Galaxy |

Changeset 1:ba271365095e (2017-10-11)

Previous changeset 0:9407a9eaad22 (2017-09-27) Next changeset 2:09ebaa5192ab (2017-10-27)

Commit message:
planemo upload for repository https://github.com/phac-nml/bio_hansel commit a0204b99a722240fe9b03b78a0786b30aa8ecc96

modified:
bio_hansel.xml

added:
test-data/SRR5646583_SMALL_1.fastq
test-data/SRR5646583_SMALL_2.fastq

diff -r 9407a9eaad22 -r ba271365095e bio_hansel.xml
--- a/bio_hansel.xml Wed Sep 27 11:50:41 2017 -0400
+++ b/bio_hansel.xml Wed Oct 11 12:35:50 2017 -0400

[

b'@@ -1,33 +1,29 @@\n-<tool id="bio_hansel" name="Hansel - Salmonella Subtyping" version="0.1.0">\n+<tool id="bio_hansel" name="Salmonella Subtyping" version="0.1.2">\n+ <description>Genome assemblies and/or whole-genome sequencing readset</description>\n <requirements>\n <requirement type="package" version="0.1.0">bio_hansel</requirement>\n <requirement type="package" version="17.2.0">attrs</requirement>\n </requirements>\n <command detect_errors="exit_code"><![CDATA[\n- ## Variables to be set.\n- #set outputResultsName = \'results.tab\'\n- #set outputMatchResultsName = \'match_results.tab\'\n- #set verboseDebuggingLevel = \'-vvv\'\n+ ## Preparing file input.\n+ #if $data_type.type == "paired":\n \n- ## Preparing file input.\n- #if $single_or_paired.type == "paired":\n+ ln -s \'$data_type.fastq_input1\' \'$data_type.fastq_input1.name\' &&\n+ ln -s \'$data_type.fastq_input2\' \'$data_type.fastq_input2.name\' &&\n+\n+ #elif $data_type.type == "collection":\n \n- ln -s \'$single_or_paired.fastq_input1\' fast_q_paired_1.fastq &&\n- ln -s \'$single_or_paired.fastq_input2\' fast_q_paired_2.fastq &&\n-\n- #elif $single_or_paired.type == "collection":\n+ ln -s \'$data_type.fastq_input1.forward\' \'$data_type.fastq_input1.forward.name\' &&\n+ ln -s \'$data_type.fastq_input1.reverse\' \'$data_type.fastq_input1.reverse.name\' &&\n \n- ln -s \'$single_or_paired.fastq_input1.forward\' fast_q_paired_1.fastq &&\n- ln -s \'$single_or_paired.fastq_input1.reverse\' fast_q_paired_2.fastq &&\n+ #elif $data_type.type == "single":\n \n- #elif $single_or_paired.type == "single":\n-\n- #if $single_or_paired.fastq_input1.is_of_type(\'fastqsanger\') or $single_or_paired.fastq_input1.is_of_type(\'fastq\'):\n- ln -s \'$single_or_paired.fastq_input1\' fast_q_single.fastq &&\n+ #if $data_type.fastq_input1.is_of_type(\'fastqsanger\') or $data_type.fastq_input1.is_of_type(\'fastq\'):\n+ ln -s \'$data_type.fastq_input1\' \'$data_type.fastq_input1.name\' &&\n #end if\n \n- #if $single_or_paired.fastq_input1.is_of_type(\'fasta\'):\n- ln -s \'$single_or_paired.fastq_input1\' fast_a_single.fasta &&\n+ #if $data_type.fastq_input1.is_of_type(\'fasta\'):\n+ ln -s \'$data_type.fastq_input1\' \'$data_type.fastq_input1.name\' &&\n #end if\n \n #end if\n@@ -36,11 +32,10 @@\n ## Checking for custom scheme.\n #if $type_of_scheme.scheme_type == "custom":\n #if $type_of_scheme.scheme_input.is_of_type(\'fasta\'):\n- ln -s \'$type_of_scheme.scheme_input\' custom_scheme.fasta &&\n+ ln -s \'$type_of_scheme.scheme_input\' \'$type_of_scheme.scheme_input.name\' &&\n #end if\n #end if\n \n-\n ## Start the actual command here\n hansel \n \n@@ -53,7 +48,7 @@\n #elif $type_of_scheme.scheme_type == "enteritidis":\n enteritidis\n #elif $type_of_scheme.scheme_type == "custom":\n- custom_scheme.fasta\n+ \'$type_of_scheme.scheme_input.name\'\n #end if\n \n \n@@ -66,29 +61,26 @@\n #end if\n \n ## Adding more parameters to the command.\n- $verboseDebuggingLevel -t "\\${GALAXY_SLOTS:-1}" -o $outputResultsName -O $outputMatchResultsName \n+ -vvv -t "\\${GALAXY_SLOTS:-1}" -o results.tab -O match_results.tab \n \n \n- ## Entering the file inputs.\n- #if $single_or_paired.type == "single":\n+ ## Entering the file inputs\n \n- #if $single_or_paired.fastq_input1.is_of_type(\'fastqsanger\') or $single_or_paired.fastq_input1.is_of_type(\'fastq\'):\n- fast_q_single.fastq\n- #end if\n+ #if $data_type.type == "single":\n+ \'$data_type.fastq_input1.name\'\n \n- #if $single_or_paired.fastq_input1.is_of_type(\'fasta\'):\n- fast_a_single.fasta\n- '..b'------+-------------------+------------+\n+ | ACGGTAAAAGAGGACTTGACTGGCGCGATTTGC | 68 | 564 | forward.fastqsanger; reverse.fastqsanger | 21097-2.2.1.1.1 | True | 2.2.1.1.1 | 21097 | True | heidelberg |\n+ +-----------------------------------+------+--------+------------------------------------------+------------------+-------------+-----------+-------------+-------------------+------------+\n+ | AACCGGCGGTATTGGCTGCGGTAAAAGTACCGT | 77 | 564 | forward.fastqsanger; reverse.fastqsanger | 157792-2.2.1.1.1 | True | 2.2.1.1.1 | 157792 | True | heidelberg |\n+ +-----------------------------------+------+--------+------------------------------------------+------------------+-------------+-----------+-------------+-------------------+------------+\n+ | CCGCTGCTTTCTGAAATCGCGCGTCGTTTCAAC | 67 | 564 | forward.fastqsanger; reverse.fastqsanger | 293728-2.2.1.1 | True | 2.2.1.1 | 293728 | True | heidelberg |\n+ +-----------------------------------+------+--------+------------------------------------------+------------------+-------------+-----------+-------------+-------------------+------------+\n+ | GAATAACAGCAAAGTGATCATGATGCCGCTGGA | 91 | 564 | forward.fastqsanger; reverse.fastqsanger | 607438-2.2.1 | True | 2.2.1 | 607438 | True | heidelberg |\n+ +-----------------------------------+------+--------+------------------------------------------+------------------+-------------+-----------+-------------+-------------------+------------+\n+ | CAGTTTTACATCCTGCGAAATGCGCAGCGTCAA | 87 | 564 | forward.fastqsanger; reverse.fastqsanger | 691203-2.2.1.1 | True | 2.2.1.1 | 691203 | True | heidelberg |\n+ +-----------------------------------+------+--------+------------------------------------------+------------------+-------------+-----------+-------------+-------------------+------------+\n+ | CAGGAGAAAGGATGCCAGGGTCAACACGTAAAC | 33 | 564 | forward.fastqsanger; reverse.fastqsanger | 944885-2.2.1.1.1 | True | 2.2.1.1.1 | 944885 | True | heidelberg |\n+ +-----------------------------------+------+--------+------------------------------------------+------------------+-------------+-----------+-------------+-------------------+------------+\n \n- GAATAACAGCAAAGTGATCATGATGCCGCTGGA 91 SRR5646583 SRR5646583_forward.fastqsanger; SRR5646583_reverse.fastqsanger 607438-2.2.1 True 2.2.1 607438 True heidelberg\n-\n- CAGTTTTACATCCTGCGAAATGCGCAGCGTCAA 87 SRR5646583 SRR5646583_forward.fastqsanger; SRR5646583_reverse.fastqsanger 691203-2.2.1.1 True 2.2.1.1 691203 True heidelberg\n+ Next 200 lines omitted.\n \n- CAGGAGAAAGGATGCCAGGGTCAACACGTAAAC 33 SRR5646583 SRR5646583_forward.fastqsanger; SRR5646583_reverse.fastqsanger 944885-2.2.1.1.1 True 2.2.1.1.1 944885 True heidelberg\n+Galaxy wrapper written by Matthew Gopez at the Public Health Agency of Canada, National Microbiology Laboratory.\n \n- [Next 200 lines omitted.]\n- \n-\n-Wrapper written by Matthew Gopez at the Public Health Agency of Canada, National Microbiology Laboratory.\n ]]></help>\n <citations>\n+ <citation type="bibtex">@ARTICLE{a1,\n+ title = {A robust genotyping scheme for *Salmonella enterica* serovar Heidelberg clones circulating in North America.},\n+ author = {Genevi\xc3\xa8ve Labb\xc3\xa9, James Robertson, Peter Kruczkiewicz, Chad R. Laing, Kim Ziebell, Aleisha R. Reimer, Lorelee Tschetter, Gary Van Domselaar, Sadjia Bekal, Kimberley A. MacDonald, Linda Hoang, Linda Chui, Danielle Daignault, Durda Slavic, Frank Pollari, E. Jane Parmley, Philip Mabon, Elissa Giang, Lok Kan Lee, Jonathan Moffat, Marisa Rankin, Joanne MacKinnon, Roger Johnson, John H.E. Nash.},\n+ url = {https://github.com/phac-nml/bio_hansel}\n+ }\n+ }</citation>\n </citations>\n </tool>\n\\ No newline at end of file\n'

diff -r 9407a9eaad22 -r ba271365095e test-data/SRR5646583_SMALL_1.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/SRR5646583_SMALL_1.fastq Wed Oct 11 12:35:50 2017 -0400

b'@@ -0,0 +1,20000 @@\n+@32927/1\n+GTGAGTAAGTTGCGCGATATTCTGCTGGATTCGGTAGTAACCAGCTCTATTGTTCTCTTACTGGTCGGCTGCTCAATGGGAATGTCATGGGCGATGACCAATGCCGATGTTCCTGAACTGATTAATGAAATGATTACCAGCGTGTCCGAAA\n++\n+AAA?ADD5F5BFGGGCCFFGGGGHHGHHHGFFFHGHGHHGCHHHHFHGHHGHEGHFHHHHHFHHHG?AEGGGEHHFGFGHGHFHFFFHHHHHGGGCHHHFGHFHHGCGFFGFGHHHHHGHHHHHBGFHHHHHGFHHFFHGHFED<FFD?ED\n+@351952/1\n+GGATTACCAGGAAGTGCTGGAAGAGTTTAACGAACATCGTAATGAGCCTGTTGATACTAACGACTTTATTGAGGCGATTGAGCGAAGTAAACGTCGCTTCCATGTTGTTGAAAATGAACAGGAGCTACTGCAAATGCTCAATGCGCCA\n++\n+CCCCCFFFBFCBFGFGFGGGGGHHHHHHHHHGGFGGGHGHHHDHHHHHHHHHHHGHHHHHHFFGGGHHHHGHFHGGGGHGHGHGGGGFGHHHGHHGGGGGGHHHHHHHHHHHHHHHGHHHHHHGHHHHHHHHHHHGHGGHHHHGGGGG\n+@37856/1\n+GCGCAGGAACGTATCGGCTTACCGTACCGGTACTGGCGAATGATGAGATGCAAATCGCGCCAGTCAAGTCCTCTTTTACCGTTACGCTGCAATCCGGCGATGCCGCCGCGCAGGTCCAGGTATCCTGTCTGCCGATTGTCCGTTATGCCAG\n++\n+CCCCCCCCFFCBG5GGGGGGGGHGGHGGGGGGGHHHHGGGGHHGHHHHHHHHGHHHGGGGGGGHHHHHHHHHHHHHHHHHGGGGGGGGGGHHHHHGGGGGGGGHGGGGGGGGGGHHHHHGGHHHHHHHHHHHHGGGGGHHHGHHGHHHHHF\n+@844740/2\n+GATCATGATTAGTCGTGCTCAAAGCGGGCCCCCACTCTACAAGTTGCAAAATTTGTTACGGGTAACTGTTATCGGTAACATTGTCCAACCGCACCATTCACGACGCAATGACCATTCGTGCCAAAAGTGAATAAGTGTGAGCTACTTCAAA\n++\n+BBBBBFFFFFFFGGFGGGGGGGGHGGGFGGGGGCFCGHHHCHHHHFFGHHFHFHHFFFHGGGEEHHHHHHHFHHGAHGHHGHFHHHHHHGGGGFFAGHFFFEGGGGCCFFFGHHHFHFFFGHHHHEHGHFFHFFF1GDFF<GHHEHFHEGG\n+@1034303/1\n+CCTGAATATTCATCATCAAACTACCGTCGCCGGAAAAACACAGCACCTTGTTGCCCGGATTCGCCAGCGCCGCGCCAATCGCCGCGGGCAGACCAAACCCCATGGTGCCCAGCCCGCCGGAAGTCAGCCACTGACGCGGACGGTTGAGCGG\n++\n+CCCCCFFFFFFFGGGGGGGGGGHHHGGGGGGGGGGGHHGHHHHHHHHHHHHHHHHHGGGGGGGGGGGGGGGGGGGGGGHHGGGGGGGGGGGGHHHHGHGGGGHGHFGFHHHHHGGGGGGGGGGGGGGGGGGGGGGGGGGGFFFFFFFFFFF\n+@79331/2\n+CCCTGGTATTCGACGTAGAGCTGCTGGATATCAAACCAGCGCCGAAAGCGGATGCTAAACCTGCCGATGCGGCTGACGCTAAAGCCGCAGATGCTGCTAAAAAATAAAAACTGAGAGCCGCCGCTTGTAATAGCGGCGGTTTTTTTTTTTT\n++\n+AAABCCFFFFFFGGGGGGGGGGHGHGGHGHHHHHHGGHHHGGGGGGGGHGGGGGGHHHHHFHHHHGGGGGGGGGGFHGGGGGHHHHGGGGGHHEGHHHHHHHHGHHHHHHGHHHHHHHHGGGGGGGGHHEHHHGGGGGG-;AEGGGAFF--\n+@234915/1\n+CACCTAATTTAACGGTCTGGTGACCAGAACCGACCGCACGCAAAAGCTTCTGAACCGATGAGGATGCTATGGGAAACACAACAATACAAACACAGAGTTTTCGTGCTGTGGATGCAGAGCAAAGCAAAAGCAAGCGCTACATTATTCCATT\n++\n+DDCDCFFFFFFFGGGGGGGGGGHHHGHHHHHGGGGGGGGGGGGGHHHHHHHHHHHHGGGGHHHHHHHHHHHHHHHHHHHHGGHHHHHHHHGHHHHHHHHHHHGHGGGHHHHHHHHHHHHHHHHGHHHHHHHHHHHFGGGGHHHHHHHHHHH\n+@238890/1\n+GTACTGGCGAATGATGAGATGCAAATCGCGCCAGTCAAGTCCTCTTTTACCGTTACGCTGCAATCCGGCGATGCCGCCGCGCAGGTCCAGGTATCCTGTCTGCCGATTGTCCGTTATGCCAGCGCGCGTCTGATGATTGACGCCCCTGCG\n++\n+BBCCCFFCCBCCGFGGGGGGGGHHHHHGGGGGGGHHHHHHHHHHHHHHHHHGGGGGGGGGGHGHHHGGGGGGGGHGGGGGGGGGGHHHHHHHHHHHHHHHHHHHGGGGGHHHGGHGHHHHHHGGGGGGGGGGHHHHHHFHHFGGGGGGGG\n+@238964/2\n+ATCGGCAGACAGGATACCTGGACCTGCGCGGCGGCATCGCCGGATTGCAGCGTAACGGTAAAAGAGGACTTGACTGGCGCGATTTGCATCTCATCATTCGCCAGTACCGGTACGGTAAGCCGATACGTTCCTGCGCTAAGATCGCTTATTG\n++\n+AAA3AB?DBFBFCGGGGGFBFFHHHHFFGGGGGCFGGHGGGGGGGGHHHGHGGGGGGGG/CGHHGHGHHHHHHGHHHHFGGFCHGHGEHGHHHHHGGEFFDGGGCFHFGC<-CAGBAEFHGG?@CCGHHH/GFECGCBCFGGF.DACEFF0\n+@135672/1\n+GAATACGGTCATATTGATATTCTGGTGAATAACGCGGGTTTGATCCGTCGTGAAGATGCGATTGATTTCACGGAAAAAGACTGGGATGACGTCATGAACCTGAACATCAAGAGCGTGTTCTTTATGTCTCAGGCGGCGGCAAAACTTTTTA\n++\n+BA@AAFBAFB?FGGGGFGGGGGHHFB4FGGFHGGGGGGEFGDHHHGHFGGGGHGHFFHHGGHHGGHFFHHHHGGGGGFGGHHHHEHHGHHGFEFHGGHHFFHHGFHHHFFFFHHC/CEFHHHHGHHHHBGHHHGCCCD-@DCAFEG0GG0.\n+@1027688/2\n+GTCTTCTATGTTACCGTCAATCAACCCGGAACTGGCCCGTATCGCTCCCGGCTTTCGTGCATTAATTATTAATGTTATTGCCGCTCCGATTCGCGATGCGCAGGTCGGAGCAATCGCGCTAAAAGAGGCCTGTCAGGCCGTATTTAACGGG\n++\n+>A11>333F33DEGGGFE1EF111BAAA000A1B0FBEEAEFG//0/A//A/EA01/0??EF211222B2222BGFH2@111/E///?EE/1>?//<<E/////0B<B@?/<0FHEECCC?CHG1.0<.<1.0/00CHC-<<.:CFHH.@.\n+@278520/1\n+GTACTGGCGAATGATGAGATGCAAATCGCGCCAGTCAAGTCCTCTTTTACCGTTACGCTGCAATCCGGCGATGCCGCCGCGCAGGTCCAGGTATCCTGTCTGCCGATTGTCCGTTATGCCAGCGCGCGTCTGATGATTGACGCCCCTGCG\n++\n+BABBBFFBBBBBGGGGGGGGGGHHHHHGGGGGGGHHGHHHHHHHHHHHHHHGGGGGFGGGGHHHHHGGGGGGGGHGGGGGGGGGGHHHHHHFGHHHGHHHHHHGGCGGGHHHGGFDEHHHHHGGGGGGGGGGHHHHHHHHHGGGGGGGGG\n+@1088790/2\n+GCTCCGGCGTGGTAACGGCATTCGCCTGCTCGCTGGTCCGCGTCGCGGCAAGCCACGGGAAAACGGTCGCATCACACTGGTCTGGTAAAGGCAGATCCGCAGTATCCTGCGGCATCACGTTGAGCCACAGCTTGCGC'..b'CGGG\n++\n+1>AAAF@>AABBFFBFEFGBGGH0A3EAEEAEA0/E///AE//0AEGCECGHHF1GEEECEGFBCGFBF111E/>EF>GBE/EECCGFCC?/CCECGCCFH??-<@?EH0EECGHH.@@-:CCG/.-@---;-;-BAA=@-@@??F?F-99\n+@47237/1\n+ATGGAATTAATTGGACTTAGTGAGAAGTGTTCATGGTGTCCCCTGCAGGAATCGAACCTGCAACTAGCCCTTAGGAGGGGCTCGTTATATCCATTTAACTAAGGGGACAACGCGGCGCCAGTATAGCGTTTTTTATTCGCCGGAGTAAGTG\n++\n+ABBBAFFFFFFFGFGGGGGGGFFHHHHHHGGHHHHFGHHHHHHHGHHHGGHGHHHHHGHHHHHHGHFHHHHHHHHHHGGGGCHFFEHHHHHHGHHHHHHHHCFEGGEGGHHFGGGGGGD/B?GFHHHGGGGGGGHHFHFGFCGDCGHHHFH\n+@1474189/1\n+TGGTAGAGCACCGGTCTCCAAAACCGGGTGTTGGGAGTTCGAGTCTCTCCGCCCCTGCCAGAAATAATCCTTAGCATCTGCTAAGGATTTTTTTTTGCCTAAAATTACCTGATTATCTGATCAGGTAATCGTAAGTTCCCTTCTTTTTCTT\n++\n+AABAB5DFBFFBGAEEEGGGGGGEEECGE?EEHHGHGEHFDGHEGHHHECEGDEEFGFCGFHEEG4FGHHHFG3FFFBGHHHGHFB3FHHFFEGGGGFHHHH11DGHHHHH0FBFG2FGHHFG<GFG2F</G0?<FF1FDDFFDGGGHBGH\n+@343204/2\n+CTAAGGAGGCATTCAGTGCGGATTCATATTCTCTTTGACCTCAATTTCCCTGGTCAGTTTCCCCATTCGTCCAGAAATGCTCCCTGCGCTCCGCCATGCGCACTAATTGTTCACAAGGCGCGTAACGAGGACCGTAAAGTGCGGCCAGGCG\n++\n+3ABBBFFA??AFGFFGGGGGGGGGCFHFHHHGHHHHHHFHHHHHFFBGHHGGHHHHHHGGHHHHHHEHHHGGGGHHHGFFHFHEHHGECFGEDEFCAGFEF?EECBGBFGHHGGFFGAGGGGDDDGGGFGGHHCCGDGFFGHGGFGCE.CC\n+@707874/1\n+GATTAAGCAACTGCTCGACGTCGGCGCGCAAACGCTTCTGATACCGATGGTGCAGAATGCCGATGAAGCGCGAAACGCCGTAGCGGCTACGCGTTATCCGCCTGCCGGTATTCGCGGCGTGGGCAGCGCGCTGGCGCGGGCATCGCGCTGG\n++\n+A>AAAFFFFF?FGFGGCG1EEF0EEEGGCGFECE/F/A1DGHGD1EFC/E@FGFEDC1@1@E>EEFGHHECEGGC@C//C</CF??//<FC/<CCCHGHCACCEAGCG--CGBC.A--@-??AEFGGG;9@@?=B-:@@@?>F/9A---;@\n+@737981/2\n+GATTAAGCAACTGCTCGACGTCGGCGCGCAAACGCTGCTGATACCGATGGTGCAGAATGCCGATGAAGCGCGAAACGCCGTAGCGGCTACGCGTTATCCGCCTGCCGGTATTCGCGGCGTGGGCAGCGCGCTGGCGCGGGCATCGCGCTTG\n++\n+>11A1F1DFFF1BGFCEGG0EE0A0E?/EE//B/A/E?1111@F1/?@??1FBBF10BBD1>E//BF1@>//></</E///<///<B@C0<//>CCEHE..<..<.<--::CH/.;@@G?A-A.B.CA@@<---9;A-----;/A-@=---\n+@156200/2\n+GTCATACAGCGGCGTTGACGGCCAGGTCTGATCAACCAGTTCGCTGCCTTCATCGCTGGCGATCAGGAATCCGCCGGGAGCGGGGCTATTCAGCGACTGGGCGGCACGCGCGGTCTCGCGAGAAATAAACGGCGCCGTTGAGGTCGTGAC\n++\n+CBABCFFFFFCCGGGGGGGGEGGGHCGHHHGHHHFGHGGFHHGGGGGHHGHHGHHGHGGGGGGGGGHHEHHHGGGGGG//DGC?FGGEHFHGFHGGFCGHHHGGGGGGGGGGGGGGGGGGFFFFFFFFFFFFFFFFF@FFFEF/BABFFF\n+@530652/2\n+ACCTTATCAGGCCTACATAAGCACTCGGCTGGTAGGCCTGATAAGCGCAGCGCCATCAGACATTGATTGGCAATTAAGCCTGTTTAGCAGCTTCTGCTGCTTTCACGATCACCGCGAAGGCGTCAGCTTTCAGAGAAGCGCCGCCTACCAG\n++\n+BBCCCFFFFFFFGGGGGGGGGGHHHHGGGGGGHHHGHHHGHHHHHHGGGGGGGGGGGHHHHHHHHHHHHGHHHHHHHHHHHHHHHHHHHHHGHHHHHHHHHHHHHHHCGFGHHGGGEGGGHGGGGGHHHHHHHGHHHGGGGGGGGGGGHHH\n+@424544/1\n+ACTACGAATACGGCGCAGCGGGCGACCGTTTTCATCAAATTCCGGTGAAATGACGTCGTTTTTCATAAAAGTGTAGTCTGCTGTGTTTGAGTTCTGAAAACGGGCATTATCCAAAGTTAGTTGCCGGATGCAAGCATGAAGCGCACTGCGG\n++\n+DDCCDDCCCDFCGGGGGGGGGGGGGGGGGGHGHHHHHHHHHHHHGGGGHHHHHHGGGGGGGGGHHHHHHHHHHHHHHHHHHHHGHHHHHHGHHHHHHHHHHGGGGGHHHHHHHHHGHHGHHHHHHGGGGGHHHHHHHHHHHGGGGGGHGGF\n+@788695/2\n+CTGCTGGTGGTTGAGCCGCCCTATGATCCTGAGTTGGACTTTCATTACCGCATCTTCAACGCCGACGGCAGTGAAGTCTCGCAGTGCGGCAATGGCGCGCGCTGTTTCGCGCGATTTGTTCGCCTGAAAGGGCTAACCAATAAACGCGACA\n++\n+BBBBBFFFF@ABGGFGGGGGGGGHHHHHHHGHHHHHHHHHHHHHHHHHHGGGGGHHHHGHGGGGGGGGGCGGHGHHGHHHHGGGGHHEGGGGHHHHGGGGGGGGGHFHGGGGGGGHGHHHHGGGGHHEHHGGGGFHHHHHGGGGGGGGGC-\n+@1399297/2\n+TTCATACAGAGATCATGACCACACATGCAACAAAAAAGCCTGCAACTCATTGAAGTTACAGGCTTTTTTAAGGTTCATGATGCATCATGAATGAATGTTTGGTGGAGCTGGCGGGAGTTGAACCCGCGTCCGAAATTCCTACATCCTCGGT\n++\n+AAABBFFFFFFCGGGGGGGGFGHGGHGHHCHHHHHHGGHGHHGHHHFFFHGHHFHGHHHHHEGHHHGHGHFHG@GFHHFHHGHFHHHHHHHHHHHHHHGHHG?FFEEFEFBE?CCCGDFFHHGFDFC@DGG@DGG.1>GG11<F0GGFGD<\n+@52275/1\n+GTCACAGTCGACGTTGGCCCCCAAATCAAGCACTACCGTTTTGCCCTTTTGCTGGTGCGGTAATACCGTCACCAACGCCGGACGCTCAATCCCCTCAAGAGGCTTGAGCAATAATTTCGCCAGCCCCATCAGCGCCCCGGTATTACCGGCG\n++\n+BBBBBFFDFA?DCEGGGGGGGGGCHHHHHGGFHHHGHGGGHGHHHHHHHHGGHHHHHH?EE?FHHHHGFFDGHHHGDGG@ECGGGDGGEHHHHGHGHHHBCHGHHCHHGFBGHHHHHHHGGGFGGGGGHHHHHGGCC?GCC-EHHEHFFG?\n+@384298/2\n+GTGTTTACACAGGAGCTGCTCCAGTTCGCTTAATGACGCCACAGTCCAGGTTGGATGAATACCCGCGGGCTGCTCGCGATGATGCGCGTTAAGCCAGCAGGTCGACAGCCCGGCGTTAATGCCGCCAAGAATATCGGATTCCGCGGTATCG\n++\n+AAABBFFFFFFFGG2GGGGGGGHHHHGGGGHGGHGHHGGGGGHHHHFHHGCGHGFHHHHHHHHHGGGGGGGGGHHGGG?FGHHHHFGGGGGEHHHHHGHFG0FCCGGGEHGGFDFCFGGGHHHFC?:@CGHBGFHGCD.EBFFGDA.9EF.\n'

diff -r 9407a9eaad22 -r ba271365095e test-data/SRR5646583_SMALL_2.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/SRR5646583_SMALL_2.fastq Wed Oct 11 12:35:50 2017 -0400