From a4a18b7d1a0b255fc727ffc24cac35d6d25d0c6e Mon Sep 17 00:00:00 2001 From: Peter Briggs Date: Wed, 3 Jan 2024 12:07:09 +0000 Subject: [PATCH 01/12] trimmomatic: import tool XML, test-data and README into IUC repo. --- tools/trimmomatic/README.rst | 156 ++++++ .../test-data/Illumina_SG_R1.fastq | 40 ++ .../test-data/Illumina_SG_R1.fastq.gz | Bin 0 -> 2205 bytes .../test-data/Illumina_SG_R1.fastqillumina | 40 ++ .../test-data/Illumina_SG_R1.fastqsolexa | 40 ++ .../test-data/Illumina_SG_R2.fastq | 40 ++ .../test-data/Illumina_SG_R2.fastq.gz | Bin 0 -> 2057 bytes .../test-data/Illumina_SG_R2.fastqillumina | 40 ++ .../test-data/Illumina_SG_R2.fastqsolexa | 40 ++ .../test-data/trimmomatic_avgqual.fastq | 16 + .../test-data/trimmomatic_maxinfo.fastq | 40 ++ .../trimmomatic_pe_r1_paired_out1.fastq | 32 ++ .../trimmomatic_pe_r1_paired_out1.fastq.gz | Bin 0 -> 893 bytes ...rimmomatic_pe_r1_paired_out1.fastqillumina | 32 ++ .../trimmomatic_pe_r1_paired_out1.fastqsolexa | 32 ++ .../trimmomatic_pe_r1_paired_out1_clip.fastq | 32 ++ .../trimmomatic_pe_r1_unpaired_out1.fastq | 0 .../trimmomatic_pe_r1_unpaired_out1.fastq.gz | Bin 0 -> 20 bytes ...mmomatic_pe_r1_unpaired_out1.fastqillumina | 0 ...rimmomatic_pe_r1_unpaired_out1.fastqsolexa | 0 .../trimmomatic_pe_r2_paired_out1.fastq | 32 ++ .../trimmomatic_pe_r2_paired_out1.fastq.gz | Bin 0 -> 1020 bytes ...rimmomatic_pe_r2_paired_out1.fastqillumina | 32 ++ .../trimmomatic_pe_r2_paired_out1.fastqsolexa | 32 ++ .../trimmomatic_pe_r2_unpaired_out1.fastq | 8 + .../trimmomatic_pe_r2_unpaired_out1.fastq.gz | Bin 0 -> 343 bytes ...mmomatic_pe_r2_unpaired_out1.fastqillumina | 8 + ...rimmomatic_pe_r2_unpaired_out1.fastqsolexa | 8 + ...trimmomatic_pe_r2_unpaired_out1_clip.fastq | 8 + .../test-data/trimmomatic_se_out1.err | 5 + .../test-data/trimmomatic_se_out1.fastq | 32 ++ .../test-data/trimmomatic_se_out1.fastq.gz | Bin 0 -> 893 bytes .../test-data/trimmomatic_se_out1.log | 10 + .../test-data/trimmomatic_se_out2.err | 4 + .../test-data/trimmomatic_se_out2.fastq | 40 ++ tools/trimmomatic/trimmomatic.xml | 529 ++++++++++++++++++ tools/trimmomatic/trimmomatic_macros.xml | 10 + 37 files changed, 1338 insertions(+) create mode 100644 tools/trimmomatic/README.rst create mode 100644 tools/trimmomatic/test-data/Illumina_SG_R1.fastq create mode 100644 tools/trimmomatic/test-data/Illumina_SG_R1.fastq.gz create mode 100644 tools/trimmomatic/test-data/Illumina_SG_R1.fastqillumina create mode 100644 tools/trimmomatic/test-data/Illumina_SG_R1.fastqsolexa create mode 100644 tools/trimmomatic/test-data/Illumina_SG_R2.fastq create mode 100644 tools/trimmomatic/test-data/Illumina_SG_R2.fastq.gz create mode 100644 tools/trimmomatic/test-data/Illumina_SG_R2.fastqillumina create mode 100644 tools/trimmomatic/test-data/Illumina_SG_R2.fastqsolexa create mode 100644 tools/trimmomatic/test-data/trimmomatic_avgqual.fastq create mode 100644 tools/trimmomatic/test-data/trimmomatic_maxinfo.fastq create mode 100644 tools/trimmomatic/test-data/trimmomatic_pe_r1_paired_out1.fastq create mode 100644 tools/trimmomatic/test-data/trimmomatic_pe_r1_paired_out1.fastq.gz create mode 100644 tools/trimmomatic/test-data/trimmomatic_pe_r1_paired_out1.fastqillumina create mode 100644 tools/trimmomatic/test-data/trimmomatic_pe_r1_paired_out1.fastqsolexa create mode 100644 tools/trimmomatic/test-data/trimmomatic_pe_r1_paired_out1_clip.fastq create mode 100644 tools/trimmomatic/test-data/trimmomatic_pe_r1_unpaired_out1.fastq create mode 100644 tools/trimmomatic/test-data/trimmomatic_pe_r1_unpaired_out1.fastq.gz create mode 100644 tools/trimmomatic/test-data/trimmomatic_pe_r1_unpaired_out1.fastqillumina create mode 100644 tools/trimmomatic/test-data/trimmomatic_pe_r1_unpaired_out1.fastqsolexa create mode 100644 tools/trimmomatic/test-data/trimmomatic_pe_r2_paired_out1.fastq create mode 100644 tools/trimmomatic/test-data/trimmomatic_pe_r2_paired_out1.fastq.gz create mode 100644 tools/trimmomatic/test-data/trimmomatic_pe_r2_paired_out1.fastqillumina create mode 100644 tools/trimmomatic/test-data/trimmomatic_pe_r2_paired_out1.fastqsolexa create mode 100644 tools/trimmomatic/test-data/trimmomatic_pe_r2_unpaired_out1.fastq create mode 100644 tools/trimmomatic/test-data/trimmomatic_pe_r2_unpaired_out1.fastq.gz create mode 100644 tools/trimmomatic/test-data/trimmomatic_pe_r2_unpaired_out1.fastqillumina create mode 100644 tools/trimmomatic/test-data/trimmomatic_pe_r2_unpaired_out1.fastqsolexa create mode 100644 tools/trimmomatic/test-data/trimmomatic_pe_r2_unpaired_out1_clip.fastq create mode 100644 tools/trimmomatic/test-data/trimmomatic_se_out1.err create mode 100644 tools/trimmomatic/test-data/trimmomatic_se_out1.fastq create mode 100644 tools/trimmomatic/test-data/trimmomatic_se_out1.fastq.gz create mode 100644 tools/trimmomatic/test-data/trimmomatic_se_out1.log create mode 100644 tools/trimmomatic/test-data/trimmomatic_se_out2.err create mode 100644 tools/trimmomatic/test-data/trimmomatic_se_out2.fastq create mode 100644 tools/trimmomatic/trimmomatic.xml create mode 100644 tools/trimmomatic/trimmomatic_macros.xml diff --git a/tools/trimmomatic/README.rst b/tools/trimmomatic/README.rst new file mode 100644 index 00000000000..fa40fc97a29 --- /dev/null +++ b/tools/trimmomatic/README.rst @@ -0,0 +1,156 @@ +Trimmomatic: flexible read trimming tool for Illumina NGS data +============================================================== + +Galaxy tool wrapper for the Trimmomatic program, which provides various functions for +manipluating Illumina FASTQ files (both single and paired-end). + +Trimmomatic has been developed within Bjorn Usadel's group at RWTH Aachen university +http://www.usadellab.org/cms/index.php?page=trimmomatic + +The reference for Trimmomatic is: + +- Bolger, A.M., Lohse, M., & Usadel, B. (2014). Trimmomatic: A flexible trimmer + for Illumina Sequence Data. Bioinformatics, btu170. + +Automated installation +====================== + +Installation via the Galaxy Tool Shed will take care of installing the tool wrapper +and the trimmomatic program and data, and setting the appropriate environment +variables. + +Controlling the available memory +================================ + +The default amount of memory avilable to trimmomatic is set to 8GB. +To change the default amount of memory you can set the environment variable +``_JAVA_OPTIONS`` to ``-XmxG``. The recommended way to +set this is in the job_conf.xml file. To change the available memory to 6GB, a +line like the below should be added: + +``-Xmx6G`` + +This will set the environment variable ``_JAVA_OPTIONS`` to ``-Xmx6G``. + +Manual Installation +=================== + +There are two files to install: + +- ``trimmomatic.xml`` (the Galaxy tool definition) +- ``trimmomatic.sh`` (the shell script wrapper) + +The suggested location is in a ``tools/trimmomatic/`` folder. You will then +need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool +by adding the line: + + + +You will also need to install trimmomatic 0.38: + +- http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.38.zip + +The tool wrapper uses the following environment variables in order to find the +appropriate files: + +- ``TRIMMOMATIC_DIR`` should point to the directory holding the + ``trimmomatic-0.36.jar`` file +- ``TRIMMOMATIC_ADAPTERS_DIR`` should point to the directory holding the adapter + sequence files (used by the ``ILLUMINACLIP`` option). + +If you want to run the functional tests, copy the sample test files under +sample test files under Galaxy's ``test-data/`` directory. Then: + + ./run_tests.sh -id trimmomatic + +You will need to have set the environment variables above. + +History +======= + +========== ====================================================================== +Version Changes +---------- ---------------------------------------------------------------------- +0.39 - Update to Trimmomatic 0.39. +0.38.1 - Bug fix: add dependency on ``coreutils`` so that ``readlink -e`` is + supported across both Linux and MacOS platforms. +0.38.0 - Update to Trimmomatic 0.38. +0.36.6 - Added trimlog and log outputs; add support for ``fastqillumina`` + and ``fastqsolexa`` input types +0.36.5 - Remove tool_dependencies.xml and always use conda to resolve tool + dependencies +0.36.4 - Add option to provide custom adapter sequences for ILLUMINACLIP + - Add options ``minAdapterLength`` and ``keepBothReads`` for ILLUMINACLIP + in palindrome mode +0.36.3 - Fix naming of output collections. Instead of all outputs being called + "Trimmomatic on collection NN" these will now be called "Trimmomatic + on collection NN: paired" or "Trimmomatic on collection NN: unpaired". +0.36.2 - Support fastqsanger.gz datatype. If fastqsanger.gz is used as input + the output will also be fastqsanger.gz. + - Use $_JAVA_OPTIONS to customize memory requirements. +0.36.1 - Reimplement to work with bioconda Trimmomatic 0.36 (toolshed version + is still supported for now). +0.36.0 - Update to Trimmomatic 0.36. +0.32.4 - Add support for ``AVGQUAL`` and ``MAXINFO`` operations. +0.32.3 - Add support for FASTQ R1/R2 pairs using dataset collections (input + can be dataset collection, in which case tool also outputs dataset + collections) and improve order and naming of output files. +0.32.2 - Use ``GALAXY_SLOTS`` to set the appropriate number of threads to use + at runtime (default is 6). +0.32.1 - Remove ``trimmomatic_adapters.loc.sample`` and hard-code adapter files + into the XML wrapper. +0.32.0 - Add tool_dependencies.xml to install Trimmomatic 0.32 automatically and + set the environment. + - Update tool versioning to use Trimmomatic version number (i.e. ``0.32``) + with tool iteration appended (i.e. ``.1``). +0.0.4 - Specify '-threads 6' in section. +0.0.3 - Added MINLEN, LEADING, TRAILING, CROP and HEADCROP options of trimmomatic. +0.0.2 - Updated ILLUMINACLIP option to use standard adapter sequences (requires + the trimmomatic_adapters.loc file; sample version is supplied) plus + cosmetic updates to wording and help text for some options. +0.0.1 - Initial version +========== ====================================================================== + + +Credits +======= + +This wrapper has been developed and is maintained by Peter Briggs (@pjbriggs). +Peter van Heusden (@pvanheus) and Marius van den Beek (@mvdbeek) contributed +support for gz compressed FastQ files. Charles Girardot (@cgirardot) and +Jelle Scholtalbers (@scholtalbers) contributed additional options to ILLUMINACLIP. +Matthias Bernt (@bernt-matthias) added log and trimlog output. +Nicola Soranzo (@nsoranzo) suggested using coreutils to enable cross-platform +support across Linux and MacOS. +Cristóbal Gallardo (@gallardoalba) updated Trimmomatic up to version 0.39. + +Developers +========== + +This tool is developed on the following GitHub repository: +https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/trimmomatic + +For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I use +the ``package_trimmomatic.sh`` script. + + +Licence (MIT) +============= + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in +all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN +THE SOFTWARE. diff --git a/tools/trimmomatic/test-data/Illumina_SG_R1.fastq b/tools/trimmomatic/test-data/Illumina_SG_R1.fastq new file mode 100644 index 00000000000..be0fe01cf06 --- /dev/null +++ b/tools/trimmomatic/test-data/Illumina_SG_R1.fastq @@ -0,0 +1,40 @@ +@MISEQ:1:000000000-A2Y1L:1:1101:19264:2433 1:N:0:NAAGGCGATAGATCGC +AGATAGCCGAAGATAAAGAGNTCATAACCGTAAAGGCCAGAGACGAGAACCACTCGCAGGCAAGGTTTGCAAGCCTCGCCAAGAATATTATAGACCCGCTTGCCAACGACTGGCATTACATCACCGTAAAGAAGGTAGGCAAGAATCACTGGATCAGCATAACAGATGAGGGTAGAGACGCCGTATCGTTTCTGGGCTAGGTTATCTGGGCCGCCTTCTTGCGTCGGCGCACAGTCACAAAGGAAATGCC ++ +?????BBB@BBBB?BBFFFF#66EAFHHHCEFEDFGHHHHF@DFHACEEF@FDFHHHHEEEHHHF?FGEHFHDEFGHHCEHEFHHHHFFFCFDFFFFBEEEEEEEEEEEB?EEEEEEEEEEEBBEE?CE?:ACCC*??CAAEECE:?ECA:?A*?EEEE?EEEE?0AAC/?8)00**0:8'8;48*?8/8?AEEEE8:A*8*0:**0**:?C?480?EE?A############################# +@MISEQ:1:000000000-A2Y1L:1:1101:18667:2435 1:N:0:NAAGGCGATAGATCGC +ATATATTCATCCGCCATTATNAGAGTCCGATTACTTTAGAACAGTGCCGCGAATCCTTCGTCAACTGTAATCCAAGCGACATTGGTTCGATTAGCACGCATGAGGCACGAGATCTACGCGTATCTCTGGTAGATACACCAGGAGGGATGAGAGTTGAGCGAGTTAGCTGTGGCCAGAGAGATGGGTCTAATCGTAGTCTACAACTGGGAGTCACATGCCACTACCGACTAATCTGGTCGCCGAACGGGAG ++ +?????BBBDDDDADDDE@FF#66CFCFHHBEHHIIIHIIHHFHHGHHHHHHHHHHIHIHIFHHHHHHEGFHIHHIIIHHHHHHHHCFHHHHHHHFFFFFFEEEEFFEFEEBBEEEFFE@E8;EEFFFEF*:AEEEEEFFFEAAEA?A?ACAEF?CEEFED2<.?AAECEAEFEEE8??A8?CAAE1?EEE?AE*888AEEEEFEEFFA8A8?ACEAEEEAE?C:??ED28.)8?< +@MISEQ:1:000000000-A2Y1L:1:1101:17523:2436 1:N:0:NAAGGCGATAGATCGC +CATCACTACCGCTCAGGAATNTGACGGCAGTCTTAGCGGCGCTCTAGTGCGGGAGGCCGTATCTTGGAATAAGGTGTCGTCAAATGCAAGGCAGGTAACCCTACACGCCGAGGTTACCACTATACTCCCGTTTCTATATTCCTGTCTCTTATACACATCTCCGAGCCCACGAGACTAAGGCGAATATCGGTTGCCGTCTTCTGCTTGAAAAAAAAAAACAAACAAGAGAAGACGACGTACTGCACCACCA ++ +?<,/<@@@@@@>@CCCE#66>ACEEEEGGGGGGGFFFEFDFFFFF=CDEFFFFEDEFFFFFC=AEBF-AA@CE;ECD5<5<==C==DEEE)83CD==@+4@DEE*D?)8):A8?EC?8***0*00:8?*)0*1:?CACC:AA?;)?EEFAEECE88*)1A*10*1:*1?:AC::A)*::*8ACEEE?########### +@MISEQ:1:000000000-A2Y1L:1:1101:15290:2442 1:N:0:NAAGGCGATAGATCGC +AAAATAATCCTAAAAAATAACCTCTATGCCGCCGAACGCTCCGCCTCTATCTTCGTAAAAACTATCTTCTCCTCCTCACCTCCATAATCAAGCATCAAGCGATCGCCCTCCGCCAACTCACCCCGCAAAATCTTATCCGCTAGCGGATTCTCAATCTCCGTCTGAATGACCCGCCTCAGCGGCCGCGCCCCATAAACCGAATCAAATCCACGCCTGTCTCTTATACACATCTCCGAGCCCACGAGACTAA ++ +?????BBBDDDDDDDDGGGGGGIIIHHFFHHHHHHHHHHEHHEHHHHHIIHHHHHFEHIIIHHIHHIHIHIIIIIHHHHHHHHHHHHHHHHDHHHHHHHHGEDFGGGGGGG;CEGEGCEGGGGG8>GGGGEGGEECEGGGGD8EDGGAEGEEGGCE:CGG8CEEGG???CEEDG.89D9DFG;FHHHHGHHFFFFHHHHECDCEFF>EFEEEE@CDFEFHHGHHHHEHDGHHFHDFHFHHHHFFHHH@FDD??DFFFFDBBEEBEEEEEEEEEEEEEEEEE,;?CEC;CEEEECB?CEEEEEEEECEEE?C?CE*0?***/:::?:*/?:A::**/:*:ACE?0:::A::***00::*/?C888??EEE############# +@MISEQ:1:000000000-A2Y1L:1:1101:15892:2446 1:N:0:NAAGGCGATAGATCGC +CTTCCCCACGGCCCAGACACAAGAGACGACCTCCATAAATCTTTTAGAGGGTGACCGCATCTCCGACGCAAACCAGGACGCCGATACCCTCGTGGTGGTGTTCGACCGTACGGATGGCGCAGACACCGACGGCACTAGTGCCACGGTATCAGGTACCACCATAACGTATGATTCGGGCACGCTCAAGGGCCAGCGTGACGGAATCGATAGAATACACTACACGGTGACTGATGGGGCCAGCCAAACCTGT ++ +?????BBBDBDDDDDDFFFFFFHIHIHHHHHHIHIFGGHFHHHHIIFHIHH?EEGHHHHHH-EGEHHCEHHHHH@FDFFEFF5@EEEFFEFE;AECCE;AEEEEEA?8?AEDDEEDFFDE2>>EEFF<<<2>D?DEEE*:C?AA<>8AEFCEE:?C?EEE?CEFEE0?:E?ACEECD8>EE>)8>E:CEEEEEED.)?AE??A?:A?*??:C0?CCE?AAA:88.88?::C:C?*8)4A?A######### +@MISEQ:1:000000000-A2Y1L:1:1101:17903:2450 1:N:0:TAAGGCGATAGATCGC +GTGCAGGGGGTGTGGTCAATCCACACTGTTGCTGAGGTGATTGGGTCTCCGGGGTCAACTCCATGAGGTAGCAGACCAGTGCCAGAGATAGTGACCACAGTGTTGGCCCTGTCTCTTATACACATCTCCGAGCCCACGAGACTAAGGCGAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAGACTTTTAAAAAACCGATCTACACCTTGACAGGCTATTAAAGGAAACTGGCCTGGTATCACAG ++ +=5===<>+5<5<+5=@CC;8CEEEEE;-8ACFDE.7C87CF-A>E>E=FFE**>>5AEDAEED-5-5AADC=D+=DDE<++3+CCD9DCD+=@3:DEEEEDD<@D*9DE99;@;@EE@;@@EEE7@@8@:@@@;9EE'449?<>>@@@@@9@@CCEE@EE+++6C8-++CECE+>DCC>@@EFFFFEEEDEE55+ACEF;-C+>EE++CBA--5A++CDC+4<<+=DE=CDEE@+@9D:D+4;@############################################################################################################################################### diff --git a/tools/trimmomatic/test-data/Illumina_SG_R1.fastq.gz b/tools/trimmomatic/test-data/Illumina_SG_R1.fastq.gz new file mode 100644 index 0000000000000000000000000000000000000000..161d1e99832c321f66c111c38b0157551eea95ae GIT binary patch literal 2205 zcmV;O2x9jiiwFpvxq(;!14(Rbb!};GVP8{6Us5qHW?^%5aR9Yg+j8T&5q#gTNYy@U zMA=?ZmTZWm2tq>;a#fD2PK7V|{~t+r59Dt0hT#Y$QeE-UsaDQ~D!j`#Aq8ndWW1zK5~ zj5pLK<4D%Caa~tsOts7<3|?0)VVJ|%0rePeD+i$sH+!33v()L58qkfu#kawYVQF>J zHZ%~cVQF^73ff1iC3av7mM!R2xLHiXiS>7IXmxzwPh{zQ(ZG?V4uSg)gB$geHcsAtttmE;RuSXl$A;T0Ddu2FCRH zd+F2kBjkjqr)MJP_#tvu*_o!4;c0+ZT8L#C8TJukP$jF#x-<=KK`XDSAb1KPvC@h@ zmL{Y5i*O<2!J@2_>1Ao{BoRk6YAFsAEXE&G2ESP44Z-Yzai(=SUUOgo=3i02cgUHM60ST6IR?XDuNPqB<>dtzuyDN!LY`juSv;T1f|5GcWVM9=LZWqX zUmPvWPC4|`g#1kJE;juglyXc(CZaTNL z55c3yemnQX2|0#`zEm(JCn3?2s7r=*tBD)js01ZBNzCE!B|uDTYJ|YWL1q;QFa3XS^KSB=el0@o`975z(rcbM5MT|o$i*{(DRK1g>%xe;u_g9 zRW7n3qov}eT?Lcm=3U*()hbOZk`ZkPOPbiMGLI@v#3;B5H|~{++>cX_c2LBJ8o`@* z%qmZ6A%{1Sb37xBUx!I)oUok?&Kc>LaxR`k4i1pB%~?F+KZ~7HzAX1CO@KzW`8XVh z^V!a4VrUZ{Z9bo;?O{T(8RmA_v{Mh3XimGnX-^?coBig?p+D!}fQ|nbIUyWdAm_0E z5ILd_CMOv_Xc{)jb;&6d@zUzxk$X@#Kldbq>b%4uZY?JQjVEDn66c!RB7&8iTQx4x zLi>B?;`{O01X;&us`DqUNWWHr>6PW?*ph%m>~kg06kBV{=!NS!N{4+_uFM`(7h#qYUNQuSP5CjJf=5D~t2XP~d` zI@dY5i4Ahg65}|>P1tnsKiOg+7d1P`oY-u3O$$APzl1>%GzLed!GPqZO-;-8rlo|! zw40{unxLZ)e~okYr`>mv!_((NWp$EY>tjx?YFrnXs~}ao#BqmEiyUnZEU|)gZgRv) ztVm(hNh*IyJZnLDCwWWJi?~iCu{r?7Q7*PCExO*~6cY93+AF1sW7CP4IWGFoZz*Opr z8ep!CoJCfryd(kS?Kd%Q&P$w6440hFk~qeZ^9?liKS7gjQig3CK9z$J!Py+67-*(s zejj~#y6a(m>*X-*675Ypkv0tFW=A>nwd=arHDAFkU=PbLOs4 zLA~OsD#fe#);5ISQr0SDi4oR`i;Bl+;-uoimff6RTI>IEqH$GTTs$cn^X|S`Z0bGd zRMx4$A(7mIDDZ{b{pCeL6l_qVtb4G7Lh-8uf^uj%PPb61Pt@6cszR4BG$k~;&3QkL z>@^I-9!`m(sOb!<7?BTLl~F32q9?u?$h+8OhD-oyz_@XPdshK9KR|S6C~5#Gf{;4f zMU&!AT?h{VO-BNXP1qdLyGZ>fVyn}RvDI-`k+c3c=O_j$l~&wMm>#|O!$pV-VCS0R zn#0e$Hz!9z4ct9&b~)p+TAXCR6gmlc={up50;bh@ta>bu&RteZQt7=?eTC!dX|2dK zMdfEo6n7c=I{U0uONb)Y+Y3D>rQ(s!T7_(lgw%h1yON7k ze@*x%o&3FD4d$HR*7ZhrPCTxZTvlscOU{jNv){h8)*O2%5qIOU% literal 0 HcmV?d00001 diff --git a/tools/trimmomatic/test-data/Illumina_SG_R1.fastqillumina b/tools/trimmomatic/test-data/Illumina_SG_R1.fastqillumina new file mode 100644 index 00000000000..940a6e3232f --- /dev/null +++ b/tools/trimmomatic/test-data/Illumina_SG_R1.fastqillumina @@ -0,0 +1,40 @@ +@MISEQ:1:000000000-A2Y1L:1:1101:19264:2433 1:N:0:NAAGGCGATAGATCGC +AGATAGCCGAAGATAAAGAGNTCATAACCGTAAAGGCCAGAGACGAGAACCACTCGCAGGCAAGGTTTGCAAGCCTCGCCAAGAATATTATAGACCCGCTTGCCAACGACTGGCATTACATCACCGTAAAGAAGGTAGGCAAGAATCACTGGATCAGCATAACAGATGAGGGTAGAGACGCCGTATCGTTTCTGGGCTAGGTTATCTGGGCCGCCTTCTTGCGTCGGCGCACAGTCACAAAGGAAATGCC ++ +^^^^^aaa_aaaa^aaeeeeBUUd`egggbdedcefgggge_ceg`bdde_eceggggdddggge^efdgegcdefggbdgdeggggeeebeceeeeaddddddddddda^dddddddddddaadd^bd^Y`bbbI^^b``ddbdY^db`Y^`I^dddd^dddd^O``bN^WHOOIIOYWFWZSWI^WNW^`ddddWY`IWIOYIIOIIY^b^SWO^dd^`BBBBBBBBBBBBBBBBBBBBBBBBBBBBB +@MISEQ:1:000000000-A2Y1L:1:1101:18667:2435 1:N:0:NAAGGCGATAGATCGC +ATATATTCATCCGCCATTATNAGAGTCCGATTACTTTAGAACAGTGCCGCGAATCCTTCGTCAACTGTAATCCAAGCGACATTGGTTCGATTAGCACGCATGAGGCACGAGATCTACGCGTATCTCTGGTAGATACACCAGGAGGGATGAGAGTTGAGCGAGTTAGCTGTGGCCAGAGAGATGGGTCTAATCGTAGTCTACAACTGGGAGTCACATGCCACTACCGACTAATCTGGTCGCCGAACGGGAG ++ +^^^^^aaacccc`cccd_eeBUUbebeggadgghhhghhggeggfgggggggggghghgheggggggdfeghgghhhggggggggbegggggggeeeeeeddddeededdaadddeed_dWZddeeedeIY`dddddeeed``d`^`^`b`de^bddedcQ[M^``dbd`dedddW^^`W^b``dP^ddd^`dIWWW`ddddeddee`W`W^`bd`ddd`d^bY^^dcQ[dYbIY^IYW^dc[]WMHW^[ +@MISEQ:1:000000000-A2Y1L:1:1101:17523:2436 1:N:0:NAAGGCGATAGATCGC +CATCACTACCGCTCAGGAATNTGACGGCAGTCTTAGCGGCGCTCTAGTGCGGGAGGCCGTATCTTGGAATAAGGTGTCGTCAAATGCAAGGCAGGTAACCCTACACGCCGAGGTTACCACTATACTCCCGTTTCTATATTCCTGTCTCTTATACACATCTCCGAGCCCACGAGACTAAGGCGAATATCGGTTGCCGTCTTCTGCTTGAAAAAAAAAAACAAACAAGAGAAGACGACGTACTGCACCACCA ++ +^[K[^aaaaaaaaaaaeeeeBU`bdbbdbVWbd\bfgdgVbgbgefg`cfgggbbbggd[cegeeeeceeeeeecececcdddddddddb`ddddZ^adddaddabdZbZSWZH^``bbddd^``^Y^dWW`ddYbd^``ddddY^IIIOYI^^``dddddd`^MWZdBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB +@MISEQ:1:000000000-A2Y1L:1:1101:15489:2437 1:N:0:NAAGGCGATAGATCGC +GAGCAGTCGGGCTCAGCGCTNTGCAAATTCTAGTTAGAAACTCACAGTTCTGACAAGCCTTAGGTCAGTGTGATTGGCGGTTAGTCAACTCGGAGAAAGCGTCTTTTCCCGACTTGAATGGTTTGTCCCGACAGTTCGTTGACTGGGGTTTCGTCAGCCTTGAGCGGGGTTCCATCCATCTTTATCGCGCCTTGGGAAAGTAGTCGGCGGGCTTCGGGGTTGGGTGAGGGCAATCCTTGTTCGGTCAAAA ++ +T\\\\]N[______]_bbbdBUU]`bddddfffffffeeedeceeeee\bcdeeeedcdeeeeeb\`daeL``_bdZdbcT[T[\\b\\cdddHWRbc\\_JS_cddI[cP[HP_ZWWWIXOZIPXWW_HQHFSZ\ddBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB +@MISEQ:1:000000000-A2Y1L:1:1101:18851:2442 1:N:0:NAAGGCGATAGATCGC +GGTATCCCCCGGCAGTGAGGATGGAGCCATGGTCTGCATCATACTCACCGTAGGTGAGAATATCCACGTCCTTCGACTCCTGGGTGCCGTCTATGGTGCCCTCTGTTACCAGGCAGTGACGGAGGACATGGTGAGGTTTCAGTACCTCTGGCCCGGCCTGGGTCACAGGGTCAGACTGGGTGACCTTCATGAAGCGTCTGGTGACGTAGCTGTGATAGTCCAGCTTGGCAACCTCTGCTGGTTGCAGAGG ++ +^^K[^aaaccccccc[eee_ebZeeeadegggbccggfgggcfgggeggd`^dd`ddgcdegggggedbegggegcgddggbegVbdegcdggbeggegge\eeececeeeeddddccdeddd[aabdabdK\\`dPYY``ddbddI^I``dee^^]c^HWHY`W^db^WIIIOIOOYW^IHOIPY^b`bbY``^ZH^dde`ddbdWWIHP`IPOIPYIP^Y`bYY`HIYYIW`bddd^BBBBBBBBBBB +@MISEQ:1:000000000-A2Y1L:1:1101:15290:2442 1:N:0:NAAGGCGATAGATCGC +AAAATAATCCTAAAAAATAACCTCTATGCCGCCGAACGCTCCGCCTCTATCTTCGTAAAAACTATCTTCTCCTCCTCACCTCCATAATCAAGCATCAAGCGATCGCCCTCCGCCAACTCACCCCGCAAAATCTTATCCGCTAGCGGATTCTCAATCTCCGTCTGAATGACCCGCCTCAGCGGCCGCGCCCCATAAACCGAATCAAATCCACGCCTGTCTCTTATACACATCTCCGAGCCCACGAGACTAA ++ +^^^^^aaaccccccccffffffhhhggeeggggggggggdggdggggghhgggggedghhhgghgghghghhhhhggggggggggggggggcggggggggfdcefffffffZbdfdfbdfffffW]ffffdffddbdffffcWdcff`dfddffbdYbffWbddff^^^bdd[cfWbbI^^]cfMW[`ffffbddfIbQ[fbbdbdIY^bd^bdXbYbYbY^bIPIIOPOYI^dWQFQ[fbdBBBBBBBB +@MISEQ:1:000000000-A2Y1L:1:1101:18106:2444 1:N:0:NAAGGCGATAGATCGC +GTAGTATTCTCATATCACAAGTCCCCAAACTGCATAAGGTGTGGAGTGGAGTGTCTCCCACTGCATTTTGTTGGTTTGGGTTGCATTTTTTGTGGCACAAAATTATCTTTAAACACTCTAAGCTCATATTTGCACATGCAACATGAATTGGAGCATTTCTTTTGCAGTCAACTGCCAGTACATTAACTCCACTCTGTAATAGTAAATCCTGTCTCTTATCCACATCTCCGAGCCCACGAGAATAAGGCGA ++ +TTKKT^Xaaaaa[[aaeeeeeeeggeadegegggecebeO`X_]XcXcefZeggggfggeeeeggggdbcbdee]dedddd_bcedeggfggggdgcfggegcegeggggeeggg_ecc^^ceeeecaaddadddddddddddddddddKZ^bdbZbddddba^bddddddddbddd^b^bdIO^IIINYYY^YIN^Y`YYIINYIY`bd^OYYY`YYIIIOOYYIN^bWWW^^dddBBBBBBBBBBBBB +@MISEQ:1:000000000-A2Y1L:1:1101:15892:2446 1:N:0:NAAGGCGATAGATCGC +CTTCCCCACGGCCCAGACACAAGAGACGACCTCCATAAATCTTTTAGAGGGTGACCGCATCTCCGACGCAAACCAGGACGCCGATACCCTCGTGGTGGTGTTCGACCGTACGGATGGCGCAGACACCGACGGCACTAGTGCCACGGTATCAGGTACCACCATAACGTATGATTCGGGCACGCTCAAGGGCCAGCGTGACGGAATCGATAGAATACACTACACGGTGACTGATGGGGCCAGCCAAACCTGT ++ +^^^^^aaacacccccceeeeeeghghgggggghgheffgegggghheghgg^ddfggggggLdfdggbdggggg_eceedeeT_dddeededZ`dbbdZ`ddddd`^W^`dccddceecdQ]]ddee[[[Q]c^cdddIYb^``[]W`debddY^b^ddd^bdeddO^Yd^`bddbcW]dd]HW]dYbddddddcMH^`d^^`^Y`^I^^YbO^bbd^```YWWMWW^YYbYb^IWHS`^`BBBBBBBBB +@MISEQ:1:000000000-A2Y1L:1:1101:17903:2450 1:N:0:TAAGGCGATAGATCGC +GTGCAGGGGGTGTGGTCAATCCACACTGTTGCTGAGGTGATTGGGTCTCCGGGGTCAACTCCATGAGGTAGCAGACCAGTGCCAGAGATAGTGACCACAGTGTTGGCCCTGTCTCTTATACACATCTCCGAGCCCACGAGACTAAGGCGAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAGACTTTTAAAAAACCGATCTACACCTTGACAGGCTATTAAAGGAAACTGGCCTGGTATCACAG ++ +\T\\\[]JT[T[JT\_bbZWbdddddZLW`becdMVbWVbeL`]d]d\eedII]]T`dc`ddcLTLT``cb\cJ\ccd[JJRJbbcXcbcJ\_RYcddddcc[_cIXcdXXZ_Z_dd_Z__dddV__W_Y___ZXddFSSX^[[dZ\d[[ZWGUZ^BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB +@MISEQ:1:000000000-A2Y1L:1:1101:15113:2451 1:N:0:TAAGGCGATAGATCGC +TCTCAGATGAGCATGCAGCAGCCCAGACTCGCCCCACGCAGTTTGCCAACCACAAGGCCATCCTCGGCCTGTCAGCCTGCCCCTCCCTCCCTCACCAGCTAGCCTCCTATGCCGCGGTAGGGGGCTCAAAGAGATTCAGACACAGCCACGTAATCATGTTACTTGCCCATTCCCCCCTCCCTCCTCCTCCTCTCCCCCCCTCTCTTCCCCTCTCCCCTCCCCTCCTCCCCTCCTGTCCCTTATACACATC ++ +\KK[\]]]_____X__bbdd_ddJJJUbWLJJbdbdJ]cbb]__deeeedddcddTTJ`bdeZLbJ]ddJJba`LLT`JJbcbJS[[J\cd\bcdd_J_XcYcJSZ_BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB diff --git a/tools/trimmomatic/test-data/Illumina_SG_R1.fastqsolexa b/tools/trimmomatic/test-data/Illumina_SG_R1.fastqsolexa new file mode 100644 index 00000000000..5cc060500a6 --- /dev/null +++ b/tools/trimmomatic/test-data/Illumina_SG_R1.fastqsolexa @@ -0,0 +1,40 @@ +@MISEQ:1:000000000-A2Y1L:1:1101:19264:2433 1:N:0:NAAGGCGATAGATCGC +AGATAGCCGAAGATAAAGAGNTCATAACCGTAAAGGCCAGAGACGAGAACCACTCGCAGGCAAGGTTTGCAAGCCTCGCCAAGAATATTATAGACCCGCTTGCCAACGACTGGCATTACATCACCGTAAAGAAGGTAGGCAAGAATCACTGGATCAGCATAACAGATGAGGGTAGAGACGCCGTATCGTTTCTGGGCTAGGTTATCTGGGCCGCCTTCTTGCGTCGGCGCACAGTCACAAAGGAAATGCC ++ +^^^^^aaa_aaaa^aaeeee>UUd`egggbdedcefgggge_ceg`bdde_eceggggdddggge^efdgegcdefggbdgdeggggeeebeceeeeaddddddddddda^dddddddddddaadd^bd^Y`bbbH^^b``ddbdY^db`Y^`H^dddd^dddd^O``bN^WGOOHHOYWEWZSWH^WNW^`ddddWY`HWHOYHHOHHY^b^SWO^dd^`>>>>>>>>>>>>>>>>>>>>>>>>>>>>> +@MISEQ:1:000000000-A2Y1L:1:1101:18667:2435 1:N:0:NAAGGCGATAGATCGC +ATATATTCATCCGCCATTATNAGAGTCCGATTACTTTAGAACAGTGCCGCGAATCCTTCGTCAACTGTAATCCAAGCGACATTGGTTCGATTAGCACGCATGAGGCACGAGATCTACGCGTATCTCTGGTAGATACACCAGGAGGGATGAGAGTTGAGCGAGTTAGCTGTGGCCAGAGAGATGGGTCTAATCGTAGTCTACAACTGGGAGTCACATGCCACTACCGACTAATCTGGTCGCCGAACGGGAG ++ +^^^^^aaacccc`cccd_ee>UUbebeggadgghhhghhggeggfgggggggggghghgheggggggdfeghgghhhggggggggbegggggggeeeeeeddddeededdaadddeed_dWZddeeedeHY`dddddeeed``d`^`^`b`de^bddedcQ[M^``dbd`dedddW^^`W^b``dP^ddd^`dHWWW`ddddeddee`W`W^`bd`ddd`d^bY^^dcQ[dYbHY^HYW^dc[]WMGW^[ +@MISEQ:1:000000000-A2Y1L:1:1101:17523:2436 1:N:0:NAAGGCGATAGATCGC +CATCACTACCGCTCAGGAATNTGACGGCAGTCTTAGCGGCGCTCTAGTGCGGGAGGCCGTATCTTGGAATAAGGTGTCGTCAAATGCAAGGCAGGTAACCCTACACGCCGAGGTTACCACTATACTCCCGTTTCTATATTCCTGTCTCTTATACACATCTCCGAGCCCACGAGACTAAGGCGAATATCGGTTGCCGTCTTCTGCTTGAAAAAAAAAAACAAACAAGAGAAGACGACGTACTGCACCACCA ++ +^[K[^aaaaaaaaaaaeeee>U`bdbbdbVWbd\bfgdgVbgbgefg`cfgggbbbggd[cegeeeeceeeeeecececcdddddddddb`ddddZ^adddaddabdZbZSWZG^``bbddd^``^Y^dWW`ddYbd^``ddddY^HHHOYH^^``dddddd`^MWZd>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> +@MISEQ:1:000000000-A2Y1L:1:1101:15489:2437 1:N:0:NAAGGCGATAGATCGC +GAGCAGTCGGGCTCAGCGCTNTGCAAATTCTAGTTAGAAACTCACAGTTCTGACAAGCCTTAGGTCAGTGTGATTGGCGGTTAGTCAACTCGGAGAAAGCGTCTTTTCCCGACTTGAATGGTTTGTCCCGACAGTTCGTTGACTGGGGTTTCGTCAGCCTTGAGCGGGGTTCCATCCATCTTTATCGCGCCTTGGGAAAGTAGTCGGCGGGCTTCGGGGTTGGGTGAGGGCAATCCTTGTTCGGTCAAAA ++ +T\\\\]N[______]_bbbd>UU]`bddddfffffffeeedeceeeee\bcdeeeedcdeeeeeb\`daeL``_bdZdbcT[T[\\b\\cdddGWRbc\\_JS_cddH[cP[GP_ZWWWHXOZHPXWW_GQGESZ\dd>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> +@MISEQ:1:000000000-A2Y1L:1:1101:18851:2442 1:N:0:NAAGGCGATAGATCGC +GGTATCCCCCGGCAGTGAGGATGGAGCCATGGTCTGCATCATACTCACCGTAGGTGAGAATATCCACGTCCTTCGACTCCTGGGTGCCGTCTATGGTGCCCTCTGTTACCAGGCAGTGACGGAGGACATGGTGAGGTTTCAGTACCTCTGGCCCGGCCTGGGTCACAGGGTCAGACTGGGTGACCTTCATGAAGCGTCTGGTGACGTAGCTGTGATAGTCCAGCTTGGCAACCTCTGCTGGTTGCAGAGG ++ +^^K[^aaaccccccc[eee_ebZeeeadegggbccggfgggcfgggeggd`^dd`ddgcdegggggedbegggegcgddggbegVbdegcdggbeggegge\eeececeeeeddddccdeddd[aabdabdK\\`dPYY``ddbddH^H``dee^^]c^GWGY`W^db^WHHHOHOOYW^HGOHPY^b`bbY``^ZG^dde`ddbdWWHGP`HPOHPYHP^Y`bYY`GHYYHW`bddd^>>>>>>>>>>> +@MISEQ:1:000000000-A2Y1L:1:1101:15290:2442 1:N:0:NAAGGCGATAGATCGC +AAAATAATCCTAAAAAATAACCTCTATGCCGCCGAACGCTCCGCCTCTATCTTCGTAAAAACTATCTTCTCCTCCTCACCTCCATAATCAAGCATCAAGCGATCGCCCTCCGCCAACTCACCCCGCAAAATCTTATCCGCTAGCGGATTCTCAATCTCCGTCTGAATGACCCGCCTCAGCGGCCGCGCCCCATAAACCGAATCAAATCCACGCCTGTCTCTTATACACATCTCCGAGCCCACGAGACTAA ++ +^^^^^aaaccccccccffffffhhhggeeggggggggggdggdggggghhgggggedghhhgghgghghghhhhhggggggggggggggggcggggggggfdcefffffffZbdfdfbdfffffW]ffffdffddbdffffcWdcff`dfddffbdYbffWbddff^^^bdd[cfWbbH^^]cfMW[`ffffbddfHbQ[fbbdbdHY^bd^bdXbYbYbY^bHPHHOPOYH^dWQEQ[fbd>>>>>>>> +@MISEQ:1:000000000-A2Y1L:1:1101:18106:2444 1:N:0:NAAGGCGATAGATCGC +GTAGTATTCTCATATCACAAGTCCCCAAACTGCATAAGGTGTGGAGTGGAGTGTCTCCCACTGCATTTTGTTGGTTTGGGTTGCATTTTTTGTGGCACAAAATTATCTTTAAACACTCTAAGCTCATATTTGCACATGCAACATGAATTGGAGCATTTCTTTTGCAGTCAACTGCCAGTACATTAACTCCACTCTGTAATAGTAAATCCTGTCTCTTATCCACATCTCCGAGCCCACGAGAATAAGGCGA ++ +TTKKT^Xaaaaa[[aaeeeeeeeggeadegegggecebeO`X_]XcXcefZeggggfggeeeeggggdbcbdee]dedddd_bcedeggfggggdgcfggegcegeggggeeggg_ecc^^ceeeecaaddadddddddddddddddddKZ^bdbZbddddba^bddddddddbddd^b^bdHO^HHHNYYY^YHN^Y`YYHHNYHY`bd^OYYY`YYHHHOOYYHN^bWWW^^ddd>>>>>>>>>>>>> +@MISEQ:1:000000000-A2Y1L:1:1101:15892:2446 1:N:0:NAAGGCGATAGATCGC +CTTCCCCACGGCCCAGACACAAGAGACGACCTCCATAAATCTTTTAGAGGGTGACCGCATCTCCGACGCAAACCAGGACGCCGATACCCTCGTGGTGGTGTTCGACCGTACGGATGGCGCAGACACCGACGGCACTAGTGCCACGGTATCAGGTACCACCATAACGTATGATTCGGGCACGCTCAAGGGCCAGCGTGACGGAATCGATAGAATACACTACACGGTGACTGATGGGGCCAGCCAAACCTGT ++ +^^^^^aaacacccccceeeeeeghghgggggghgheffgegggghheghgg^ddfggggggLdfdggbdggggg_eceedeeT_dddeededZ`dbbdZ`ddddd`^W^`dccddceecdQ]]ddee[[[Q]c^cdddHYb^``[]W`debddY^b^ddd^bdeddO^Yd^`bddbcW]dd]GW]dYbddddddcMG^`d^^`^Y`^H^^YbO^bbd^```YWWMWW^YYbYb^HWGS`^`>>>>>>>>> +@MISEQ:1:000000000-A2Y1L:1:1101:17903:2450 1:N:0:TAAGGCGATAGATCGC +GTGCAGGGGGTGTGGTCAATCCACACTGTTGCTGAGGTGATTGGGTCTCCGGGGTCAACTCCATGAGGTAGCAGACCAGTGCCAGAGATAGTGACCACAGTGTTGGCCCTGTCTCTTATACACATCTCCGAGCCCACGAGACTAAGGCGAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAGACTTTTAAAAAACCGATCTACACCTTGACAGGCTATTAAAGGAAACTGGCCTGGTATCACAG ++ +\T\\\[]JT[T[JT\_bbZWbdddddZLW`becdMVbWVbeL`]d]d\eedHH]]T`dc`ddcLTLT``cb\cJ\ccd[JJRJbbcXcbcJ\_RYcddddcc[_cHXcdXXZ_Z_dd_Z__dddV__W_Y___ZXddESSX^[[dZ\d[[ZWFUZ^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> +@MISEQ:1:000000000-A2Y1L:1:1101:15113:2451 1:N:0:TAAGGCGATAGATCGC +TCTCAGATGAGCATGCAGCAGCCCAGACTCGCCCCACGCAGTTTGCCAACCACAAGGCCATCCTCGGCCTGTCAGCCTGCCCCTCCCTCCCTCACCAGCTAGCCTCCTATGCCGCGGTAGGGGGCTCAAAGAGATTCAGACACAGCCACGTAATCATGTTACTTGCCCATTCCCCCCTCCCTCCTCCTCCTCTCCCCCCCTCTCTTCCCCTCTCCCCTCCCCTCCTCCCCTCCTGTCCCTTATACACATC ++ +\KK[\]]]_____X__bbdd_ddJJJUbWLJJbdbdJ]cbb]__deeeedddcddTTJ`bdeZLbJ]ddJJba`LLT`JJbcbJS[[J\cd\bcdd_J_XcYcJSZ_>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> diff --git a/tools/trimmomatic/test-data/Illumina_SG_R2.fastq b/tools/trimmomatic/test-data/Illumina_SG_R2.fastq new file mode 100644 index 00000000000..086f796457a --- /dev/null +++ b/tools/trimmomatic/test-data/Illumina_SG_R2.fastq @@ -0,0 +1,40 @@ +@MISEQ:1:000000000-A2Y1L:1:1101:19264:2433 2:N:0:NAAGGCGATAGATCGC +GCCGATATGCAGATGCCGTTGATTGCTGCCAGCATAGCAGCCATTGCCGGCATATCCTTTGTGACTGTGCGCCGACGCAAGAAGGCGGCCCAGATAACCTAGCCCAGAAACGATACGGCGTCTCTACCCTCATCTGTTATGCTGATCCAGTGATTCTTGCCTACCTTCTTTACGGTGATGTAATGCCAGTCGTTGGCAAGCGGGTCTATAATATTCTTGGCGAGGCTTGCAAACCTGGCCTGCGAGTGGT ++ +??A??ABBDDDDDDDDFFEEEFHIIIIHHIIHIFHIIHHHFHHIIIIIHHHFHHIIIIIIFFFHHIIHGDEHHAAEHHHHFHHHHD=EBBEEEEEFFFFEEEECEFFEEFFF8*??AA?;>DEEEFFFF*?8AECFEFFFFFFEAEEECFFFCEEEFFFFFFEEFEACEEC?CAACEFEEEFE?0?EACAAAEEAACEEA*.48.'0*1::A?CAA?CC::4''4'00'8:?A8?E############## +@MISEQ:1:000000000-A2Y1L:1:1101:18667:2435 2:N:0:NAAGGCGATAGATCGC +GATGACATCAGCACAGGTTCCGCTTCCGCTGTCGCAACGACGTGGCTGCCATCGATTATATTCAATTCTGAGTGCTGCCGTAGGGCTAGATGTAAGACTCACGTTCGGCGACCAGATTAGTCGGTAGTGGCATGTGACTCCCCGTTGTAGACTACGATTAGACCCATCTCTCTGGCCACAGCTAACTCGCTCAACTCTCATCCCTCCTGGGGTATCTACCAGCGATACGCGTAGAACTCGTGCCTCATGC ++ +?????BBBDDDDDDDDGFFGGGHHHHIHHHHHHHIHHHHIHBCEEHFFHHHIIHFHHHIIIIIIIHIFBGFGFHHHHIHE@EEEHHFFHHFF?CFHHHHHGGGGGGGGGGGGGGGGGGGECGGG;EE:CEGGG?#################################################################################################################### +@MISEQ:1:000000000-A2Y1L:1:1101:17523:2436 2:N:0:NAAGGCGATAGATCGC +GAATATAGAAACGGGAGTATAGTGGTAACCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTAGNNCGCCGCTAAGACTGCCGTCAAATTCCTGAGCGGTAGTGATGCTGTCTCTTATACACATCTGACGCTGCCGACGAGCGATCTAGTGTAGATCTCGGGGGGCGCCGGCACATTCAAAAAAAAAAAACAGGAAAATGACATAGGCGTGTGTGA ++ +??AAABBBDDDDDEDDGGCFGGHHIFFHHH################################################################66?=##466@@EEEGCGGC>CE*0*1C:?################################################################# +@MISEQ:1:000000000-A2Y1L:1:1101:15489:2437 2:N:0:NAAGGCGATAGATCGC +GTCCACGTGAAATCCCGAGCGTCCCTCTCCCTCCCGAGAACCCGGTCTATATCCCACGATTTTTGACCGAACAAGGATTGACCTCATCCAACTCCGAAGCCCGCCGCCTACTTTCCCAAGGCGCGATAAAGATTGATGGAACCCCGCCCAAGGCTGACGAAATCCCCGCCAACGAACTGTCGGGCCGACCCATTCAAGTGGGGAAAAAAACCTTTCCCCGGGTTGACAAACCGCCAAACAACCTCACCAA ++ +????9B???AD9?BDDEEDDDDHHHHHFHFHFFHHHHHHHHHEHH>CEGHHFGHHGHH=FHHHHC+CGEBCCCE6BB)).).:AAAEE?A?A################################################################################################################################## +@MISEQ:1:000000000-A2Y1L:1:1101:18851:2442 2:N:0:NAAGGCGATAGATCGC +TCTCCTCAGTACGGGGGAGGAGGTTCGCTCGGCGGACGTGCGGCCCTACGCCAGACTCTACCACATGGTTCAGCAGGAGCTGGAGCACCGCGCTGTGTCCGGGGACTGGGAATACACCATCAGCCCCGGCGAGGAGTGGCAAGAGACGGAGCCTCTGCAACCAGCAGAGGTTGCCAAGCTGGACTATCACAGCTACGTCACCAGACGCTTCATGAAGGTCACCCAGTCTGACCCTGTGAACCAGGCCGGG ++ +A??A?BBBDDDDDDDDGGGGGGHEFHHGEHHHIHEHHHHHDHBEHGFFFEGGDEEDGGGGGEGGEECE?EGCEGEGGGCEEEGGCEEGG4D;;4AGGGGGG8>GGA?EGGGEEGEEGGGCGGEGEGGGGD81,;;;;3B,3B;;*:B;1;''0::0*1:A*:;>DD'4'8.::AA>D22>DA>''0..08?*:A*1?:*0?########################################################################################################################## +@MISEQ:1:000000000-A2Y1L:1:1101:18106:2444 2:N:0:NAAGGCGATAGATCGC +GAGTTACTATTACAGAGTGGAGCTAATGTACTGGCAGTTGACTGCAAAAGAAATGCTCCAATTCATGTTGCATGTGCAAATATGAGCTTAGAGTGTTTAAAGATAATTTTGTGCCACAAAAAATGCAACCCAAACCAACAAAATGCAGTGGGAGACACTCCACTCCACACCTTATGCAGTTTGGGGACTTGTGATATGAGAATACTACCTGTCTCTTATACACATCTGACGCTGCCGACGAGCGAACAAG ++ +?????BBBDDDDDDDDGCFGFGIIIIIHFHIIIIHIHFG=EHHIGIIIIFHIHDGHGHHHIHIH=CGHGGHFHHHFHFGHHFH/ACDFGG?FE?CDFFHHHHHIIHFHHI>CEDGFHHHHHHHHDFHHFHHHFFAFFGGGGGGEDEG>>DACC;?EGG>CEEA>AEACCEE?:C::CC:::C:CEG######### +@MISEQ:1:000000000-A2Y1L:1:1101:15892:2446 2:N:0:NAAGGCGATAGATCGC +GTATTGCTGGCACCATCAGTCACCGTGTAGTGTATTCTATCGATTCCGTCACGCTGGCCCTTGAGCGTGCCCGAATCATACGTTATGGTGGTACCTGATACCGTGGCACTAGTGCCGTCGGTGTCTGCGCCATCCGTACGGTCGAACACCACCACGAGGGTATCGGCGTCCTGGTTTGCGTCGGGGATGCGGTCACCCTCTAAAAGATTTATGGAGGTCGTCTCTTGTGTCTGGGCCGGGGGGAAGATGT ++ +?????BBBDDDDDDDDGGGGGGIIHIIFHHHIHHIFHGHGGHHIHIIDEFFHEF@DFHIIHIIIGHACDCFFHHHIHIIHIHGHHHBGFGEEHHHHFHFFHHDFDCEGGFGGFGGG@DBEEEEGC>CEEGGGGGGE0?CDGGGD>EE2CE8CEGEE<>>>):CEEGDA'428CE:?9CC4828>'4<)0:>'04)1?E*8:1CC??):CCEECC**8)0548?C*:?:*010*:CC############## +@MISEQ:1:000000000-A2Y1L:1:1101:17903:2450 2:N:0:TAAGGCGATAGATCGC +GGCCAACACTGTGGTCACTATCTCTGGCACTGGTCTGCTACCACATGGAGTTGACACCGGAGACCCAATCACCACAGCAACAGTGTGGATTGACCACACCCCCTGCACCTGTCTCTTATACACATCTGACGCTGCCGACGAGCGATCTAGTGTAGATCTCCGTGGGCGCCGCATCATTAAAAAAAAAAAAAAAAAACATAACTCTCAAACGCGAATAGAGCAAGAAACAGACAGCTAAAGTACAAACAAT ++ +55DDD880:?#################################################################################################### +@MISEQ:1:000000000-A2Y1L:1:1101:15113:2451 2:N:0:TAAGGCGATAGATCGC +GAGGGGAGGAGGGGAAGGGAGAGGGGAAGAGAGGAGAGGAGAGGAGGAGGAGAGAAGGGGGAATGAGCAAGTAACATAATTACATAGCTGTGTCTGAATCTCTTTGAGCACCCTACCTCGGCATAGGAGGCTAGCTGGTGAGGGAGGGAGGGGCAGACTGACAGGCCGAGGATGGCCTTGTGGTTGGCAAACTCCGTGGGGCGAGTCTGGGCTGCTGCATGCGCATCTGAGACTGGCTCTTGTACACATC ++ +?????@9@B?B?BBBBEEEFB@@EEHEC?BF-CE@DDEH,5+5C,>@+CE+NqMW&9x(8{@Fb+lWQlec)r%v(q@B4q_f5vWX z*YepP{@49Wd%CXG>U=o$r7wo^afoR%|-N22lb-X)Cl*0M`J3tAbcPu zvCV}T$ZFL#SGZd~R>xoyPb_sUzNc2O;<*p(s<2m^<>~p!Ij^624z;8dV@%6k%cAvi zM|)Y8w6O1&&3j60E;+lay+~MIj8rL0|-Gll(KoqHTCy6%`(lQJe*EwUfq7iqN!Qo}Oc)vLu z4#TxkVv+IVVEZ<5j{R^3a=yHa97G5Fn)r3`(tCyy;hW6Y7+pY-tlk6u*|N435kUUF{v&co#ZP#lh zX-13*$<6&7Znv=2Ri}C0Zui^$$oQfG(tp_Te*L!kVrkg#d*#%Ru6dOlowbcg3DqG zy>E{IgxA1D4zpb`%z|GqUkI&i#3kH}*&{z?MGjQXuc8&pqEctc(E<>06P7tH8L}g1 zz{_Heej<2cr4OhR);afKntE^MhO6$^VL~L`@Hef569#3IpjJRK$}TbvA{&(^$}37d zjoY>&?btZ$AOl4?H{*yO&xtnnSgL(z={E|{wrw!C=~|ug5#$^X=k`yLL-rUW|Kd)B|k2y#SA>msg#0b8iZn$`o2A8el5jpbS2cO;YH> zbnSMNmX~?=GEY-8&QmvSHtjeQjFTY7pNC}EkZ=`Q23KbFjE~bt#tyGmu_2Q{rsBPiC zQUj8?m%j5=h*VCoXyUDxIbJac3FBR@7=-F@DV4=YBlbkH8S}93kV*`$f25FA=A>-e zx29Oy$gc{XJG-@W2^ryP!O*K{J5w?z#<8^g>?NpHa+(2Y!@`}Z>bnN6kRJgsB+JE8 z^3>(vq!9B}F(xvBqpnDsu3pn9ZGd$~q)d8Mu_Tu>SjaUFiI*t(2(;3OX+lEMwseq1 z-F}em!EJgazrVsc!}$Q@yswZ;O~Lacijd|_gO+S5Zq27m+=@*XvPQNySx7!iWQ<3s zu_=LzS%ZCAq>*f-KxIqTvYgwzD)y<2Qfd}2jEg1P@=V@ZV-mJlCDY1crDpz>esYab z44F*){s=iNz{@>ZVx?Dt13IHKw45DMy7o$(#PNZO7}T?YEta%`kQv zx}44?jGAWHwkmKD%s_1&0+{?&&iQg~ky{`i7+ka$u?d8lR1q{xu(^DVxS(9_m9J~fNJ6NKy z&Xh8cb39%M9t92HGus)8kR=|8cV6lNPhQExPIe?L6n4v&wZqc?TEq=|NM zUSx+fR>e6a9LYpv^C4(}3&YUo6~2BH%+*f-SPP-yX););`7D5#?O*e z(khwEVdoSMyB^R>)2nJ8Mc@>6bN_0GfimxQ^E_!Jfqst7G|A}oX2M||4*pymywXWK nYRcsY-|w9p+;HfJ?J(k$PbX~q$xS~PPfz~`xUFeaL>2%5=Pvw{ literal 0 HcmV?d00001 diff --git a/tools/trimmomatic/test-data/Illumina_SG_R2.fastqillumina b/tools/trimmomatic/test-data/Illumina_SG_R2.fastqillumina new file mode 100644 index 00000000000..4e98d004ce9 --- /dev/null +++ b/tools/trimmomatic/test-data/Illumina_SG_R2.fastqillumina @@ -0,0 +1,40 @@ +@MISEQ:1:000000000-A2Y1L:1:1101:19264:2433 2:N:0:NAAGGCGATAGATCGC +GCCGATATGCAGATGCCGTTGATTGCTGCCAGCATAGCAGCCATTGCCGGCATATCCTTTGTGACTGTGCGCCGACGCAAGAAGGCGGCCCAGATAACCTAGCCCAGAAACGATACGGCGTCTCTACCCTCATCTGTTATGCTGATCCAGTGATTCTTGCCTACCTTCTTTACGGTGATGTAATGCCAGTCGTTGGCAAGCGGGTCTATAATATTCTTGGCGAGGCTTGCAAACCTGGCCTGCGAGTGGT ++ +^^`^^`aacccccccceedddeghhhhgghhgheghhgggegghhhhhgggegghhhhhheeegghhgfcdgg``dggggeggggc\daadddddeeeeddddbdeeddeeeWI^^``^Z]cdddeeeeI^W`dbedeeeeeed`dddbeeebdddeeeeeedded`bddb^b``bdeddded^O^d`b```dd``bdd`IMSWMFOIPYY`^b``^bbYYSFFSFOOFWY^`W^dBBBBBBBBBBBBBB +@MISEQ:1:000000000-A2Y1L:1:1101:18667:2435 2:N:0:NAAGGCGATAGATCGC +GATGACATCAGCACAGGTTCCGCTTCCGCTGTCGCAACGACGTGGCTGCCATCGATTATATTCAATTCTGAGTGCTGCCGTAGGGCTAGATGTAAGACTCACGTTCGGCGACCAGATTAGTCGGTAGTGGCATGTGACTCCCCGTTGTAGACTACGATTAGACCCATCTCTCTGGCCACAGCTAACTCGCTCAACTCTCATCCCTCCTGGGGTATCTACCAGCGATACGCGTAGAACTCGTGCCTCATGC ++ +^^^^^aaaccccccccfeefffgggghggggggghgggghgabddgeeggghhgeggghhhhhhhgheafefegggghgd_dddggeeggee^begggggfffffffffffffffffffdbfffZddYbdfff^BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB +@MISEQ:1:000000000-A2Y1L:1:1101:17523:2436 2:N:0:NAAGGCGATAGATCGC +GAATATAGAAACGGGAGTATAGTGGTAACCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTAGNNCGCCGCTAAGACTGCCGTCAAATTCCTGAGCGGTAGTGATGCTGTCTCTTATACACATCTGACGCTGCCGACGAGCGATCTAGTGTAGATCTCGGGGGGCGCCGGCACATTCAAAAAAAAAAAACAGGAAAATGACATAGGCGTGTGTGA ++ +^^```aaacccccdccffbeffggheegggBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBUU^\BBSUU__dddfbffb]bd[dfddfdfbdfdffffWW[^P^b^dfbd^ddb^bb^bbdffbffbfbW^bb`b[``FQQQW]IOIPbY^BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB +@MISEQ:1:000000000-A2Y1L:1:1101:15489:2437 2:N:0:NAAGGCGATAGATCGC +GTCCACGTGAAATCCCGAGCGTCCCTCTCCCTCCCGAGAACCCGGTCTATATCCCACGATTTTTGACCGAACAAGGATTGACCTCATCCAACTCCGAAGCCCGCCGCCTACTTTCCCAAGGCGCGATAAAGATTGATGGAACCCCGCCCAAGGCTGACGAAATCCCCGCCAACGAACTGTCGGGCCGACCCATTCAAGTGGGGAAAAAAACCTTTCCCCGGGTTGACAAACCGCCAAACAACCTCACCAA ++ +^^^^Xa^^^`cX^accddccccgggggegegeegggggggggdgg]bdfggefggfgg\eggggbJbfdabb[be_KSbe_beaeeeece^aSac__cH]bdUaaHHMHMY```dd^`^`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB +@MISEQ:1:000000000-A2Y1L:1:1101:18851:2442 2:N:0:NAAGGCGATAGATCGC +TCTCCTCAGTACGGGGGAGGAGGTTCGCTCGGCGGACGTGCGGCCCTACGCCAGACTCTACCACATGGTTCAGCAGGAGCTGGAGCACCGCGCTGTGTCCGGGGACTGGGAATACACCATCAGCCCCGGCGAGGAGTGGCAAGAGACGGAGCCTCTGCAACCAGCAGAGGTTGCCAAGCTGGACTATCACAGCTACGTCACCAGACGCTTCATGAAGGTCACCCAGTCTGACCCTGTGAACCAGGCCGGG ++ +`^^`^aaaccccccccffffffgdeggfdggghgdgggggcgadgfeeedffcddcfffffdffddbd^dfbdfdfffbdddffbddffScZZS`ffffffW]ff`^dfffddfddfffbffdfdffffcW[``cdbdbdff^bbbYWbbFFWYbY^bbdI^HObbOYI^YbY^bbbW^bbdbXIYYbbbb^bIYYMbdffdbXXbSFHHMOOIYbY^IPOYbbBBBBBBBBBBBBBBBBBBBBBBBBBB +@MISEQ:1:000000000-A2Y1L:1:1101:15290:2442 2:N:0:NAAGGCGATAGATCGC +GCGTGGATTTGATTCGGTTTATGGGGCGCGGCCGCTGAGGCGGGTCATTCAGACGGAGATTGAGAATCCGCTAGCGGATAAGATTTTGCGGGGGGAGTTGGCGGAGGGCGATCGCTTGATGCTTGATTATGGAGGGGAGGGGGAGAAGATAGGTTTTACGAAAATAGAGGCGGAGGGGTCGGCGGCATAGAGGGTAATTTTTTGGGTTTTTTTCTGTGTCTTATACACAACTGAACGTGCCGACGAGCGG ++ +^^^^^_^accccccccedddeeghhgdggggcgggggdggggggW`ceeeceecPcZ]PKZZZZRaKRaZZIYaZPZFFOYYOIPY`IYZ]ccFSFWMYY``]cQQ]c`]FFOMMOW^IY`IP^YIO^BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB +@MISEQ:1:000000000-A2Y1L:1:1101:18106:2444 2:N:0:NAAGGCGATAGATCGC +GAGTTACTATTACAGAGTGGAGCTAATGTACTGGCAGTTGACTGCAAAAGAAATGCTCCAATTCATGTTGCATGTGCAAATATGAGCTTAGAGTGTTTAAAGATAATTTTGTGCCACAAAAAATGCAACCCAAACCAACAAAATGCAGTGGGAGACACTCCACTCCACACCTTATGCAGTTTGGGGACTTGTGATATGAGAATACTACCTGTCTCTTATACACATCTGACGCTGCCGACGAGCGAACAAG ++ +^^^^^aaaccccccccfbefefhhhhhgeghhhhghgef\dgghfhhhheghgcfgfggghghg\bfgffgegggegefggegN`bceff^ed^bceeggggghhgeggh]bdcfeggggggggceggegggee`eeffffffdcdf]]c`bbZ^dff]bdd`]`d`bbdd^YbYYbbYYYbYbd[b[XbY^b^I^bddbbbIYb^b^dY^YbYbYbbbbdY^bPIOIPPMWbHQ^FSW]fBBBBBBBBB +@MISEQ:1:000000000-A2Y1L:1:1101:15892:2446 2:N:0:NAAGGCGATAGATCGC +GTATTGCTGGCACCATCAGTCACCGTGTAGTGTATTCTATCGATTCCGTCACGCTGGCCCTTGAGCGTGCCCGAATCATACGTTATGGTGGTACCTGATACCGTGGCACTAGTGCCGTCGGTGTCTGCGCCATCCGTACGGTCGAACACCACCACGAGGGTATCGGCGTCCTGGTTTGCGTCGGGGATGCGGTCACCCTCTAAAAGATTTATGGAGGTCGTCTCTTGTGTCTGGGCCGGGGGGAAGATGT ++ +^^^^^aaaccccccccffffffhhghheggghgghegfgffgghghhcdeegde_ceghhghhhfg`bcbeeggghghhghgfgggafefddggggegeeggcecbdffeffefff_caddddfb]bddffffffdO^bcfffc]ddQbdWbdfdd[]]]HYbddfc`FSQWbdY^XbbSWQW]FS[HOY]FOSHP^dIWYPbb^^HYbbddbbIIWHOTSW^bIY^YIOPOIYbbBBBBBBBBBBBBBB +@MISEQ:1:000000000-A2Y1L:1:1101:17903:2450 2:N:0:TAAGGCGATAGATCGC +GGCCAACACTGTGGTCACTATCTCTGGCACTGGTCTGCTACCACATGGAGTTGACACCGGAGACCCAATCACCACAGCAACAGTGTGGATTGACCACACCCCCTGCACCTGTCTCTTATACACATCTGACGCTGCCGACGAGCGATCTAGTGTAGATCTCCGTGGGCGCCGCATCATTAAAAAAAAAAAAAAAAAACATAACTCTCAAACGCGAATAGAGCAAGAAACAGACAGCTAAAGTACAAACAAT ++ +TT[^^^^^cccaaccaeeeeeebgghhgghhhhhhhgfgghhhhggfghhgegghhhhgggbcghhhgeeghhhhhbeeghgdbfbfdghg\eggggggggggeZeeeeecceeeeeeedeeeededace`dd`dd_ddcc]cccWWOY^BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB +@MISEQ:1:000000000-A2Y1L:1:1101:15113:2451 2:N:0:TAAGGCGATAGATCGC +GAGGGGAGGAGGGGAAGGGAGAGGGGAAGAGAGGAGAGGAGAGGAGGAGGAGAGAAGGGGGAATGAGCAAGTAACATAATTACATAGCTGTGTCTGAATCTCTTTGAGCACCCTACCTCGGCATAGGAGGCTAGCTGGTGAGGGAGGGAGGGGCAGACTGACAGGCCGAGGATGGCCTTGTGGTTGGCAAACTCCGTGGGGCGAGTCTGGGCTGCTGCATGCGCATCTGAGACTGGCTCTTGTACACATC ++ +^^^^^_X_a^a^aaaadddea__ddgdb^aeLbd_ccdgKTJTbK]_JbdJ[^\dLbedbdggcacK^ceeKScccaeZ\aZZaacZcKaS\adddddbaKKaaZ^b^bddddIZZbY`b^bZ^bbY`ddd^dW`bdYOY`^``W`SM^^W^WQSWHWY`bddd^dHSZ^Z^BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB diff --git a/tools/trimmomatic/test-data/Illumina_SG_R2.fastqsolexa b/tools/trimmomatic/test-data/Illumina_SG_R2.fastqsolexa new file mode 100644 index 00000000000..8cc54dfac6c --- /dev/null +++ b/tools/trimmomatic/test-data/Illumina_SG_R2.fastqsolexa @@ -0,0 +1,40 @@ +@MISEQ:1:000000000-A2Y1L:1:1101:19264:2433 2:N:0:NAAGGCGATAGATCGC +GCCGATATGCAGATGCCGTTGATTGCTGCCAGCATAGCAGCCATTGCCGGCATATCCTTTGTGACTGTGCGCCGACGCAAGAAGGCGGCCCAGATAACCTAGCCCAGAAACGATACGGCGTCTCTACCCTCATCTGTTATGCTGATCCAGTGATTCTTGCCTACCTTCTTTACGGTGATGTAATGCCAGTCGTTGGCAAGCGGGTCTATAATATTCTTGGCGAGGCTTGCAAACCTGGCCTGCGAGTGGT ++ +^^`^^`aacccccccceedddeghhhhgghhgheghhgggegghhhhhgggegghhhhhheeegghhgfcdgg``dggggeggggc\daadddddeeeeddddbdeeddeeeWH^^``^Z]cdddeeeeH^W`dbedeeeeeed`dddbeeebdddeeeeeedded`bddb^b``bdeddded^O^d`b```dd``bdd`HMSWMEOHPYY`^b``^bbYYSEESEOOEWY^`W^d>>>>>>>>>>>>>> +@MISEQ:1:000000000-A2Y1L:1:1101:18667:2435 2:N:0:NAAGGCGATAGATCGC +GATGACATCAGCACAGGTTCCGCTTCCGCTGTCGCAACGACGTGGCTGCCATCGATTATATTCAATTCTGAGTGCTGCCGTAGGGCTAGATGTAAGACTCACGTTCGGCGACCAGATTAGTCGGTAGTGGCATGTGACTCCCCGTTGTAGACTACGATTAGACCCATCTCTCTGGCCACAGCTAACTCGCTCAACTCTCATCCCTCCTGGGGTATCTACCAGCGATACGCGTAGAACTCGTGCCTCATGC ++ +^^^^^aaaccccccccfeefffgggghggggggghgggghgabddgeeggghhgeggghhhhhhhgheafefegggghgd_dddggeeggee^begggggfffffffffffffffffffdbfffZddYbdfff^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> +@MISEQ:1:000000000-A2Y1L:1:1101:17523:2436 2:N:0:NAAGGCGATAGATCGC +GAATATAGAAACGGGAGTATAGTGGTAACCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTAGNNCGCCGCTAAGACTGCCGTCAAATTCCTGAGCGGTAGTGATGCTGTCTCTTATACACATCTGACGCTGCCGACGAGCGATCTAGTGTAGATCTCGGGGGGCGCCGGCACATTCAAAAAAAAAAAACAGGAAAATGACATAGGCGTGTGTGA ++ +^^```aaacccccdccffbeffggheeggg>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>UU^\>>SUU__dddfbffb]bd[dfddfdfbdfdffffWW[^P^b^dfbd^ddb^bb^bbdffbffbfbW^bb`b[``EQQQW]HOHPbY^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> +@MISEQ:1:000000000-A2Y1L:1:1101:15489:2437 2:N:0:NAAGGCGATAGATCGC +GTCCACGTGAAATCCCGAGCGTCCCTCTCCCTCCCGAGAACCCGGTCTATATCCCACGATTTTTGACCGAACAAGGATTGACCTCATCCAACTCCGAAGCCCGCCGCCTACTTTCCCAAGGCGCGATAAAGATTGATGGAACCCCGCCCAAGGCTGACGAAATCCCCGCCAACGAACTGTCGGGCCGACCCATTCAAGTGGGGAAAAAAACCTTTCCCCGGGTTGACAAACCGCCAAACAACCTCACCAA ++ +^^^^Xa^^^`cX^accddccccgggggegegeegggggggggdgg]bdfggefggfgg\eggggbJbfdabb[be_KSbe_beaeeeece^aSac__cG]bdUaaGGMGMY```dd^`^`>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> +@MISEQ:1:000000000-A2Y1L:1:1101:18851:2442 2:N:0:NAAGGCGATAGATCGC +TCTCCTCAGTACGGGGGAGGAGGTTCGCTCGGCGGACGTGCGGCCCTACGCCAGACTCTACCACATGGTTCAGCAGGAGCTGGAGCACCGCGCTGTGTCCGGGGACTGGGAATACACCATCAGCCCCGGCGAGGAGTGGCAAGAGACGGAGCCTCTGCAACCAGCAGAGGTTGCCAAGCTGGACTATCACAGCTACGTCACCAGACGCTTCATGAAGGTCACCCAGTCTGACCCTGTGAACCAGGCCGGG ++ +`^^`^aaaccccccccffffffgdeggfdggghgdgggggcgadgfeeedffcddcfffffdffddbd^dfbdfdfffbdddffbddffScZZS`ffffffW]ff`^dfffddfddfffbffdfdffffcW[``cdbdbdff^bbbYWbbEEWYbY^bbdH^GObbOYH^YbY^bbbW^bbdbXHYYbbbb^bHYYMbdffdbXXbSEGGMOOHYbY^HPOYbb>>>>>>>>>>>>>>>>>>>>>>>>>> +@MISEQ:1:000000000-A2Y1L:1:1101:15290:2442 2:N:0:NAAGGCGATAGATCGC +GCGTGGATTTGATTCGGTTTATGGGGCGCGGCCGCTGAGGCGGGTCATTCAGACGGAGATTGAGAATCCGCTAGCGGATAAGATTTTGCGGGGGGAGTTGGCGGAGGGCGATCGCTTGATGCTTGATTATGGAGGGGAGGGGGAGAAGATAGGTTTTACGAAAATAGAGGCGGAGGGGTCGGCGGCATAGAGGGTAATTTTTTGGGTTTTTTTCTGTGTCTTATACACAACTGAACGTGCCGACGAGCGG ++ +^^^^^_^accccccccedddeeghhgdggggcgggggdggggggW`ceeeceecPcZ]PKZZZZRaKRaZZHYaZPZEEOYYOHPY`HYZ]ccESEWMYY``]cQQ]c`]EEOMMOW^HY`HP^YHO^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> +@MISEQ:1:000000000-A2Y1L:1:1101:18106:2444 2:N:0:NAAGGCGATAGATCGC +GAGTTACTATTACAGAGTGGAGCTAATGTACTGGCAGTTGACTGCAAAAGAAATGCTCCAATTCATGTTGCATGTGCAAATATGAGCTTAGAGTGTTTAAAGATAATTTTGTGCCACAAAAAATGCAACCCAAACCAACAAAATGCAGTGGGAGACACTCCACTCCACACCTTATGCAGTTTGGGGACTTGTGATATGAGAATACTACCTGTCTCTTATACACATCTGACGCTGCCGACGAGCGAACAAG ++ +^^^^^aaaccccccccfbefefhhhhhgeghhhhghgef\dgghfhhhheghgcfgfggghghg\bfgffgegggegefggegN`bceff^ed^bceeggggghhgeggh]bdcfeggggggggceggegggee`eeffffffdcdf]]c`bbZ^dff]bdd`]`d`bbdd^YbYYbbYYYbYbd[b[XbY^b^H^bddbbbHYb^b^dY^YbYbYbbbbdY^bPHOHPPMWbGQ^ESW]f>>>>>>>>> +@MISEQ:1:000000000-A2Y1L:1:1101:15892:2446 2:N:0:NAAGGCGATAGATCGC +GTATTGCTGGCACCATCAGTCACCGTGTAGTGTATTCTATCGATTCCGTCACGCTGGCCCTTGAGCGTGCCCGAATCATACGTTATGGTGGTACCTGATACCGTGGCACTAGTGCCGTCGGTGTCTGCGCCATCCGTACGGTCGAACACCACCACGAGGGTATCGGCGTCCTGGTTTGCGTCGGGGATGCGGTCACCCTCTAAAAGATTTATGGAGGTCGTCTCTTGTGTCTGGGCCGGGGGGAAGATGT ++ +^^^^^aaaccccccccffffffhhghheggghgghegfgffgghghhcdeegde_ceghhghhhfg`bcbeeggghghhghgfgggafefddggggegeeggcecbdffeffefff_caddddfb]bddffffffdO^bcfffc]ddQbdWbdfdd[]]]GYbddfc`ESQWbdY^XbbSWQW]ES[GOY]EOSGP^dHWYPbb^^GYbbddbbHHWGOTSW^bHY^YHOPOHYbb>>>>>>>>>>>>>> +@MISEQ:1:000000000-A2Y1L:1:1101:17903:2450 2:N:0:TAAGGCGATAGATCGC +GGCCAACACTGTGGTCACTATCTCTGGCACTGGTCTGCTACCACATGGAGTTGACACCGGAGACCCAATCACCACAGCAACAGTGTGGATTGACCACACCCCCTGCACCTGTCTCTTATACACATCTGACGCTGCCGACGAGCGATCTAGTGTAGATCTCCGTGGGCGCCGCATCATTAAAAAAAAAAAAAAAAAACATAACTCTCAAACGCGAATAGAGCAAGAAACAGACAGCTAAAGTACAAACAAT ++ +TT[^^^^^cccaaccaeeeeeebgghhgghhhhhhhgfgghhhhggfghhgegghhhhgggbcghhhgeeghhhhhbeeghgdbfbfdghg\eggggggggggeZeeeeecceeeeeeedeeeededace`dd`dd_ddcc]cccWWOY^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> +@MISEQ:1:000000000-A2Y1L:1:1101:15113:2451 2:N:0:TAAGGCGATAGATCGC +GAGGGGAGGAGGGGAAGGGAGAGGGGAAGAGAGGAGAGGAGAGGAGGAGGAGAGAAGGGGGAATGAGCAAGTAACATAATTACATAGCTGTGTCTGAATCTCTTTGAGCACCCTACCTCGGCATAGGAGGCTAGCTGGTGAGGGAGGGAGGGGCAGACTGACAGGCCGAGGATGGCCTTGTGGTTGGCAAACTCCGTGGGGCGAGTCTGGGCTGCTGCATGCGCATCTGAGACTGGCTCTTGTACACATC ++ +^^^^^_X_a^a^aaaadddea__ddgdb^aeLbd_ccdgKTJTbK]_JbdJ[^\dLbedbdggcacK^ceeKScccaeZ\aZZaacZcKaS\adddddbaKKaaZ^b^bddddHZZbY`b^bZ^bbY`ddd^dW`bdYOY`^``W`SM^^W^WQSWGWY`bddd^dGSZ^Z^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> diff --git a/tools/trimmomatic/test-data/trimmomatic_avgqual.fastq b/tools/trimmomatic/test-data/trimmomatic_avgqual.fastq new file mode 100644 index 00000000000..3785c69b1f4 --- /dev/null +++ b/tools/trimmomatic/test-data/trimmomatic_avgqual.fastq @@ -0,0 +1,16 @@ +@MISEQ:1:000000000-A2Y1L:1:1101:18667:2435 1:N:0:NAAGGCGATAGATCGC +ATATATTCATCCGCCATTATNAGAGTCCGATTACTTTAGAACAGTGCCGCGAATCCTTCGTCAACTGTAATCCAAGCGACATTGGTTCGATTAGCACGCATGAGGCACGAGATCTACGCGTATCTCTGGTAGATACACCAGGAGGGATGAGAGTTGAGCGAGTTAGCTGTGGCCAGAGAGATGGGTCTAATCGTAGTCTACAACTGGGAGTCACATGCCACTACCGACTAATCTGGTCGCCGAACGGGAG ++ +?????BBBDDDDADDDE@FF#66CFCFHHBEHHIIIHIIHHFHHGHHHHHHHHHHIHIHIFHHHHHHEGFHIHHIIIHHHHHHHHCFHHHHHHHFFFFFFEEEEFFEFEEBBEEEFFE@E8;EEFFFEF*:AEEEEEFFFEAAEA?A?ACAEF?CEEFED2<.?AAECEAEFEEE8??A8?CAAE1?EEE?AE*888AEEEEFEEFFA8A8?ACEAEEEAE?C:??ED28.)8?< +@MISEQ:1:000000000-A2Y1L:1:1101:15290:2442 1:N:0:NAAGGCGATAGATCGC +AAAATAATCCTAAAAAATAACCTCTATGCCGCCGAACGCTCCGCCTCTATCTTCGTAAAAACTATCTTCTCCTCCTCACCTCCATAATCAAGCATCAAGCGATCGCCCTCCGCCAACTCACCCCGCAAAATCTTATCCGCTAGCGGATTCTCAATCTCCGTCTGAATGACCCGCCTCAGCGGCCGCGCCCCATAAACCGAATCAAATCCACGCCTGTCTCTTATACACATCTCCGAGCCCACGAGACTAA ++ +?????BBBDDDDDDDDGGGGGGIIIHHFFHHHHHHHHHHEHHEHHHHHIIHHHHHFEHIIIHHIHHIHIHIIIIIHHHHHHHHHHHHHHHHDHHHHHHHHGEDFGGGGGGG;CEGEGCEGGGGG8>GGGGEGGEECEGGGGD8EDGGAEGEEGGCE:CGG8CEEGG???CEEDG.89D9DFG;FHHHHGHHFFFFHHHHECDCEFF>EFEEEE@CDFEFHHGHHHHEHDGHHFHDFHFHHHHFFHHH@FDD??DFFFFDBBEEBEEEEEEEEEEEEEEEEE,;?CEC;CEEEECB?CEEEEEEEECEEE?C?CE*0?***/:::?:*/?:A::**/:*:ACE?0:::A::***00::*/?C888??EEE############# +@MISEQ:1:000000000-A2Y1L:1:1101:15892:2446 1:N:0:NAAGGCGATAGATCGC +CTTCCCCACGGCCCAGACACAAGAGACGACCTCCATAAATCTTTTAGAGGGTGACCGCATCTCCGACGCAAACCAGGACGCCGATACCCTCGTGGTGGTGTTCGACCGTACGGATGGCGCAGACACCGACGGCACTAGTGCCACGGTATCAGGTACCACCATAACGTATGATTCGGGCACGCTCAAGGGCCAGCGTGACGGAATCGATAGAATACACTACACGGTGACTGATGGGGCCAGCCAAACCTGT ++ +?????BBBDBDDDDDDFFFFFFHIHIHHHHHHIHIFGGHFHHHHIIFHIHH?EEGHHHHHH-EGEHHCEHHHHH@FDFFEFF5@EEEFFEFE;AECCE;AEEEEEA?8?AEDDEEDFFDE2>>EEFF<<<2>D?DEEE*:C?AA<>8AEFCEE:?C?EEE?CEFEE0?:E?ACEECD8>EE>)8>E:CEEEEEED.)?AE??A?:A?*??:C0?CCE?AAA:88.88?::C:C?*8)4A?A######### diff --git a/tools/trimmomatic/test-data/trimmomatic_maxinfo.fastq b/tools/trimmomatic/test-data/trimmomatic_maxinfo.fastq new file mode 100644 index 00000000000..9ab47faeb4b --- /dev/null +++ b/tools/trimmomatic/test-data/trimmomatic_maxinfo.fastq @@ -0,0 +1,40 @@ +@MISEQ:1:000000000-A2Y1L:1:1101:19264:2433 1:N:0:NAAGGCGATAGATCGC +AGATAGCCGAAGATAAAGAGNTCATAACCGTAAAGGCCAGAGACGAGAACCACTCGCAGGCAAGGTTTGCAAGCCTCGCCAAGAATATTATAGACCCGCTTGCCAACGACTGGCATTACATCACCGTAAAGAAGG ++ +?????BBB@BBBB?BBFFFF#66EAFHHHCEFEDFGHHHHF@DFHACEEF@FDFHHHHEEEHHHF?FGEHFHDEFGHHCEHEFHHHHFFFCFDFFFFBEEEEEEEEEEEB?EEEEEEEEEEEBBEE?CE?:ACCC +@MISEQ:1:000000000-A2Y1L:1:1101:18667:2435 1:N:0:NAAGGCGATAGATCGC +ATATATTCATCCGCCATTATNAGAGTCCGATTACTTTAGAACAGTGCCGCGAATCCTTCGTCAACTGTAATCCAAGCGACATTGGTTCGATTAGCACGCATGAGGCACGAGATCTACGCGTATCTCTGG ++ +?????BBBDDDDADDDE@FF#66CFCFHHBEHHIIIHIIHHFHHGHHHHHHHHHHIHIHIFHHHHHHEGFHIHHIIIHHHHHHHHCFHHHHHHHFFFFFFEEEEFFEFEEBBEEEFFE@E8;EEFFFEF +@MISEQ:1:000000000-A2Y1L:1:1101:17523:2436 1:N:0:NAAGGCGATAGATCGC +CATCACTACCGCTCAGGAATNTGACGGCAGTCTTAGCGGCGCTCTAGTGCGGGAGGCCGTATCTTGGAATAAGGTGTCGTCAAATGCAAGGCAGGTAACCCTACACGCCG ++ +?<,/<@@@@@@>@CCCE#66>ACEEEEGGGGGGGFFFEFDFFFFF=CDEFFFFEDEFFFFFC=AEBF-AA@CE;ECD5<5<==C==DEEE +@MISEQ:1:000000000-A2Y1L:1:1101:18851:2442 1:N:0:NAAGGCGATAGATCGC +GGTATCCCCCGGCAGTGAGGATGGAGCCATGGTCTGCATCATACTCACCGTAGGTGAGAATATCCACGTCCTTCGACTCCTGGGTGCCGTCTATGGTGCCCTCTGTTACCAGGCAGTGACGGAGGACATGG ++ +??,GGGGEGGEECEGGGGD8EDGGAEGEEGGCE:CGG8CEEGG???CEE9D9DFG;FHHHHGHHFFFFHHHHECDCEFF>EFEEEE@CDFEFHHGHHHHEHDGHHFHDFHFHHHHFFHHH@FDD??DFFFFDBBEEBEEEEEEEEEEEEEEEEE +@MISEQ:1:000000000-A2Y1L:1:1101:15892:2446 1:N:0:NAAGGCGATAGATCGC +CTTCCCCACGGCCCAGACACAAGAGACGACCTCCATAAATCTTTTAGAGGGTGACCGCATCTCCGACGCAAACCAGGACGCCGATACCCTCGTGGTGGTGTTCGACCGTACGGATGGCGC ++ +?????BBBDBDDDDDDFFFFFFHIHIHHHHHHIHIFGGHFHHHHIIFHIHH?EEGHHHHHH-EGEHHCEHHHHH@FDFFEFF5@EEEFFEFE;AECCE;AEEEEEA?8?AEDDEEDFFDE +@MISEQ:1:000000000-A2Y1L:1:1101:17903:2450 1:N:0:TAAGGCGATAGATCGC +GTGCAGGGGGTGTGGTCAATCCACACTGTTGCTGAGGTGATTGGGTCTCCGGGGTCAACTCCATGAGGTAGCAGACCAG ++ +=5===<>+5<5<+5=@CC;8CEEEEE;-8ACFDE.7C87CF-A>E>E=FFE**>>5AEDAEED-5-5AADC=D+=DDE< +@MISEQ:1:000000000-A2Y1L:1:1101:15113:2451 1:N:0:TAAGGCGATAGATCGC +TCTCAGATGAGCATGCAGCAGCCCAGACTCGCCCCACGCAGTTTGCCAACCACAAGGCCATCCTCGGCCTGTCAGCCT ++ +=,,<=>>>@@@@@9@@CCEE@EE+++6C8-++CECE+>DCC>@@EFFFFEEEDEE55+ACEF;-C+>EE++CBA--5A diff --git a/tools/trimmomatic/test-data/trimmomatic_pe_r1_paired_out1.fastq b/tools/trimmomatic/test-data/trimmomatic_pe_r1_paired_out1.fastq new file mode 100644 index 00000000000..b8b03e3e426 --- /dev/null +++ b/tools/trimmomatic/test-data/trimmomatic_pe_r1_paired_out1.fastq @@ -0,0 +1,32 @@ +@MISEQ:1:000000000-A2Y1L:1:1101:19264:2433 1:N:0:NAAGGCGATAGATCGC +AGATAGCCGAAGATAAAGAGNT ++ +?????BBB@BBBB?BBFFFF#6 +@MISEQ:1:000000000-A2Y1L:1:1101:18667:2435 1:N:0:NAAGGCGATAGATCGC +ATATATTCATCCGCCATTATNA ++ +?????BBBDDDDADDDE@FF#6 +@MISEQ:1:000000000-A2Y1L:1:1101:17523:2436 1:N:0:NAAGGCGATAGATCGC +CATCACTACCGCTCAGGAATNTGACGGCAGTCTTAGCGGCGCTCTAGTGCGGGAGGCCGTATCTTGGAATAAGGTGTCGTCAAATGCAAGGCAGGTAACCCTACACGCCGAGG ++ +?<,/<@@@@@@>@CCCE#6 +@MISEQ:1:000000000-A2Y1L:1:1101:18851:2442 1:N:0:NAAGGCGATAGATCGC +GGTATCCCCCGGCAGTGAGGATGGAGCCATGGTCTGCATCATACTCACCGTAGGTGAGAATATCCACGTCCTTCGACTCCTGGGTGCCGTCTATGGTGCCCTCTGTTACCAGGCAGTGACGGAGGACATGGTGAGGTTTCAGTACCTCTGGCCCGGCCTGG ++ +??,D?)8 +@MISEQ:1:000000000-A2Y1L:1:1101:15290:2442 1:N:0:NAAGGCGATAGATCGC +AAAATAATCCTAAAAAATAACCTCTATGCCGCCGAACGCTCCGCCTCTATCTTCGTAAAAACTATCTTCTCCTCCTCACCTCCATAATCAAGCATCAAGCGATCGCCCTCCGCCAACTCACCCCGCAAAATCTTATCCGCTAGCGGATTCTCAATCTCCGTCTGAATGACCCGCCTCAGCGGCCGCGCCCCATAAACCGAATCAAATCCACGCCTGTCTCTTA ++ +?????BBBDDDDDDDDGGGGGGIIIHHFFHHHHHHHHHHEHHEHHHHHIIHHHHHFEHIIIHHIHHIHIHIIIIIHHHHHHHHHHHHHHHHDHHHHHHHHGEDFGGGGGGG;CEGEGCEGGGGG8>GGGGEGGEECEGGGGD8EDGGAEGEEGGCE:CGG8CEEGG???CEEDG.8>EEFF<<<2>D?DEEE*:C?AA<>8AEFCEE:?C?EEE?CEFEE0?:E?ACEECD8>EE>)8>E:CEEEEEED.)?AE??A?:A?*??:C0?CCE?AAA:88.88?::C:C?*8 +@MISEQ:1:000000000-A2Y1L:1:1101:17903:2450 1:N:0:TAAGGCGATAGATCGC +GTGCAGGGGG ++ +=5===<>+5< diff --git a/tools/trimmomatic/test-data/trimmomatic_pe_r1_paired_out1.fastq.gz b/tools/trimmomatic/test-data/trimmomatic_pe_r1_paired_out1.fastq.gz new file mode 100644 index 0000000000000000000000000000000000000000..6fadae3de812df4a9c7fbfda35311f52926c9671 GIT binary patch literal 893 zcmV-@1A_b?iwFP!00000|BY44uG=^a-RCO`%<87?oy0c}M{z7OluQMf2~bp<`Trm3 zIg|qwEiw%)%alZs5)VmF|K7gmZ($oY5Be(If7^dBv)yjcow~y=bi0p_Pup-0n{XE~ zQH=;^CP^ni8!-d*BRrt@mo85EH9f=>cxRD%i?_QHL7NhGpMDtrgN} za1(^w3?~Jesb16_X~xS8Uj|<0LCt-lS<#NY=8Ia%<)}r=Y(k}*Zi}vMmk-QB-pjC5T$2GWlj&V%!t$zXe?zH(| z97H_8=|PcY;Jy&|rk4j#5Ar_kK5xR0A$MzoiO9G2|xp`3)tf>PhpxDcw;TCo z;U`KD#&VjQUOQ{HZ0Jb+$R0e=Bb)k+0|-Pg)EsaZR0QxiBfdkzP}hXl-upqgh0AO0 z24nrm>i{{llLkIfUxj6HH1Fau2(BDyF6n;3G$Un6Vkv2T1s zAGG}m()$|}$0#vKM6?9mM3{vx34QgxZx=DQ1j T2*db!KdgQLF55A#f(QTr%jvXj literal 0 HcmV?d00001 diff --git a/tools/trimmomatic/test-data/trimmomatic_pe_r1_paired_out1.fastqillumina b/tools/trimmomatic/test-data/trimmomatic_pe_r1_paired_out1.fastqillumina new file mode 100644 index 00000000000..2ffed9a16bc --- /dev/null +++ b/tools/trimmomatic/test-data/trimmomatic_pe_r1_paired_out1.fastqillumina @@ -0,0 +1,32 @@ +@MISEQ:1:000000000-A2Y1L:1:1101:19264:2433 1:N:0:NAAGGCGATAGATCGC +AGATAGCCGAAGATAAAGAGNT ++ +^^^^^aaa_aaaa^aaeeeeBU +@MISEQ:1:000000000-A2Y1L:1:1101:18667:2435 1:N:0:NAAGGCGATAGATCGC +ATATATTCATCCGCCATTATNA ++ +^^^^^aaacccc`cccd_eeBU +@MISEQ:1:000000000-A2Y1L:1:1101:17523:2436 1:N:0:NAAGGCGATAGATCGC +CATCACTACCGCTCAGGAATNTGACGGCAGTCTTAGCGGCGCTCTAGTGCGGGAGGCCGTATCTTGGAATAAGGTGTCGTCAAATGCAAGGCAGGTAACCCTACACGCCGAGG ++ +^[K[^aaaaaaaaaaaeeeeBU`bdbbdbVWbd\bfgdgVbgbgefg`cfgggbbbggd[cegeeeeceeeeeecececcdddddddddb`ddddZ^adddaddabdZbZSWZ +@MISEQ:1:000000000-A2Y1L:1:1101:15489:2437 1:N:0:NAAGGCGATAGATCGC +GAGCAGTCGGGCTCAGCGCTNT ++ +T\\\\]N[______]_bbbdBU +@MISEQ:1:000000000-A2Y1L:1:1101:18851:2442 1:N:0:NAAGGCGATAGATCGC +GGTATCCCCCGGCAGTGAGGATGGAGCCATGGTCTGCATCATACTCACCGTAGGTGAGAATATCCACGTCCTTCGACTCCTGGGTGCCGTCTATGGTGCCCTCTGTTACCAGGCAGTGACGGAGGACATGGTGAGGTTTCAGTACCTCTGGCCCGGCCTGG ++ +^^K[^aaaccccccc[eee_ebZeeeadegggbccggfgggcfgggeggd`^dd`ddgcdegggggedbegggegcgddggbegVbdegcdggbeggegge\eeececeeeeddddccdeddd[aabdabdK\\`dPYY``ddbddI^I``dee^^]c^HW +@MISEQ:1:000000000-A2Y1L:1:1101:15290:2442 1:N:0:NAAGGCGATAGATCGC +AAAATAATCCTAAAAAATAACCTCTATGCCGCCGAACGCTCCGCCTCTATCTTCGTAAAAACTATCTTCTCCTCCTCACCTCCATAATCAAGCATCAAGCGATCGCCCTCCGCCAACTCACCCCGCAAAATCTTATCCGCTAGCGGATTCTCAATCTCCGTCTGAATGACCCGCCTCAGCGGCCGCGCCCCATAAACCGAATCAAATCCACGCCTGTCTCTTA ++ +^^^^^aaaccccccccffffffhhhggeeggggggggggdggdggggghhgggggedghhhgghgghghghhhhhggggggggggggggggcggggggggfdcefffffffZbdfdfbdfffffW]ffffdffddbdffffcWdcff`dfddffbdYbffWbddff^^^bdd[cfWbbI^^]cfMW[`ffffbddfIbQ[fbbdbdIY^bd^bdXbYbYbY^b +@MISEQ:1:000000000-A2Y1L:1:1101:15892:2446 1:N:0:NAAGGCGATAGATCGC +CTTCCCCACGGCCCAGACACAAGAGACGACCTCCATAAATCTTTTAGAGGGTGACCGCATCTCCGACGCAAACCAGGACGCCGATACCCTCGTGGTGGTGTTCGACCGTACGGATGGCGCAGACACCGACGGCACTAGTGCCACGGTATCAGGTACCACCATAACGTATGATTCGGGCACGCTCAAGGGCCAGCGTGACGGAATCGATAGAATACACTACACGGTGACTGATGGGG ++ +^^^^^aaacacccccceeeeeeghghgggggghgheffgegggghheghgg^ddfggggggLdfdggbdggggg_eceedeeT_dddeededZ`dbbdZ`ddddd`^W^`dccddceecdQ]]ddee[[[Q]c^cdddIYb^``[]W`debddY^b^ddd^bdeddO^Yd^`bddbcW]dd]HW]dYbddddddcMH^`d^^`^Y`^I^^YbO^bbd^```YWWMWW^YYbYb^IW +@MISEQ:1:000000000-A2Y1L:1:1101:17903:2450 1:N:0:TAAGGCGATAGATCGC +GTGCAGGGGG ++ +\T\\\[]JT[ diff --git a/tools/trimmomatic/test-data/trimmomatic_pe_r1_paired_out1.fastqsolexa b/tools/trimmomatic/test-data/trimmomatic_pe_r1_paired_out1.fastqsolexa new file mode 100644 index 00000000000..5f2fb494fd3 --- /dev/null +++ b/tools/trimmomatic/test-data/trimmomatic_pe_r1_paired_out1.fastqsolexa @@ -0,0 +1,32 @@ +@MISEQ:1:000000000-A2Y1L:1:1101:19264:2433 1:N:0:NAAGGCGATAGATCGC +AGATAGCCGAAGATAAAGAGNT ++ +^^^^^aaa_aaaa^aaeeee>U +@MISEQ:1:000000000-A2Y1L:1:1101:18667:2435 1:N:0:NAAGGCGATAGATCGC +ATATATTCATCCGCCATTATNA ++ +^^^^^aaacccc`cccd_ee>U +@MISEQ:1:000000000-A2Y1L:1:1101:17523:2436 1:N:0:NAAGGCGATAGATCGC +CATCACTACCGCTCAGGAATNTGACGGCAGTCTTAGCGGCGCTCTAGTGCGGGAGGCCGTATCTTGGAATAAGGTGTCGTCAAATGCAAGGCAGGTAACCCTACACGCCGAGG ++ +^[K[^aaaaaaaaaaaeeee>U`bdbbdbVWbd\bfgdgVbgbgefg`cfgggbbbggd[cegeeeeceeeeeecececcdddddddddb`ddddZ^adddaddabdZbZSWZ +@MISEQ:1:000000000-A2Y1L:1:1101:15489:2437 1:N:0:NAAGGCGATAGATCGC +GAGCAGTCGGGCTCAGCGCTNT ++ +T\\\\]N[______]_bbbd>U +@MISEQ:1:000000000-A2Y1L:1:1101:18851:2442 1:N:0:NAAGGCGATAGATCGC +GGTATCCCCCGGCAGTGAGGATGGAGCCATGGTCTGCATCATACTCACCGTAGGTGAGAATATCCACGTCCTTCGACTCCTGGGTGCCGTCTATGGTGCCCTCTGTTACCAGGCAGTGACGGAGGACATGGTGAGGTTTCAGTACCTC ++ +^^K[^aaaccccccc[eee_ebZeeeadegggbccggfgggcfgggeggd`^dd`ddgcdegggggedbegggegcgddggbegVbdegcdggbeggegge\eeececeeeeddddccdeddd[aabdabdK\\`dPYY``ddbddH^ +@MISEQ:1:000000000-A2Y1L:1:1101:15290:2442 1:N:0:NAAGGCGATAGATCGC +AAAATAATCCTAAAAAATAACCTCTATGCCGCCGAACGCTCCGCCTCTATCTTCGTAAAAACTATCTTCTCCTCCTCACCTCCATAATCAAGCATCAAGCGATCGCCCTCCGCCAACTCACCCCGCAAAATCTTATCCGCTAGCGGATTCTCAATCTCCGTCTGAATGACCCGCCTCAGCGGCCGCGCCCCATAAACCGAATCAAATCCACGCCTGTCTCTTA ++ +^^^^^aaaccccccccffffffhhhggeeggggggggggdggdggggghhgggggedghhhgghgghghghhhhhggggggggggggggggcggggggggfdcefffffffZbdfdfbdfffffW]ffffdffddbdffffcWdcff`dfddffbdYbffWbddff^^^bdd[cfWbbH^^]cfMW[`ffffbddfHbQ[fbbdbdHY^bd^bdXbYbYbY^b +@MISEQ:1:000000000-A2Y1L:1:1101:15892:2446 1:N:0:NAAGGCGATAGATCGC +CTTCCCCACGGCCCAGACACAAGAGACGACCTCCATAAATCTTTTAGAGGGTGACCGCATCTCCGACGCAAACCAGGACGCCGATACCCTCGTGGTGGTGTTCGACCGTACGGATGGCGCAGACACCGACGGCACTAGTGCCACGGTATCAGGTACCACCATAACGTATGATTCGGGCACGCTCAAGGGCCAGCGTGACGGAATCGATAGAATACACTACACGGTGACTGATGGGG ++ +^^^^^aaacacccccceeeeeeghghgggggghgheffgegggghheghgg^ddfggggggLdfdggbdggggg_eceedeeT_dddeededZ`dbbdZ`ddddd`^W^`dccddceecdQ]]ddee[[[Q]c^cdddHYb^``[]W`debddY^b^ddd^bdeddO^Yd^`bddbcW]dd]GW]dYbddddddcMG^`d^^`^Y`^H^^YbO^bbd^```YWWMWW^YYbYb^HW +@MISEQ:1:000000000-A2Y1L:1:1101:17903:2450 1:N:0:TAAGGCGATAGATCGC +GTGCAGGGGG ++ +\T\\\[]JT[ diff --git a/tools/trimmomatic/test-data/trimmomatic_pe_r1_paired_out1_clip.fastq b/tools/trimmomatic/test-data/trimmomatic_pe_r1_paired_out1_clip.fastq new file mode 100644 index 00000000000..9a778b127a5 --- /dev/null +++ b/tools/trimmomatic/test-data/trimmomatic_pe_r1_paired_out1_clip.fastq @@ -0,0 +1,32 @@ +@MISEQ:1:000000000-A2Y1L:1:1101:19264:2433 1:N:0:NAAGGCGATAGATCGC +AGATAGCCGAAGATAAAGAGNT ++ +?????BBB@BBBB?BBFFFF#6 +@MISEQ:1:000000000-A2Y1L:1:1101:18667:2435 1:N:0:NAAGGCGATAGATCGC +ATATATTCATCCGCCATTATNA ++ +?????BBBDDDDADDDE@FF#6 +@MISEQ:1:000000000-A2Y1L:1:1101:17523:2436 1:N:0:NAAGGCGATAGATCGC +CATCACTACCGCTCAGGAATNTGACGGCAGTCTTAGCGGCGCTCTAGTGCGGGAGGCCGTATCTTGGAATAAGGTGTCGTCAAATGCAAGGCAGGTAACCCTACACGCCGAGG ++ +?<,/<@@@@@@>@CCCE#6 +@MISEQ:1:000000000-A2Y1L:1:1101:18851:2442 1:N:0:NAAGGCGATAGATCGC +GGTATCCCCCGGCAGTGAGGATGGAGCCATGGTCTGCATCATACTCACCGTAGGTGAGAATATCCACGTCCTTCGACTCCTGGGTGCCGTCTATGGTGCCCTCTGTTACCAGGCAGTGACGGAGGACATGGTGAGGTTTCAGTACCTCTGGCCCGGCCTGG ++ +??,D?)8 +@MISEQ:1:000000000-A2Y1L:1:1101:15290:2442 1:N:0:NAAGGCGATAGATCGC +AAAATAATCCTAAAAAATAACCTCTATGCCGCCGAACGCTCCGCCTCTATCTTCGTAAAAACTATCTTCTCCTCCTCACCTCCATAATCAAGCATCAAGCGATCGCCCTCCGCCAACTCACCCCGCAAAATCTTATCCGCTAGCGGATTCTCAATCTCCGTCTGAATGACCCGCCTCAGCGGCCGCGCCCCATAAACCGAATCAAATCCACGC ++ +?????BBBDDDDDDDDGGGGGGIIIHHFFHHHHHHHHHHEHHEHHHHHIIHHHHHFEHIIIHHIHHIHIHIIIIIHHHHHHHHHHHHHHHHDHHHHHHHHGEDFGGGGGGG;CEGEGCEGGGGG8>GGGGEGGEECEGGGGD8EDGGAEGEEGGCE:CGG8CEEGG???CEEDG.8>EEFF<<<2>D?DEEE*:C?AA<>8AEFCEE:?C?EEE?CEFEE0?:E?ACEECD8>EE>)8>E:CEEEEEED.)?AE??A?:A?*??:C0?CCE?AAA:88.88?::C:C?*8 +@MISEQ:1:000000000-A2Y1L:1:1101:17903:2450 1:N:0:TAAGGCGATAGATCGC +GTGCAGGGGG ++ +=5===<>+5< diff --git a/tools/trimmomatic/test-data/trimmomatic_pe_r1_unpaired_out1.fastq b/tools/trimmomatic/test-data/trimmomatic_pe_r1_unpaired_out1.fastq new file mode 100644 index 00000000000..e69de29bb2d diff --git a/tools/trimmomatic/test-data/trimmomatic_pe_r1_unpaired_out1.fastq.gz b/tools/trimmomatic/test-data/trimmomatic_pe_r1_unpaired_out1.fastq.gz new file mode 100644 index 0000000000000000000000000000000000000000..0239669d57f6148035ad2dc4a6d54ae7db678e85 GIT binary patch literal 20 Scmb2|=3oGW|I82?NCE&DbOE&h literal 0 HcmV?d00001 diff --git a/tools/trimmomatic/test-data/trimmomatic_pe_r1_unpaired_out1.fastqillumina b/tools/trimmomatic/test-data/trimmomatic_pe_r1_unpaired_out1.fastqillumina new file mode 100644 index 00000000000..e69de29bb2d diff --git a/tools/trimmomatic/test-data/trimmomatic_pe_r1_unpaired_out1.fastqsolexa b/tools/trimmomatic/test-data/trimmomatic_pe_r1_unpaired_out1.fastqsolexa new file mode 100644 index 00000000000..e69de29bb2d diff --git a/tools/trimmomatic/test-data/trimmomatic_pe_r2_paired_out1.fastq b/tools/trimmomatic/test-data/trimmomatic_pe_r2_paired_out1.fastq new file mode 100644 index 00000000000..0deb9f729af --- /dev/null +++ b/tools/trimmomatic/test-data/trimmomatic_pe_r2_paired_out1.fastq @@ -0,0 +1,32 @@ +@MISEQ:1:000000000-A2Y1L:1:1101:19264:2433 2:N:0:NAAGGCGATAGATCGC +GCCGATATGCAGATGCCGTTGATTGCTGCCAGCATAGCAGCCATTGCCGGCATATCCTTTGTGACTGTGCGCCGACGCAAGAAGGCGGCCCAGATAACCTAGCCCAGAAACGATACGGCGTCTCTACCCTCATCTGTTATGCTGATCCAGTGATTCTTGCCTACCTTCTTTACGGTGATGTAATGCCAGTCGTTGGCAAG ++ +??A??ABBDDDDDDDDFFEEEFHIIIIHHIIHIFHIIHHHFHHIIIIIHHHFHHIIIIIIFFFHHIIHGDEHHAAEHHHHFHHHHD=EBBEEEEEFFFFEEEECEFFEEFFF8*??AA?;>DEEEFFFF*?8AECFEFFFFFFEAEEECFFFCEEEFFFFFFEEFEACEEC?CAACEFEEEFE?0?EACAAAEEAACEEA +@MISEQ:1:000000000-A2Y1L:1:1101:18667:2435 2:N:0:NAAGGCGATAGATCGC +GATGACATCAGCACAGGTTCCGCTTCCGCTGTCGCAACGACGTGGCTGCCATCGATTATATTCAATTCTGAGTGCTGCCGTAGGGCTAGATGTAAGACTCACGTTCGGCGACCAGATTAGTCGGTAGTGGCATG ++ +?????BBBDDDDDDDDGFFGGGHHHHIHHHHHHHIHHHHIHBCEEHFFHHHIIHFHHHIIIIIIIHIFBGFGFHHHHIHE@EEEHHFFHHFF?CFHHHHHGGGGGGGGGGGGGGGGGGGECGGG;EE:CEGGG? +@MISEQ:1:000000000-A2Y1L:1:1101:17523:2436 2:N:0:NAAGGCGATAGATCGC +GAATATAGAAACGGGAGTATAGTGGTAACC ++ +??AAABBBDDDDDEDDGGCFGGHHIFFHHH +@MISEQ:1:000000000-A2Y1L:1:1101:15489:2437 2:N:0:NAAGGCGATAGATCGC +GTCCACGTGAAATCCCGAGCGTCCCTCTCCCTCCCGAGAACCCGGTCTATATCCCACGATTTTTGACCGAACAAGGATTGACCTCATCCAACTCCGAAGCCCGCC ++ +????9B???AD9?BDDEEDDDDHHHHHFHFHFFHHHHHHHHHEHH>CEGHHFGHHGHH=FHHHHC+CGEBCCCE6BB +@MISEQ:1:000000000-A2Y1L:1:1101:18851:2442 2:N:0:NAAGGCGATAGATCGC +TCTCCTCAGTACGGGGGAGGAGGTTCGCTCGGCGGACGTGCGGCCCTACGCCAGACTCTACCACATGGTTCAGCAGGAGCTGGAGCACCGCGCTGTGTCCGGGGACTGGGAATACACCATCAGCCCCGGCGAGGAGTGGCAAGAGACGGA ++ +A??A?BBBDDDDDDDDGGGGGGHEFHHGEHHHIHEHHHHHDHBEHGFFFEGGDEEDGGGGGEGGEECE?EGCEGEGGGCEEEGGCEEGG4D;;4AGGGGGG8>GGA?EGGGEEGEEGGGCGGEGEGGGGD81,; +@MISEQ:1:000000000-A2Y1L:1:1101:15892:2446 2:N:0:NAAGGCGATAGATCGC +GTATTGCTGGCACCATCAGTCACCGTGTAGTGTATTCTATCGATTCCGTCACGCTGGCCCTTGAGCGTGCCCGAATCATACGTTATGGTGGTACCTGATACCGTGGCACTAGTGCCGTCGGTGTCTGCGCCATCCGTACGGTCGAACACCACCACGAGGGTATCGGCG ++ +?????BBBDDDDDDDDGGGGGGIIHIIFHHHIHHIFHGHGGHHIHIIDEFFHEF@DFHIIHIIIGHACDCFFHHHIHIIHIHGHHHBGFGEEHHHHFHFFHHDFDCEGGFGGFGGG@DBEEEEGC>CEEGGGGGGE0?CDGGGD>EE2CE8CEGEE<>>>):CEEGDA +@MISEQ:1:000000000-A2Y1L:1:1101:17903:2450 2:N:0:TAAGGCGATAGATCGC +GGCCAACACTGTGGTCACTATCTCTGGCACTGGTCTGCTACCACATGGAGTTGACACCGGAGACCCAATCACCACAGCAACAGTGTGGATTGACCACACCCCCTGCACCTGTCTCTTATACACATCTGACGCTGCCGACGAGCGATCTAG ++ +55DDD880:? diff --git a/tools/trimmomatic/test-data/trimmomatic_pe_r2_paired_out1.fastq.gz b/tools/trimmomatic/test-data/trimmomatic_pe_r2_paired_out1.fastq.gz new file mode 100644 index 0000000000000000000000000000000000000000..5ce15fecbfb30b4c2da7b67c848f51025ef167b1 GIT binary patch literal 1020 zcmVYyLMzsq5`xBD5{tK|BrNL z=*_k`O?MSXmMEH%W=Klc-*11GKgQj-eJj7F{a?G^AldD+WL?K4y&=auGMPV&9}`wCp^oN*HUXKrM4SNL)~s{ zx7KQt?4QkBt!g&UrL~k$X|T2YT9&1-K!pa26~56KzGAvGU#7f{ew~L@tf~#2L}fH= z9oAJU?6kBZGut9yBqeFk%EnEfH5k60Ape>|@mvTx>PF?+Fk z{eD1YbzuPHIxmMMU$6NKzB(<-CwzT4?tsf-{|FatpPsG+A#OZ89v&6`idZ4WGRqOU0S6(Z76Or6DCXFX7IDFt?>N zXL@ia(&52)kZR`QK$lL;ETY=|kS~`*3UkAR$!02Gq)3q;v*CGoNh!k$qhQ8b#{ukq z?1}sH_J0v~rH$0%q@cGcduwi?tVFJrI9;sU3JTTVlEQUmSa0uK#f?_w|7DJCj|6_efsKfql)06f=mV&Z8*ePO-v3)PWZJS2i#m zVquN;Wl=_4z7(frl3kr>5tJ4WVRKClwg1YWDol&F8p#uHZ%Q%X-FfEZ0mIse1gHb>O*8@-}(nb~etPr&9J-2Kr=qnWpK>NS*wNGwb=h zWrjU&S62E@thiE9+$e-Oap)^e5|Olf%qHDb#G8VSU-v*U>39>B_gp7U5-8GpTtIq6 zvu+^4aa?4QRz~i?!SVPa8UR0uSmG=mLy!jjc&~Hfm2><|1G4Y82 literal 0 HcmV?d00001 diff --git a/tools/trimmomatic/test-data/trimmomatic_pe_r2_paired_out1.fastqillumina b/tools/trimmomatic/test-data/trimmomatic_pe_r2_paired_out1.fastqillumina new file mode 100644 index 00000000000..1cb1312f730 --- /dev/null +++ b/tools/trimmomatic/test-data/trimmomatic_pe_r2_paired_out1.fastqillumina @@ -0,0 +1,32 @@ +@MISEQ:1:000000000-A2Y1L:1:1101:19264:2433 2:N:0:NAAGGCGATAGATCGC +GCCGATATGCAGATGCCGTTGATTGCTGCCAGCATAGCAGCCATTGCCGGCATATCCTTTGTGACTGTGCGCCGACGCAAGAAGGCGGCCCAGATAACCTAGCCCAGAAACGATACGGCGTCTCTACCCTCATCTGTTATGCTGATCCAGTGATTCTTGCCTACCTTCTTTACGGTGATGTAATGCCAGTCGTTGGCAAG ++ +^^`^^`aacccccccceedddeghhhhgghhgheghhgggegghhhhhgggegghhhhhheeegghhgfcdgg``dggggeggggc\daadddddeeeeddddbdeeddeeeWI^^``^Z]cdddeeeeI^W`dbedeeeeeed`dddbeeebdddeeeeeedded`bddb^b``bdeddded^O^d`b```dd``bdd` +@MISEQ:1:000000000-A2Y1L:1:1101:18667:2435 2:N:0:NAAGGCGATAGATCGC +GATGACATCAGCACAGGTTCCGCTTCCGCTGTCGCAACGACGTGGCTGCCATCGATTATATTCAATTCTGAGTGCTGCCGTAGGGCTAGATGTAAGACTCACGTTCGGCGACCAGATTAGTCGGTAGTGGCATG ++ +^^^^^aaaccccccccfeefffgggghggggggghgggghgabddgeeggghhgeggghhhhhhhgheafefegggghgd_dddggeeggee^begggggfffffffffffffffffffdbfffZddYbdfff^ +@MISEQ:1:000000000-A2Y1L:1:1101:17523:2436 2:N:0:NAAGGCGATAGATCGC +GAATATAGAAACGGGAGTATAGTGGTAACC ++ +^^```aaacccccdccffbeffggheeggg +@MISEQ:1:000000000-A2Y1L:1:1101:15489:2437 2:N:0:NAAGGCGATAGATCGC +GTCCACGTGAAATCCCGAGCGTCCCTCTCCCTCCCGAGAACCCGGTCTATATCCCACGATTTTTGACCGAACAAGGATTGACCTCATCCAACTCCGAAGCCCGCC ++ +^^^^Xa^^^`cX^accddccccgggggegegeegggggggggdgg]bdfggefggfgg\eggggbJbfdabb[be_KSbe_beaeeeece^aSac__cH]bdUaa +@MISEQ:1:000000000-A2Y1L:1:1101:18851:2442 2:N:0:NAAGGCGATAGATCGC +TCTCCTCAGTACGGGGGAGGAGGTTCGCTCGGCGGACGTGCGGCCCTACGCCAGACTCTACCACATGGTTCAGCAGGAGCTGGAGCACCGCGCTGTGTCCGGGGACTGGGAATACACCATCAGCCCCGGCGAGGAGTGGCAAGAGACGGA ++ +`^^`^aaaccccccccffffffgdeggfdggghgdgggggcgadgfeeedffcddcfffffdffddbd^dfbdfdfffbdddffbddffScZZS`ffffffW]ff`^dfffddfddfffbffdfdffffcW[``cdbdbdff^bbbYWbb +@MISEQ:1:000000000-A2Y1L:1:1101:15290:2442 2:N:0:NAAGGCGATAGATCGC +GCGTGGATTTGATTCGGTTTATGGGGCGCGGCCGCTGAGGCGGGTCATTCAGACGGAGATT ++ +^^^^^_^accccccccedddeeghhgdggggcgggggdggggggW`ceeeceecPcZ]PKZ +@MISEQ:1:000000000-A2Y1L:1:1101:15892:2446 2:N:0:NAAGGCGATAGATCGC +GTATTGCTGGCACCATCAGTCACCGTGTAGTGTATTCTATCGATTCCGTCACGCTGGCCCTTGAGCGTGCCCGAATCATACGTTATGGTGGTACCTGATACCGTGGCACTAGTGCCGTCGGTGTCTGCGCCATCCGTACGGTCGAACACCACCACGAGGGTATCGGCG ++ +^^^^^aaaccccccccffffffhhghheggghgghegfgffgghghhcdeegde_ceghhghhhfg`bcbeeggghghhghgfgggafefddggggegeeggcecbdffeffefff_caddddfb]bddffffffdO^bcfffc]ddQbdWbdfdd[]]]HYbddfc` +@MISEQ:1:000000000-A2Y1L:1:1101:17903:2450 2:N:0:TAAGGCGATAGATCGC +GGCCAACACTGTGGTCACTATCTCTGGCACTGGTCTGCTACCACATGGAGTTGACACCGGAGACCCAATCACCACAGCAACAGTGTGGATTGACCACACCCCCTGCACCTGTCTCTTATACACATCTGACGCTGCCGACGAGCGATCTAG ++ +TT[^^^^^cccaaccaeeeeeebgghhgghhhhhhhgfgghhhhggfghhgegghhhhgggbcghhhgeeghhhhhbeeghgdbfbfdghg\eggggggggggeZeeeeecceeeeeeedeeeededace`dd`dd_ddcc]cccWWOY^ diff --git a/tools/trimmomatic/test-data/trimmomatic_pe_r2_paired_out1.fastqsolexa b/tools/trimmomatic/test-data/trimmomatic_pe_r2_paired_out1.fastqsolexa new file mode 100644 index 00000000000..6dd0bb9fe41 --- /dev/null +++ b/tools/trimmomatic/test-data/trimmomatic_pe_r2_paired_out1.fastqsolexa @@ -0,0 +1,32 @@ +@MISEQ:1:000000000-A2Y1L:1:1101:19264:2433 2:N:0:NAAGGCGATAGATCGC +GCCGATATGCAGATGCCGTTGATTGCTGCCAGCATAGCAGCCATTGCCGGCATATCCTTTGTGACTGTGCGCCGACGCAAGAAGGCGGCCCAGATAACCTAGCCCAGAAACGATACGGCGTCTCTACCCTCATCTGTTATGCTGATCCAGTGATTCTTGCCTACCTTCTTTACGGTGATGTAATGCCAGTCGTTGGCAAG ++ +^^`^^`aacccccccceedddeghhhhgghhgheghhgggegghhhhhgggegghhhhhheeegghhgfcdgg``dggggeggggc\daadddddeeeeddddbdeeddeeeWH^^``^Z]cdddeeeeH^W`dbedeeeeeed`dddbeeebdddeeeeeedded`bddb^b``bdeddded^O^d`b```dd``bdd` +@MISEQ:1:000000000-A2Y1L:1:1101:18667:2435 2:N:0:NAAGGCGATAGATCGC +GATGACATCAGCACAGGTTCCGCTTCCGCTGTCGCAACGACGTGGCTGCCATCGATTATATTCAATTCTGAGTGCTGCCGTAGGGCTAGATGTAAGACTCACGTTCGGCGACCAGATTAGTCGGTAGTGGCATG ++ +^^^^^aaaccccccccfeefffgggghggggggghgggghgabddgeeggghhgeggghhhhhhhgheafefegggghgd_dddggeeggee^begggggfffffffffffffffffffdbfffZddYbdfff^ +@MISEQ:1:000000000-A2Y1L:1:1101:17523:2436 2:N:0:NAAGGCGATAGATCGC +GAATATAGAAACGGGAGTATAGTGGTAACC ++ +^^```aaacccccdccffbeffggheeggg +@MISEQ:1:000000000-A2Y1L:1:1101:15489:2437 2:N:0:NAAGGCGATAGATCGC +GTCCACGTGAAATCCCGAGCGTCCCTCTCCCTCCCGAGAACCCGGTCTATATCCCACGATTTTTGACCGAACAAGGATTGACCTCATCCAACTCCGAAGCCCGCC ++ +^^^^Xa^^^`cX^accddccccgggggegegeegggggggggdgg]bdfggefggfgg\eggggbJbfdabb[be_KSbe_beaeeeece^aSac__cG]bdUaa +@MISEQ:1:000000000-A2Y1L:1:1101:18851:2442 2:N:0:NAAGGCGATAGATCGC +TCTCCTCAGTACGGGGGAGGAGGTTCGCTCGGCGGACGTGCGGCCCTACGCCAGACTCTACCACATGGTTCAGCAGGAGCTGGAGCACCGCGCTGTGTCCGGGGACTGGGAATACACCATCAGCCCCGGCGAGGAGTGGCAAGAGACGGA ++ +`^^`^aaaccccccccffffffgdeggfdggghgdgggggcgadgfeeedffcddcfffffdffddbd^dfbdfdfffbdddffbddffScZZS`ffffffW]ff`^dfffddfddfffbffdfdffffcW[``cdbdbdff^bbbYWbb +@MISEQ:1:000000000-A2Y1L:1:1101:15290:2442 2:N:0:NAAGGCGATAGATCGC +GCGTGGATTTGATTCGGTTTATGGGGCGCGGCCGCTGAGGCGGGTCATTCAGACGGAGATT ++ +^^^^^_^accccccccedddeeghhgdggggcgggggdggggggW`ceeeceecPcZ]PKZ +@MISEQ:1:000000000-A2Y1L:1:1101:15892:2446 2:N:0:NAAGGCGATAGATCGC +GTATTGCTGGCACCATCAGTCACCGTGTAGTGTATTCTATCGATTCCGTCACGCTGGCCCTTGAGCGTGCCCGAATCATACGTTATGGTGGTACCTGATACCGTGGCACTAGTGCCGTCGGTGTCTGCGCCATCCGTACGGTCGAACACCACCACGAGGGTATCGGCG ++ +^^^^^aaaccccccccffffffhhghheggghgghegfgffgghghhcdeegde_ceghhghhhfg`bcbeeggghghhghgfgggafefddggggegeeggcecbdffeffefff_caddddfb]bddffffffdO^bcfffc]ddQbdWbdfdd[]]]GYbddfc` +@MISEQ:1:000000000-A2Y1L:1:1101:17903:2450 2:N:0:TAAGGCGATAGATCGC +GGCCAACACTGTGGTCACTATCTCTGGCACTGGTCTGCTACCACATGGAGTTGACACCGGAGACCCAATCACCACAGCAACAGTGTGGATTGACCACACCCCCTGCACCTGTCTCTTATACACATCTGACGCTGCCGACGAGCGATCTAG ++ +TT[^^^^^cccaaccaeeeeeebgghhgghhhhhhhgfgghhhhggfghhgegghhhhgggbcghhhgeeghhhhhbeeghgdbfbfdghg\eggggggggggeZeeeeecceeeeeeedeeeededace`dd`dd_ddcc]cccWWOY^ diff --git a/tools/trimmomatic/test-data/trimmomatic_pe_r2_unpaired_out1.fastq b/tools/trimmomatic/test-data/trimmomatic_pe_r2_unpaired_out1.fastq new file mode 100644 index 00000000000..07bd12523c5 --- /dev/null +++ b/tools/trimmomatic/test-data/trimmomatic_pe_r2_unpaired_out1.fastq @@ -0,0 +1,8 @@ +@MISEQ:1:000000000-A2Y1L:1:1101:18106:2444 2:N:0:NAAGGCGATAGATCGC +GAGTTACTATTACAGAGTGGAGCTAATGTACTGGCAGTTGACTGCAAAAGAAATGCTCCAATTCATGTTGCATGTGCAAATATGAGCTTAGAGTGTTTAAAGATAATTTTGTGCCACAAAAAATGCAACCCAAACCAACAAAATGCAGTGGGAGACACTCCACTCCACACCTTATGCAGTTTGGGGACTTGTGATATGAGAATACTACCTGTCTCTTATACACA ++ +?????BBBDDDDDDDDGCFGFGIIIIIHFHIIIIHIHFG=EHHIGIIIIFHIHDGHGHHHIHIH=CGHGGHFHHHFHFGHHFH/ACDFGG?FE?CDFFHHHHHIIHFHHI>CEDGFHHHHHHHHDFHHFHHHFFAFFGGGGGGEDEG>>DACC;?EGG>CEEA>AEACCEE?:C::CC:::C:CE{zMi&*fXbVu<4%dpi7t4@5#3A>P9H8V|?g@!=3}af~-2RaP>>VdX(d&4`U$ zl6wjPpG-XtwlmaCCP2wkYz)tgo#q*+o=2lzZ)-1u;Wge5a1vAR)4LF{_aPU2kNF5F zMxfua3Q)|pv^l{i@_yTmelw;9OAQsy^&%P`hvdjPmkr8Qt1gaKTURjjDy=O&j9@F; zv>|}+%CHsGhEvt$GjXY^sY-(38Bo1jTPBvGYXm5@t%a3p)eb45(^N3(dlFUfg(edC zA}Ml=j04Sb;met0;z-vUMcUJ8_ytg9S9G2N003u>r3?T7 literal 0 HcmV?d00001 diff --git a/tools/trimmomatic/test-data/trimmomatic_pe_r2_unpaired_out1.fastqillumina b/tools/trimmomatic/test-data/trimmomatic_pe_r2_unpaired_out1.fastqillumina new file mode 100644 index 00000000000..bbbc217d7bd --- /dev/null +++ b/tools/trimmomatic/test-data/trimmomatic_pe_r2_unpaired_out1.fastqillumina @@ -0,0 +1,8 @@ +@MISEQ:1:000000000-A2Y1L:1:1101:18106:2444 2:N:0:NAAGGCGATAGATCGC +GAGTTACTATTACAGAGTGGAGCTAATGTACTGGCAGTTGACTGCAAAAGAAATGCTCCAATTCATGTTGCATGTGCAAATATGAGCTTAGAGTGTTTAAAGATAATTTTGTGCCACAAAAAATGCAACCCAAACCAACAAAATGCAGTGGGAGACACTCCACTCCACACCTTATGCAGTTTGGGGACTTGTGATATGAGAATACTACCTGTCTCTTATACACA ++ +^^^^^aaaccccccccfbefefhhhhhgeghhhhghgef\dgghfhhhheghgcfgfggghghg\bfgffgegggegefggegN`bceff^ed^bceeggggghhgeggh]bdcfeggggggggceggegggee`eeffffffdcdf]]c`bbZ^dff]bdd`]`d`bbdd^YbYYbbYYYbYbd[b[XbY^b^I^bddbbbIYb^b^dY^YbYbYbbbbdY^b +@MISEQ:1:000000000-A2Y1L:1:1101:15113:2451 2:N:0:TAAGGCGATAGATCGC +GAGGGGAGGAGGGGAAGGGAGAGGGGAAGAGAGGAGAGGAG ++ +^^^^^_X_a^a^aaaadddea__ddgdb^aeLbd_ccdgKT diff --git a/tools/trimmomatic/test-data/trimmomatic_pe_r2_unpaired_out1.fastqsolexa b/tools/trimmomatic/test-data/trimmomatic_pe_r2_unpaired_out1.fastqsolexa new file mode 100644 index 00000000000..6137bf8a275 --- /dev/null +++ b/tools/trimmomatic/test-data/trimmomatic_pe_r2_unpaired_out1.fastqsolexa @@ -0,0 +1,8 @@ +@MISEQ:1:000000000-A2Y1L:1:1101:18106:2444 2:N:0:NAAGGCGATAGATCGC +GAGTTACTATTACAGAGTGGAGCTAATGTACTGGCAGTTGACTGCAAAAGAAATGCTCCAATTCATGTTGCATGTGCAAATATGAGCTTAGAGTGTTTAAAGATAATTTTGTGCCACAAAAAATGCAACCCAAACCAACAAAATGCAGTGGGAGACACTCCACTCCACACCTTATGCAGTTTGGGGACTTGTGATATGAGAATACTACCTGTCTCTTATACACA ++ +^^^^^aaaccccccccfbefefhhhhhgeghhhhghgef\dgghfhhhheghgcfgfggghghg\bfgffgegggegefggegN`bceff^ed^bceeggggghhgeggh]bdcfeggggggggceggegggee`eeffffffdcdf]]c`bbZ^dff]bdd`]`d`bbdd^YbYYbbYYYbYbd[b[XbY^b^H^bddbbbHYb^b^dY^YbYbYbbbbdY^b +@MISEQ:1:000000000-A2Y1L:1:1101:15113:2451 2:N:0:TAAGGCGATAGATCGC +GAGGGGAGGAGGGGAAGGGAGAGGGGAAGAGAGGAGAGGAG ++ +^^^^^_X_a^a^aaaadddea__ddgdb^aeLbd_ccdgKT diff --git a/tools/trimmomatic/test-data/trimmomatic_pe_r2_unpaired_out1_clip.fastq b/tools/trimmomatic/test-data/trimmomatic_pe_r2_unpaired_out1_clip.fastq new file mode 100644 index 00000000000..fee78d4412c --- /dev/null +++ b/tools/trimmomatic/test-data/trimmomatic_pe_r2_unpaired_out1_clip.fastq @@ -0,0 +1,8 @@ +@MISEQ:1:000000000-A2Y1L:1:1101:18106:2444 2:N:0:NAAGGCGATAGATCGC +GAGTTACTATTACAGAGTGGAGCTAATGTACTGGCAGTTGACTGCAAAAGAAATGCTCCAATTCATGTTGCATGTGCAAATATGAGCTTAGAGTGTTTAAAGATAATTTTGTGCCACAAAAAATGCAACCCAAACCAACAAAATGCAGTGGGAGACACTCCACTCCACACCTTATGCAGTTTGGGGACTTGTGATATGAGAATACTAC ++ +?????BBBDDDDDDDDGCFGFGIIIIIHFHIIIIHIHFG=EHHIGIIIIFHIHDGHGHHHIHIH=CGHGGHFHHHFHFGHHFH/ACDFGG?FE?CDFFHHHHHIIHFHHI>CEDGFHHHHHHHHDFHHFHHHFFAFFGGGGGGEDEG>>DACC;?EGG>CEEA>AEACCEE?:C::CC:::C:CE/<@@@@@@>@CCCE#6 +@MISEQ:1:000000000-A2Y1L:1:1101:18851:2442 1:N:0:NAAGGCGATAGATCGC +GGTATCCCCCGGCAGTGAGGATGGAGCCATGGTCTGCATCATACTCACCGTAGGTGAGAATATCCACGTCCTTCGACTCCTGGGTGCCGTCTATGGTGCCCTCTGTTACCAGGCAGTGACGGAGGACATGGTGAGGTTTCAGTACCTCTGGCCCGGCCTGG ++ +??,D?)8 +@MISEQ:1:000000000-A2Y1L:1:1101:15290:2442 1:N:0:NAAGGCGATAGATCGC +AAAATAATCCTAAAAAATAACCTCTATGCCGCCGAACGCTCCGCCTCTATCTTCGTAAAAACTATCTTCTCCTCCTCACCTCCATAATCAAGCATCAAGCGATCGCCCTCCGCCAACTCACCCCGCAAAATCTTATCCGCTAGCGGATTCTCAATCTCCGTCTGAATGACCCGCCTCAGCGGCCGCGCCCCATAAACCGAATCAAATCCACGCCTGTCTCTTA ++ +?????BBBDDDDDDDDGGGGGGIIIHHFFHHHHHHHHHHEHHEHHHHHIIHHHHHFEHIIIHHIHHIHIHIIIIIHHHHHHHHHHHHHHHHDHHHHHHHHGEDFGGGGGGG;CEGEGCEGGGGG8>GGGGEGGEECEGGGGD8EDGGAEGEEGGCE:CGG8CEEGG???CEEDG.8>EEFF<<<2>D?DEEE*:C?AA<>8AEFCEE:?C?EEE?CEFEE0?:E?ACEECD8>EE>)8>E:CEEEEEED.)?AE??A?:A?*??:C0?CCE?AAA:88.88?::C:C?*8 +@MISEQ:1:000000000-A2Y1L:1:1101:17903:2450 1:N:0:TAAGGCGATAGATCGC +GTGCAGGGGG ++ +=5===<>+5< diff --git a/tools/trimmomatic/test-data/trimmomatic_se_out1.fastq.gz b/tools/trimmomatic/test-data/trimmomatic_se_out1.fastq.gz new file mode 100644 index 0000000000000000000000000000000000000000..6fadae3de812df4a9c7fbfda35311f52926c9671 GIT binary patch literal 893 zcmV-@1A_b?iwFP!00000|BY44uG=^a-RCO`%<87?oy0c}M{z7OluQMf2~bp<`Trm3 zIg|qwEiw%)%alZs5)VmF|K7gmZ($oY5Be(If7^dBv)yjcow~y=bi0p_Pup-0n{XE~ zQH=;^CP^ni8!-d*BRrt@mo85EH9f=>cxRD%i?_QHL7NhGpMDtrgN} za1(^w3?~Jesb16_X~xS8Uj|<0LCt-lS<#NY=8Ia%<)}r=Y(k}*Zi}vMmk-QB-pjC5T$2GWlj&V%!t$zXe?zH(| z97H_8=|PcY;Jy&|rk4j#5Ar_kK5xR0A$MzoiO9G2|xp`3)tf>PhpxDcw;TCo z;U`KD#&VjQUOQ{HZ0Jb+$R0e=Bb)k+0|-Pg)EsaZR0QxiBfdkzP}hXl-upqgh0AO0 z24nrm>i{{llLkIfUxj6HH1Fau2(BDyF6n;3G$Un6Vkv2T1s zAGG}m()$|}$0#vKM6?9mM3{vx34QgxZx=DQ1j T2*db!KdgQLF55A#f(QTr%jvXj literal 0 HcmV?d00001 diff --git a/tools/trimmomatic/test-data/trimmomatic_se_out1.log b/tools/trimmomatic/test-data/trimmomatic_se_out1.log new file mode 100644 index 00000000000..84ed576c66b --- /dev/null +++ b/tools/trimmomatic/test-data/trimmomatic_se_out1.log @@ -0,0 +1,10 @@ +MISEQ:1:000000000-A2Y1L:1:1101:19264:2433 1:N:0:NAAGGCGATAGATCGC 22 0 22 228 +MISEQ:1:000000000-A2Y1L:1:1101:18667:2435 1:N:0:NAAGGCGATAGATCGC 22 0 22 228 +MISEQ:1:000000000-A2Y1L:1:1101:17523:2436 1:N:0:NAAGGCGATAGATCGC 113 0 113 137 +MISEQ:1:000000000-A2Y1L:1:1101:15489:2437 1:N:0:NAAGGCGATAGATCGC 22 0 22 228 +MISEQ:1:000000000-A2Y1L:1:1101:18851:2442 1:N:0:NAAGGCGATAGATCGC 161 0 161 89 +MISEQ:1:000000000-A2Y1L:1:1101:15290:2442 1:N:0:NAAGGCGATAGATCGC 223 0 223 27 +MISEQ:1:000000000-A2Y1L:1:1101:18106:2444 1:N:0:NAAGGCGATAGATCGC 0 0 0 0 +MISEQ:1:000000000-A2Y1L:1:1101:15892:2446 1:N:0:NAAGGCGATAGATCGC 236 0 236 14 +MISEQ:1:000000000-A2Y1L:1:1101:17903:2450 1:N:0:TAAGGCGATAGATCGC 10 0 10 240 +MISEQ:1:000000000-A2Y1L:1:1101:15113:2451 1:N:0:TAAGGCGATAGATCGC 0 0 0 0 diff --git a/tools/trimmomatic/test-data/trimmomatic_se_out2.err b/tools/trimmomatic/test-data/trimmomatic_se_out2.err new file mode 100644 index 00000000000..dc66ba2b282 --- /dev/null +++ b/tools/trimmomatic/test-data/trimmomatic_se_out2.err @@ -0,0 +1,4 @@ +TrimmomaticSE: Started with arguments: + -threads 1 fastq_in.fastqsanger fastq_out.fastqsanger SLIDINGWINDOW:4:20 -trimlog trimlog -phred33 +Input Reads: 10 Surviving: 8 (80.00%) Dropped: 2 (20.00%) +TrimmomaticSE: Completed successfully diff --git a/tools/trimmomatic/test-data/trimmomatic_se_out2.fastq b/tools/trimmomatic/test-data/trimmomatic_se_out2.fastq new file mode 100644 index 00000000000..bc06f5ccf12 --- /dev/null +++ b/tools/trimmomatic/test-data/trimmomatic_se_out2.fastq @@ -0,0 +1,40 @@ +@MISEQ:1:000000000-A2Y1L:1:1101:19264:2433 1:N:0:NAAGGCGATAGATCGC +AGATAGCCGA ++ +?????BBB@B +@MISEQ:1:000000000-A2Y1L:1:1101:18667:2435 1:N:0:NAAGGCGATAGATCGC +ATATATTCAT ++ +?????BBBDD +@MISEQ:1:000000000-A2Y1L:1:1101:17523:2436 1:N:0:NAAGGCGATAGATCGC +CATCACTACC ++ +?<,/<@@ +@MISEQ:1:000000000-A2Y1L:1:1101:18851:2442 1:N:0:NAAGGCGATAGATCGC +GGTATCCCCC ++ +??,+5< +@MISEQ:1:000000000-A2Y1L:1:1101:15113:2451 1:N:0:TAAGGCGATAGATCGC +TCTCAGATGA ++ +=,,<=>>>@@ diff --git a/tools/trimmomatic/trimmomatic.xml b/tools/trimmomatic/trimmomatic.xml new file mode 100644 index 00000000000..ef2b21b1be0 --- /dev/null +++ b/tools/trimmomatic/trimmomatic.xml @@ -0,0 +1,529 @@ + + flexible read trimming tool for Illumina NGS data + + trimmomatic_macros.xml + + + trimmomatic + + coreutils + + &1 | tee trimmomatic.log && + if [ -z "\$(tail -1 trimmomatic.log | grep "Completed successfully")" ]; then echo "Trimmomatic did not finish successfully" >&2 ; exit 1 ; fi + && + #if $readtype.single_or_paired == "pair_of_files" + mv fastq_out_r1_paired.'$r1_ext' '${fastq_out_r1_paired}' && + mv fastq_out_r1_unpaired.'$r1_ext' '${fastq_out_r1_unpaired}' && + mv fastq_out_r2_paired.'$r2_ext' '${fastq_out_r2_paired}' && + mv fastq_out_r2_unpaired.'$r2_ext' '${fastq_out_r2_unpaired}' + #elif $readtype.single_or_paired == "collection" + mv fastq_out_r1_paired.'$r1_ext' '${fastq_out_paired.forward}' && + mv fastq_out_r1_unpaired.'$r1_ext' '${fastq_out_unpaired.forward}' && + mv fastq_out_r2_paired.'$r2_ext' '${fastq_out_paired.reverse}' && + mv fastq_out_r2_unpaired.'$r2_ext' '${fastq_out_unpaired.reverse}' + #else + mv fastq_out.'$fastq_in.extension' '${fastq_out}' + #end if + ]]> + + #set from_text_area = '' +#if str( $illuminaclip.do_illuminaclip ) == "yes" and str( $illuminaclip.adapter_type.standard_or_custom ) == "custom": +#set from_text_area = $illuminaclip.adapter_type.adapter_text +#end if +${from_text_area} + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + readtype['single_or_paired'] == "pair_of_files" + + + readtype['single_or_paired'] == "pair_of_files" + + + readtype['single_or_paired'] == "pair_of_files" + + + readtype['single_or_paired'] == "pair_of_files" + + + readtype['single_or_paired'] == 'se' + + + readtype['single_or_paired'] == "collection" + + + + + readtype['single_or_paired'] == "collection" + + + + + output_logs + + + output_err + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 10.1093/bioinformatics/btu170 + + diff --git a/tools/trimmomatic/trimmomatic_macros.xml b/tools/trimmomatic/trimmomatic_macros.xml new file mode 100644 index 00000000000..e6fd28adc09 --- /dev/null +++ b/tools/trimmomatic/trimmomatic_macros.xml @@ -0,0 +1,10 @@ + + + if [ -z "\$TRIMMOMATIC_JAR_PATH" ]; then export TRIMMOMATIC_JAR_PATH=\$(dirname \$(readlink -e \$(which trimmomatic))); fi + if [ -z "\$TRIMMOMATIC_ADAPTERS_PATH" ]; then export TRIMMOMATIC_ADAPTERS_PATH=\$(dirname \$(readlink -e \$(which trimmomatic)))/adapters; fi + 0.39 + 0 + From f6a26f02ccd19d0c35ea002c92bf5d5d233e5eee Mon Sep 17 00:00:00 2001 From: Peter Briggs Date: Wed, 3 Jan 2024 12:24:25 +0000 Subject: [PATCH 02/12] trimmomatic: add initial .shed.yml file. --- tools/trimmomatic/.shed.yml | 11 +++++++++++ 1 file changed, 11 insertions(+) create mode 100644 tools/trimmomatic/.shed.yml diff --git a/tools/trimmomatic/.shed.yml b/tools/trimmomatic/.shed.yml new file mode 100644 index 00000000000..7cde6b41fde --- /dev/null +++ b/tools/trimmomatic/.shed.yml @@ -0,0 +1,11 @@ +name: trimmomatic +owner: iuc +description: A flexible read trimming tool for Illumina NGS data +homepage_url: http://www.usadellab.org/cms/?page=trimmomatic +long_description: | + Trimmomatic performs a variety of useful trimming tasks for + illumina paired-end and single ended data.8 +remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/main/packages/trimmomatic +type: unrestricted +categories: +- Fastq Manipulation From 4fb171f4fca7b656441a9a0f9bc67ef3da99e27e Mon Sep 17 00:00:00 2001 From: Peter Briggs Date: Mon, 8 Jan 2024 10:09:29 +0000 Subject: [PATCH 03/12] trimmomatic: set tool owner to 'pjbriggs' in .shed.yml file. --- tools/trimmomatic/.shed.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tools/trimmomatic/.shed.yml b/tools/trimmomatic/.shed.yml index 7cde6b41fde..a56a59ca15a 100644 --- a/tools/trimmomatic/.shed.yml +++ b/tools/trimmomatic/.shed.yml @@ -1,5 +1,5 @@ name: trimmomatic -owner: iuc +owner: pjbriggs description: A flexible read trimming tool for Illumina NGS data homepage_url: http://www.usadellab.org/cms/?page=trimmomatic long_description: | From 58050918ebf00c0e782d4371a395f40f55a6e6e0 Mon Sep 17 00:00:00 2001 From: Peter Briggs Date: Mon, 8 Jan 2024 11:15:33 +0000 Subject: [PATCH 04/12] trimmomatic: bump the Galaxy tool version to 'galaxy1'. --- tools/trimmomatic/trimmomatic_macros.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tools/trimmomatic/trimmomatic_macros.xml b/tools/trimmomatic/trimmomatic_macros.xml index e6fd28adc09..f5dcad5065a 100644 --- a/tools/trimmomatic/trimmomatic_macros.xml +++ b/tools/trimmomatic/trimmomatic_macros.xml @@ -6,5 +6,5 @@ if [ -z "\$TRIMMOMATIC_JAR_PATH" ]; then export TRIMMOMATIC_JAR_PATH=\$(dirname \$(readlink -e \$(which trimmomatic))); fi if [ -z "\$TRIMMOMATIC_ADAPTERS_PATH" ]; then export TRIMMOMATIC_ADAPTERS_PATH=\$(dirname \$(readlink -e \$(which trimmomatic)))/adapters; fi 0.39 - 0 + 1 From ddbb0db11911c7967b957132d17de91d993672a4 Mon Sep 17 00:00:00 2001 From: Peter Briggs Date: Mon, 8 Jan 2024 11:26:44 +0000 Subject: [PATCH 05/12] trimmomatic: update 'credits' in tool help, to say it's part of the IUC repo. --- tools/trimmomatic/trimmomatic.xml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/tools/trimmomatic/trimmomatic.xml b/tools/trimmomatic/trimmomatic.xml index ef2b21b1be0..3daf38dca01 100644 --- a/tools/trimmomatic/trimmomatic.xml +++ b/tools/trimmomatic/trimmomatic.xml @@ -499,9 +499,11 @@ reads. **Credits** -This Galaxy tool has been developed within the Bioinformatics Core Facility at the -University of Manchester, with contributions from Peter van Heusden, Marius -van den Beek, Jelle Scholtalbers, Charles Girardot, Matthias Bernt and Cristóbal Gallardo. +This Galaxy tool was originally developed within the Bioinformatics Core +Facility at the University of Manchester, with contributions from Peter van +Heusden, Marius van den Beek, Jelle Scholtalbers, Charles Girardot, Matthias +Bernt and Cristóbal Gallardo. It is now maintained as part of the IUC tool +collection. It runs the Trimmomatic program which has been developed within Bjorn Usadel's group at RWTH Aachen university. From 7490a900b79aad5451d9524a04539c973ab6d834 Mon Sep 17 00:00:00 2001 From: Peter Briggs Date: Mon, 8 Jan 2024 11:28:40 +0000 Subject: [PATCH 06/12] trimmomatic: update/overhaul README.rst associated with the tool. --- tools/trimmomatic/README.rst | 149 ++++++++++++++--------------------- 1 file changed, 59 insertions(+), 90 deletions(-) diff --git a/tools/trimmomatic/README.rst b/tools/trimmomatic/README.rst index fa40fc97a29..9639b7e7dd3 100644 --- a/tools/trimmomatic/README.rst +++ b/tools/trimmomatic/README.rst @@ -12,13 +12,6 @@ The reference for Trimmomatic is: - Bolger, A.M., Lohse, M., & Usadel, B. (2014). Trimmomatic: A flexible trimmer for Illumina Sequence Data. Bioinformatics, btu170. -Automated installation -====================== - -Installation via the Galaxy Tool Shed will take care of installing the tool wrapper -and the trimmomatic program and data, and setting the appropriate environment -variables. - Controlling the available memory ================================ @@ -32,107 +25,83 @@ line like the below should be added: This will set the environment variable ``_JAVA_OPTIONS`` to ``-Xmx6G``. -Manual Installation -=================== - -There are two files to install: - -- ``trimmomatic.xml`` (the Galaxy tool definition) -- ``trimmomatic.sh`` (the shell script wrapper) - -The suggested location is in a ``tools/trimmomatic/`` folder. You will then -need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool -by adding the line: - - - -You will also need to install trimmomatic 0.38: - -- http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.38.zip - -The tool wrapper uses the following environment variables in order to find the -appropriate files: - -- ``TRIMMOMATIC_DIR`` should point to the directory holding the - ``trimmomatic-0.36.jar`` file -- ``TRIMMOMATIC_ADAPTERS_DIR`` should point to the directory holding the adapter - sequence files (used by the ``ILLUMINACLIP`` option). - -If you want to run the functional tests, copy the sample test files under -sample test files under Galaxy's ``test-data/`` directory. Then: - - ./run_tests.sh -id trimmomatic - -You will need to have set the environment variables above. - History ======= -========== ====================================================================== -Version Changes ----------- ---------------------------------------------------------------------- -0.39 - Update to Trimmomatic 0.39. -0.38.1 - Bug fix: add dependency on ``coreutils`` so that ``readlink -e`` is - supported across both Linux and MacOS platforms. -0.38.0 - Update to Trimmomatic 0.38. -0.36.6 - Added trimlog and log outputs; add support for ``fastqillumina`` - and ``fastqsolexa`` input types -0.36.5 - Remove tool_dependencies.xml and always use conda to resolve tool - dependencies -0.36.4 - Add option to provide custom adapter sequences for ILLUMINACLIP - - Add options ``minAdapterLength`` and ``keepBothReads`` for ILLUMINACLIP - in palindrome mode -0.36.3 - Fix naming of output collections. Instead of all outputs being called - "Trimmomatic on collection NN" these will now be called "Trimmomatic - on collection NN: paired" or "Trimmomatic on collection NN: unpaired". -0.36.2 - Support fastqsanger.gz datatype. If fastqsanger.gz is used as input - the output will also be fastqsanger.gz. - - Use $_JAVA_OPTIONS to customize memory requirements. -0.36.1 - Reimplement to work with bioconda Trimmomatic 0.36 (toolshed version - is still supported for now). -0.36.0 - Update to Trimmomatic 0.36. -0.32.4 - Add support for ``AVGQUAL`` and ``MAXINFO`` operations. -0.32.3 - Add support for FASTQ R1/R2 pairs using dataset collections (input - can be dataset collection, in which case tool also outputs dataset - collections) and improve order and naming of output files. -0.32.2 - Use ``GALAXY_SLOTS`` to set the appropriate number of threads to use - at runtime (default is 6). -0.32.1 - Remove ``trimmomatic_adapters.loc.sample`` and hard-code adapter files - into the XML wrapper. -0.32.0 - Add tool_dependencies.xml to install Trimmomatic 0.32 automatically and - set the environment. - - Update tool versioning to use Trimmomatic version number (i.e. ``0.32``) - with tool iteration appended (i.e. ``.1``). -0.0.4 - Specify '-threads 6' in section. -0.0.3 - Added MINLEN, LEADING, TRAILING, CROP and HEADCROP options of trimmomatic. -0.0.2 - Updated ILLUMINACLIP option to use standard adapter sequences (requires - the trimmomatic_adapters.loc file; sample version is supplied) plus - cosmetic updates to wording and help text for some options. -0.0.1 - Initial version -========== ====================================================================== +============== ================================================================ +Version Changes +-------------- ---------------------------------------------------------------- +0.39+galaxy1 - Relocated to the ``tools-iuc`` repository +0.39 - Update to Trimmomatic 0.39. +0.38.1 - Bug fix: add dependency on ``coreutils`` so that + ``readlink -e`` is supported across both Linux and MacOS + platforms. +0.38.0 - Update to Trimmomatic 0.38. +0.36.6 - Added trimlog and log outputs; add support for + ``fastqillumina`` and ``fastqsolexa`` input types +0.36.5 - Remove tool_dependencies.xml and always use conda to resolve + tool dependencies +0.36.4 - Add option to provide custom adapter sequences for + ILLUMINACLIP + - Add options ``minAdapterLength`` and ``keepBothReads`` for + ILLUMINACLIP in palindrome mode +0.36.3 - Fix naming of output collections. Instead of all outputs being + called "Trimmomatic on collection NN" these will now be called + "Trimmomatic on collection NN: paired" or "Trimmomatic on + collection NN: unpaired". +0.36.2 - Support fastqsanger.gz datatype. If fastqsanger.gz is used as + input the output will also be fastqsanger.gz. + - Use $_JAVA_OPTIONS to customize memory requirements. +0.36.1 - Reimplement to work with bioconda Trimmomatic 0.36 (toolshed + version is still supported for now). +0.36.0 - Update to Trimmomatic 0.36. +0.32.4 - Add support for ``AVGQUAL`` and ``MAXINFO`` operations. +0.32.3 - Add support for FASTQ R1/R2 pairs using dataset collections + (input can be dataset collection, in which case tool also + outputs dataset collections) and improve order and naming of + output files. +0.32.2 - Use ``GALAXY_SLOTS`` to set the appropriate number of threads + to use at runtime (default is 6). +0.32.1 - Remove ``trimmomatic_adapters.loc.sample`` and hard-code + adapter files into the XML wrapper. +0.32.0 - Add tool_dependencies.xml to install Trimmomatic 0.32 + automatically and set the environment. + - Update tool versioning to use Trimmomatic version number (i.e. + ``0.32``) with tool iteration appended (i.e. ``.1``). +0.0.4 - Specify '-threads 6' in section. +0.0.3 - Added MINLEN, LEADING, TRAILING, CROP and HEADCROP options of + trimmomatic. +0.0.2 - Updated ILLUMINACLIP option to use standard adapter sequences + (requires the trimmomatic_adapters.loc file; sample version is + supplied) plus cosmetic updates to wording and help text for + some options. +0.0.1 - Initial version +============== ================================================================ Credits ======= -This wrapper has been developed and is maintained by Peter Briggs (@pjbriggs). +This wrapper was originally developed and maintained by Peter Briggs +(@pjbriggs). Peter van Heusden (@pvanheus) and Marius van den Beek (@mvdbeek) contributed support for gz compressed FastQ files. Charles Girardot (@cgirardot) and -Jelle Scholtalbers (@scholtalbers) contributed additional options to ILLUMINACLIP. +Jelle Scholtalbers (@scholtalbers) contributed additional options to +ILLUMINACLIP. Matthias Bernt (@bernt-matthias) added log and trimlog output. Nicola Soranzo (@nsoranzo) suggested using coreutils to enable cross-platform support across Linux and MacOS. Cristóbal Gallardo (@gallardoalba) updated Trimmomatic up to version 0.39. +Peter Briggs wishes to acknowledge the help from Matthia Bernt +(@bernt-matthias) with relocating the tool in the IUC tool repository, +and the IUC for taking on responsibility for the tool. Developers ========== -This tool is developed on the following GitHub repository: -https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/trimmomatic - -For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I use -the ``package_trimmomatic.sh`` script. - +The Trimmomatic tool is now maintained as part of the ``tools-iuc`` repository +on GitHub: +https://github.com/galaxyproject/tools-iuc/tools/tree/main/trimmomatic Licence (MIT) ============= From 1970dc801423bbe8185264938c54531ee11291c3 Mon Sep 17 00:00:00 2001 From: Peter Briggs Date: Mon, 8 Jan 2024 16:07:19 +0000 Subject: [PATCH 07/12] Add 'pjbriggs' as owner for trimmomatic tool wrapper. --- .github/CODEOWNERS | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS index 616d6d13841..cb34d2e65bf 100644 --- a/.github/CODEOWNERS +++ b/.github/CODEOWNERS @@ -28,4 +28,5 @@ /tools/seurat/ @nsoranzo /tools/sickle/ @nsoranzo /tools/stringtie/ @nsoranzo +/tools/trimmomatic/ @pjbriggs /tools/ucsc_tools/ @nsoranzo From 11b9c8ec1e2b3affe1ff6edc6cbe6a2fe50cd084 Mon Sep 17 00:00:00 2001 From: Peter Briggs Date: Mon, 8 Jan 2024 16:18:24 +0000 Subject: [PATCH 08/12] trimmomatic: update 'coreutils' version in requirements (needed for conda). --- tools/trimmomatic/trimmomatic.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tools/trimmomatic/trimmomatic.xml b/tools/trimmomatic/trimmomatic.xml index 3daf38dca01..a5bcc76e125 100644 --- a/tools/trimmomatic/trimmomatic.xml +++ b/tools/trimmomatic/trimmomatic.xml @@ -10,7 +10,7 @@ See similar fix for snpSift https://github.com/galaxyproject/tools-iuc/commit/b5e2080a7afdea9fa476895693b6115824c6fbb9 --> - coreutils + coreutils Date: Mon, 8 Jan 2024 16:20:28 +0000 Subject: [PATCH 09/12] trimmomatic: add 'num_expected_outputs' attribute to tests. --- tools/trimmomatic/trimmomatic.xml | 28 ++++++++++++++-------------- 1 file changed, 14 insertions(+), 14 deletions(-) diff --git a/tools/trimmomatic/trimmomatic.xml b/tools/trimmomatic/trimmomatic.xml index a5bcc76e125..080b41f2ed6 100644 --- a/tools/trimmomatic/trimmomatic.xml +++ b/tools/trimmomatic/trimmomatic.xml @@ -252,7 +252,7 @@ ${from_text_area} - + @@ -265,14 +265,14 @@ ${from_text_area} - + - + @@ -283,7 +283,7 @@ ${from_text_area} - + @@ -294,7 +294,7 @@ ${from_text_area} - + @@ -305,7 +305,7 @@ ${from_text_area} - + @@ -316,7 +316,7 @@ ${from_text_area} - + @@ -324,7 +324,7 @@ ${from_text_area} - + @@ -343,7 +343,7 @@ ${from_text_area} - + @@ -362,7 +362,7 @@ ${from_text_area} - + @@ -370,7 +370,7 @@ ${from_text_area} - + @@ -379,7 +379,7 @@ ${from_text_area} - + @@ -392,7 +392,7 @@ ${from_text_area} - + @@ -408,7 +408,7 @@ ${from_text_area} - + From 2291a1c59d2983e98cc89bfc1f89aaf24578f431 Mon Sep 17 00:00:00 2001 From: Peter Briggs Date: Thu, 11 Jan 2024 15:04:18 +0000 Subject: [PATCH 10/12] trimmomatic: use 're_match' to handle variable threads in tests using 'err_file'. --- tools/trimmomatic/test-data/trimmomatic_se_out1.err.re_match | 5 +++++ tools/trimmomatic/test-data/trimmomatic_se_out2.err.re_match | 4 ++++ tools/trimmomatic/trimmomatic.xml | 4 ++-- 3 files changed, 11 insertions(+), 2 deletions(-) create mode 100644 tools/trimmomatic/test-data/trimmomatic_se_out1.err.re_match create mode 100644 tools/trimmomatic/test-data/trimmomatic_se_out2.err.re_match diff --git a/tools/trimmomatic/test-data/trimmomatic_se_out1.err.re_match b/tools/trimmomatic/test-data/trimmomatic_se_out1.err.re_match new file mode 100644 index 00000000000..acf37d677a5 --- /dev/null +++ b/tools/trimmomatic/test-data/trimmomatic_se_out1.err.re_match @@ -0,0 +1,5 @@ +TrimmomaticSE: Started with arguments: + -threads [0-9]+ fastq_in\.fastqsanger fastq_out\.fastqsanger SLIDINGWINDOW:4:20 -trimlog trimlog +Quality encoding detected as phred33 +Input Reads: 10 Surviving: 8 \(80\.00%\) Dropped: 2 \(20\.00%\) +TrimmomaticSE: Completed successfully diff --git a/tools/trimmomatic/test-data/trimmomatic_se_out2.err.re_match b/tools/trimmomatic/test-data/trimmomatic_se_out2.err.re_match new file mode 100644 index 00000000000..fc7882a8cbf --- /dev/null +++ b/tools/trimmomatic/test-data/trimmomatic_se_out2.err.re_match @@ -0,0 +1,4 @@ +TrimmomaticSE: Started with arguments: + -threads [0-9]+ fastq_in\.fastqsanger fastq_out\.fastqsanger SLIDINGWINDOW:4:20 -trimlog trimlog -phred33 +Input Reads: 10 Surviving: 8 \(80\.00%\) Dropped: 2 \(20\.00%\) +TrimmomaticSE: Completed successfully diff --git a/tools/trimmomatic/trimmomatic.xml b/tools/trimmomatic/trimmomatic.xml index 080b41f2ed6..80b999d5d08 100644 --- a/tools/trimmomatic/trimmomatic.xml +++ b/tools/trimmomatic/trimmomatic.xml @@ -263,7 +263,7 @@ ${from_text_area} - + @@ -420,7 +420,7 @@ ${from_text_area} - + Date: Thu, 11 Jan 2024 15:22:20 +0000 Subject: [PATCH 11/12] trimmomatic: change 'do_illuminaclip' from 'boolean' to 'select' (fix linting error). --- tools/trimmomatic/trimmomatic.xml | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/tools/trimmomatic/trimmomatic.xml b/tools/trimmomatic/trimmomatic.xml index 80b999d5d08..06f031857ba 100644 --- a/tools/trimmomatic/trimmomatic.xml +++ b/tools/trimmomatic/trimmomatic.xml @@ -38,7 +38,7 @@ SE -threads \${GALAXY_SLOTS:-6} fastq_in.'$fastq_in.extension' fastq_out.'$fastq_in.extension' #end if ## ILLUMINACLIP option - #if $illuminaclip.do_illuminaclip + #if $illuminaclip.do_illuminaclip == "yes" #if $illuminaclip.adapter_type.standard_or_custom == "custom" #if $readtype.single_or_paired in ["pair_of_files","collection"] ILLUMINACLIP:$adapter_file_from_text:$illuminaclip.seed_mismatches:$illuminaclip.palindrome_clip_threshold:$illuminaclip.simple_clip_threshold:$illuminaclip.min_adapter_len:$illuminaclip.keep_both_reads @@ -134,7 +134,10 @@ ${from_text_area} - + + + + @@ -384,7 +387,7 @@ ${from_text_area} - + @@ -397,7 +400,7 @@ ${from_text_area} - + From 3219c062d4e03dcef710dde37ba455b486dde878 Mon Sep 17 00:00:00 2001 From: Peter Briggs Date: Thu, 11 Jan 2024 16:22:56 +0000 Subject: [PATCH 12/12] trimmomatic: remove @pjbriggs from CODEOWNERS (as doesn't have write access). --- .github/CODEOWNERS | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS index cb34d2e65bf..616d6d13841 100644 --- a/.github/CODEOWNERS +++ b/.github/CODEOWNERS @@ -28,5 +28,4 @@ /tools/seurat/ @nsoranzo /tools/sickle/ @nsoranzo /tools/stringtie/ @nsoranzo -/tools/trimmomatic/ @pjbriggs /tools/ucsc_tools/ @nsoranzo