26.9007\t27.5\t23.5\t30.5\t21\t32.5\n+104-105\t26.5735\t26.5\t23.5\t30\t20.5\t32\n+106-107\t25.5966\t26.5\t22.5\t29\t19.5\t31.5\n+108\t27.2314\t27\t24\t30\t22\t32\n+>>END_MODULE\n+>>Per tile sequence quality\tfail\n+#Tile\tBase\tMean\n+0\t1\t-29.4857\n+0\t2\t-28.7721\n+0\t3\t-28.5832\n+0\t4\t-28.7282\n+0\t5\t-28.9662\n+0\t6\t-28.9765\n+0\t7\t-29.0324\n+0\t8\t-28.9563\n+0\t9\t-28.4479\n+0\t10\t-28.2935\n+0\t11\t-28.6264\n+0\t12\t-28.711\n+0\t13\t-28.5163\n+0\t14\t-28.3915\n+0\t15\t-28.2392\n+0\t16\t-28.5304\n+0\t17\t-28.3975\n+0\t18\t-28.5859\n+0\t19\t-28.6272\n+0\t20\t-28.1273\n+0\t21\t-28.2058\n+0\t22\t-28.1046\n+0\t23\t-28.3908\n+0\t24\t-28.0801\n+0\t25\t-28.0111\n+0\t26\t-27.9571\n+0\t27\t-28.1062\n+0\t28\t-27.7915\n+0\t29\t-27.6043\n+0\t30\t-27.7709\n+0\t31\t-27.5781\n+0\t32\t-27.8211\n+0\t33\t-27.6197\n+0\t34\t-27.447\n+0\t35\t-27.3368\n+0\t36\t-27.2226\n+0\t37\t-27.2582\n+0\t38\t-27.2825\n+0\t39\t-26.7901\n+0\t40\t-26.9377\n+0\t41\t-27.17\n+0\t42\t-27.1488\n+0\t43\t-26.1931\n+0\t44\t-26.6119\n+0\t45\t-26.5613\n+0\t46\t-26.7864\n+0\t47\t-26.3367\n+0\t48\t-26.2903\n+0\t49\t-25.7095\n+0\t50\t-26.3457\n+0\t51\t-26.0927\n+0\t52\t-25.7055\n+0\t53\t-24.9716\n+0\t54\t-26\n+0\t55\t-30.4161\n+0\t56\t-30.3869\n+0\t57\t-30.1825\n+0\t58\t-29.6569\n+0\t59\t-30.0876\n+0\t60\t-30.146\n+0\t61\t-30.4891\n+0\t62\t-30.9197\n+0\t63\t-30.0511\n+0\t64\t-29.5255\n+0\t65\t-30.0956\n+0\t66\t-30.4559\n+0\t67\t-30.0588\n+0\t68\t-30.1176\n+0\t69\t-29.9853\n+0\t70\t-30.4191\n+0\t71\t-30.1029\n+0\t72\t-30.2206\n+0\t73\t-30.2132\n+0\t74\t-29.2721\n+0\t75\t-29.25\n+0\t76\t-29.7206\n+0\t77\t-29.8015\n+0\t78\t-29.7794\n+0\t79\t-29.6838\n+0\t80\t-29.5956\n+0\t81\t-29.4412\n+0\t82\t-29.3824\n+0\t83\t-29.375\n+0\t84\t-29.6176\n+0\t85\t-29.1544\n+0\t86\t-29.2059\n+0\t87\t-29.0074\n+0\t88\t-28.8162\n+0\t89\t-28.3603\n+0\t90\t-28.0809\n+0\t91\t-28.8309\n+0\t92\t-28.5882\n+0\t93\t-28.1618\n+0\t94\t-27.8897\n+0\t95\t-28.0074\n+0\t96\t-28.1471\n+0\t97\t-27.6471\n+0\t98\t-27.5662\n+0\t99\t-27.4485\n+0\t100\t-27.4044\n+0\t101\t-26.9265\n+0\t102\t-27.2132\n+0\t103\t-26.5882\n+0\t104\t-26.8603\n+0\t105\t-26.2868\n+0\t106\t-26.0588\n+0\t107\t-25.1343\n+0\t108\t-27.2314\n+1\t1\t0.904969'..b'5\n+82\t6\n+83\t5\n+84\t4\n+85\t4.5\n+86\t4.5\n+87\t4\n+88\t3.5\n+89\t3\n+90\t3\n+91\t3\n+92\t3\n+93\t3\n+94\t3.5\n+95\t4.5\n+96\t5\n+97\t4\n+98\t3\n+99\t3\n+100\t3\n+>>END_MODULE\n+>>Per base N content\tpass\n+#Base\tN-Count\n+1\t0\n+2\t0\n+3\t0\n+4\t0\n+5\t0\n+6\t0\n+7\t0\n+8\t0\n+9\t0\n+10-11\t0\n+12-13\t0\n+14-15\t0\n+16-17\t0\n+18-19\t0\n+20-21\t0\n+22-23\t0\n+24-25\t0\n+26-27\t0\n+28-29\t0\n+30-31\t0\n+32-33\t0\n+34-35\t0\n+36-37\t0\n+38-39\t0\n+40-41\t0\n+42-43\t0\n+44-45\t0\n+46-47\t0\n+48-49\t0\n+50-51\t0\n+52-53\t0\n+54-55\t0\n+56-57\t0\n+58-59\t0\n+60-61\t0\n+62-63\t0\n+64-65\t0\n+66-67\t0\n+68-69\t0\n+70-71\t0\n+72-73\t0\n+74-75\t0\n+76-77\t0\n+78-79\t0\n+80-81\t0\n+82-83\t0\n+84-85\t0\n+86-87\t0\n+88-89\t0\n+90-91\t0\n+92-93\t0\n+94-95\t0\n+96-97\t0\n+98-99\t0\n+100-101\t0\n+102-103\t0\n+104-105\t0\n+106-107\t0\n+108\t0\n+>>END_MODULE\n+>>Sequence Length Distribution\twarn\n+#Length\tCount\n+1\t1.0\n+3\t5.0\n+4\t9.0\n+5\t5.0\n+6\t5.0\n+7\t5.0\n+8\t7.0\n+9\t8.0\n+10\t4.0\n+11\t3.0\n+12\t6.0\n+13\t6.0\n+14\t6.0\n+15\t7.0\n+16\t6.0\n+17\t9.0\n+18\t7.0\n+19\t4.0\n+20\t6.0\n+21\t6.0\n+22\t2.0\n+23\t9.0\n+24\t3.0\n+25\t9.0\n+26\t11.0\n+27\t8.0\n+28\t5.0\n+29\t3.0\n+30\t3.0\n+31\t7.0\n+32\t8.0\n+33\t3.0\n+34\t11.0\n+35\t8.0\n+36\t8.0\n+37\t6.0\n+38\t7.0\n+39\t5.0\n+40\t10.0\n+41\t5.0\n+42\t9.0\n+43\t14.0\n+44\t7.0\n+45\t6.0\n+46\t7.0\n+47\t13.0\n+48\t7.0\n+49\t17.0\n+50\t11.0\n+51\t5.0\n+52\t5.0\n+53\t2.0\n+54\t2.0\n+64\t1.0\n+98\t3.0\n+106\t2.0\n+107\t13.0\n+108\t121.0\n+>>END_MODULE\n+>>Sequence Duplication Levels\tpass\n+#Total Deduplicated Percentage\t99.5927\n+#Duplication Level\tPercentage of deduplicated\tPercentage of total\n+1\t99.7955\t99.389\n+2\t0\t0\n+3\t0.204499\t0.610998\n+4\t0\t0\n+5\t0\t0\n+6\t0\t0\n+7\t0\t0\n+8\t0\t0\n+9\t0\t0\n+>10\t0\t0\n+>50\t0\t0\n+>100\t0\t0\n+>500\t0\t0\n+>1k\t0\t0\n+>5k\t0\t0\n+>10k+\t0\t0\n+>>END_MODULE\n+>>Overrepresented sequences\tpass\n+>>END_MODULE\n+>>Adapter Content\tpass\n+#Position\tIllumina Universal Adapter\tIllumina Small RNA 3 prime Adapter\tIllumina Small RNA 5 prime Adapter\tNextera Transposase Sequence\tSOLID Small RNA Adapter\n+1\t0\t0\t0\t0\t0\n+2\t0\t0\t0\t0\t0\n+3\t0\t0\t0\t0\t0\n+4\t0\t0\t0\t0\t0\n+5\t0\t0\t0\t0\t0\n+6\t0\t0\t0\t0\t0\n+7\t0\t0\t0\t0\t0\n+8\t0\t0\t0\t0\t0\n+9\t0\t0\t0\t0\t0\n+10\t0\t0\t0\t0\t0\n+11\t0\t0\t0\t0\t0\n+12\t0\t0\t0\t0\t0\n+13\t0\t0\t0\t0\t0\n+14\t0\t0\t0\t0\t0\n+15\t0\t0\t0\t0\t0\n+16\t0\t0\t0\t0\t0\n+17\t0\t0\t0\t0\t0\n+18\t0\t0\t0\t0\t0\n+19\t0\t0\t0\t0\t0\n+20\t0.0203874\t0\t0\t0\t0\n+21\t0.0203874\t0\t0\t0\t0\n+22\t0.0203874\t0\t0\t0\t0\n+23\t0.0203874\t0\t0\t0\t0\n+24\t0.0203874\t0\t0\t0\t0\n+25\t0.0203874\t0\t0\t0\t0\n+26\t0.0203874\t0\t0\t0\t0\n+27\t0.0203874\t0\t0\t0\t0\n+28\t0.0203874\t0\t0\t0\t0\n+29\t0.0203874\t0\t0\t0\t0\n+30\t0.0203874\t0\t0\t0\t0\n+31\t0.0203874\t0\t0\t0\t0\n+32\t0.0203874\t0\t0\t0\t0\n+33\t0.0203874\t0\t0\t0\t0\n+34\t0.0203874\t0\t0\t0\t0\n+35\t0.0203874\t0\t0\t0\t0\n+36\t0.0203874\t0\t0\t0\t0\n+37\t0.0203874\t0\t0\t0\t0\n+38\t0.0407747\t0\t0\t0\t0\n+39\t0.0611621\t0\t0\t0\t0\n+40\t0.0611621\t0\t0\t0\t0\n+41\t0.0611621\t0\t0\t0\t0\n+42\t0.0611621\t0\t0\t0\t0\n+43\t0.0611621\t0\t0\t0\t0\n+44\t0.0611621\t0\t0\t0\t0\n+45\t0.0611621\t0\t0\t0\t0\n+46\t0.0611621\t0\t0\t0\t0\n+47\t0.0611621\t0\t0\t0\t0\n+48\t0.0611621\t0\t0\t0\t0\n+49\t0.0611621\t0\t0\t0\t0\n+50\t0.0611621\t0\t0\t0\t0\n+51\t0.0611621\t0\t0\t0\t0\n+52\t0.0611621\t0\t0\t0\t0\n+53\t0.0611621\t0\t0\t0\t0\n+54\t0.0611621\t0\t0\t0\t0\n+55\t0.0611621\t0\t0\t0\t0\n+56\t0.0611621\t0\t0\t0\t0\n+57\t0.0611621\t0\t0\t0\t0\n+58\t0.0611621\t0\t0\t0\t0\n+59\t0.0611621\t0\t0\t0\t0\n+60\t0.0611621\t0\t0\t0\t0\n+61\t0.0611621\t0\t0\t0\t0\n+62\t0.0611621\t0\t0\t0\t0\n+63\t0.0611621\t0\t0\t0\t0\n+64\t0.0611621\t0\t0\t0\t0\n+65\t0.0611621\t0\t0\t0\t0\n+66\t0.0611621\t0\t0\t0\t0\n+67\t0.0611621\t0\t0\t0\t0\n+68\t0.0611621\t0\t0\t0\t0\n+69\t0.0611621\t0\t0\t0\t0\n+70\t0.0611621\t0\t0\t0\t0\n+71\t0.0611621\t0\t0\t0\t0\n+72\t0.0611621\t0\t0\t0\t0\n+73\t0.0611621\t0\t0\t0\t0\n+74\t0.0815494\t0\t0\t0\t0\n+75\t0.0815494\t0\t0\t0\t0\n+76\t0.0815494\t0\t0\t0\t0\n+77\t0.0815494\t0\t0\t0\t0\n+78\t0.0815494\t0\t0\t0\t0\n+79\t0.0815494\t0\t0\t0\t0\n+80\t0.0815494\t0\t0\t0\t0\n+81\t0.0815494\t0\t0\t0\t0\n+82\t0.0815494\t0\t0\t0\t0\n+83\t0.0815494\t0\t0\t0\t0\n+84\t0.0815494\t0\t0\t0\t0\n+85\t0.0815494\t0\t0\t0\t0\n+86\t0.0815494\t0\t0\t0\t0\n+87\t0.0815494\t0\t0\t0\t0\n+88\t0.0815494\t0\t0\t0\t0\n+89\t0.0815494\t0\t0\t0\t0\n+90\t0.0815494\t0\t0\t0\t0\n+91\t0.0815494\t0\t0\t0\t0\n+92\t0.101937\t0\t0\t0\t0\n+93\t0.122324\t0\t0\t0\t0\n+94\t0.122324\t0\t0\t0\t0\n+95\t0.122324\t0\t0\t0\t0\n+96\t0.122324\t0\t0\t0\t0\n+97\t0.122324\t0\t0\t0\t0\n+98\t0.122324\t0\t0\t0\t0\n+99\t0.122324\t0\t0\t0\t0\n+100\t0.122324\t0\t0\t0\t0\n+101\t0.122324\t0\t0\t0\t0\n+102\t0.122324\t0\t0\t0\t0\n+103\t0.122324\t0\t0\t0\t0\n+104\t0.122324\t0\t0\t0\t0\n+105\t0.122324\t0\t0\t0\t0\n+106\t0.122324\t0\t0\t0\t0\n+107\t0.122324\t0\t0\t0\t0\n+108\t0.122324\t0\t0\t0\t0\n+>>END_MODULE\n'

diff -r 000000000000 -r e462044ece67 test-data/fastqc_report_subsample_summary.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fastqc_report_subsample_summary.txt Tue Jun 04 14:14:49 2024 +0000

@@ -0,0 +1,11 @@
+PASS Basic Statistics 1000trimmed_fastq
+PASS Per base sequence quality 1000trimmed_fastq
+FAIL Per tile sequence quality 1000trimmed_fastq
+PASS Per sequence quality scores 1000trimmed_fastq
+FAIL Per base sequence content 1000trimmed_fastq
+WARN Per sequence GC content 1000trimmed_fastq
+PASS Per base N content 1000trimmed_fastq
+WARN Sequence Length Distribution 1000trimmed_fastq
+PASS Sequence Duplication Levels 1000trimmed_fastq
+PASS Overrepresented sequences 1000trimmed_fastq
+PASS Adapter Content 1000trimmed_fastq

diff -r 000000000000 -r e462044ece67 test-data/hisat_output_1.bam

Binary file test-data/hisat_output_1.bam has changed

diff -r 000000000000 -r e462044ece67 test-data/limits.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/limits.txt Tue Jun 04 14:14:49 2024 +0000

@@ -0,0 +1,81 @@
+# For each of the modules you can choose to not run that
+# module at all by setting the value below to 1 for the
+# modules you want to remove.
+duplication ignore 0
+kmer ignore 1
+n_content ignore 0
+overrepresented ignore 0
+quality_base ignore 0
+sequence ignore 0
+gc_sequence ignore 0
+quality_sequence ignore 0
+tile ignore 0
+sequence_length ignore 0
+adapter ignore 0
+
+# For the duplication module the value is the percentage
+# remaining after deduplication.  Measured levels below
+# these limits trigger the warning / error.
+duplication warn 70
+duplication error 50
+
+# For the kmer module the filter is on the -log10 binomial
+# pvalue for the most significant Kmer, so 5 would be
+# 10^-5 = p<0.00001
+kmer warn 2
+kmer error 5
+
+# For the N module the filter is on the percentage of Ns
+# at any position in the library
+n_content warn 5
+n_content error 20
+
+# For the overrepresented seqs the warn value sets the
+# threshold for the overrepresented sequences to be reported
+# at all as the proportion of the library which must be seen
+# as a single sequence
+overrepresented warn 0.1
+overrepresented error 1
+
+# The per base quality filter uses two values, one for the value
+# of the lower quartile, and the other for the value of the
+# median quality.  Failing either of these will trigger the alert
+quality_base_lower warn 10
+quality_base_lower error 5
+quality_base_median warn 25
+quality_base_median error 20
+
+# The per base sequence content module tests the maximum deviation
+# between A and T or C and G
+sequence warn 10
+sequence error 20
+
+# The per sequence GC content tests the maximum deviation between
+# the theoretical distribution and the real distribution
+gc_sequence warn 15
+gc_sequence error 30
+
+# The per sequence quality module tests the phred score which is
+# most frequently observed
+quality_sequence warn 27
+quality_sequence error 20
+
+# The per tile module tests the maximum phred score loss between
+# and individual tile and the average for that base across all tiles
+tile warn 5
+tile error 10
+
+# The sequence length module tests are binary, so the values here
+# simply turn them on or off.  The actual tests warn if you have
+# sequences of different length, and error if you have sequences
+# of zero length.
+
+sequence_length warn 1
+sequence_length error 1
+
+# The adapter module's warnings and errors are based on the
+# percentage of reads in the library which have been observed
+# to contain an adapter associated Kmer at any point
+
+adapter warn 5
+adapter error 10

diff -r 000000000000 -r e462044ece67 test-data/summary.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/summary.txt Tue Jun 04 14:14:49 2024 +0000