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Changeset 16:cd7e644cae1d (2021-10-08)

Previous changeset 15:084bbd8ba7b8 (2019-07-30)

Commit message:
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"

modified:
test-data/paired_collection_example_pair1_results3.fastq.gz
test-data/paired_collection_example_pair2_results3.fastq.gz
test-data/paired_collection_example_results3.txt
test-data/paired_collection_example_results3gz.txt
test-data/paired_collection_example_unpair1_results3.fastq.gz
test-data/paired_collection_example_unpair2_results3.fastq.gz
test-data/paired_example_pair1_results2.fastq.gz
test-data/paired_example_pair2_results2.fastq.gz
test-data/paired_example_results2.txt
test-data/paired_example_results2gz.txt
test-data/sanger_full_range_report_results1.txt
test-data/sanger_full_range_report_results1gz.txt
test-data/sanger_full_range_results1.fastq.gz
test-data/sanger_full_range_results2.fastq.gz
test-data/sanger_full_range_results3.fastq.gz
trim_galore.xml

added:
macros.xml
test-data/mec_reads_pair1.fastqsanger
test-data/mec_reads_pair2.fastqsanger
test-data/paired_hardtrimmed3_pair1_.fastqsanger
test-data/paired_hardtrimmed3_pair2_.fastqsanger
test-data/paired_hardtrimmed5_pair1_.fastqsanger
test-data/paired_hardtrimmed5_pair2_.fastqsanger
test-data/trimmed_polyA_reads_pair1.fastqsanger
test-data/trimmed_polyA_reads_pair2.fastqsanger

diff -r 084bbd8ba7b8 -r cd7e644cae1d macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Fri Oct 08 09:57:52 2021 +0000

[

@@ -0,0 +1,66 @@
+<macros>
+    <token name="@TOOL_VERSION@">0.6.7</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">trim-galore</requirement>
+        </requirements>
+    </xml>
+    <xml name="xrefs">
+        <xrefs>
+            <xref type="bio.tools">trim_galore</xref>
+        </xrefs>
+    </xml>
+    <xml name="adapter_trimming">
+        <conditional name="trimming">
+            <param name="trimming_select" type="select" label="Adapter sequence to be trimmed">
+                <option value="">Automatic detection</option>
+                <option value="--illumina">Illumina universal</option>
+                <option value="--nextera">Nextera transposase</option>
+                <option value="--small_rna">Illumina small RNA adapters</option>
+                <option value="user">User defined adapter sequence</option>
+            </param>
+            <when value=""/>
+            <when value="--illumina"/>
+            <when value="--nextera"/>
+            <when value="--small_rna"/>
+            <when value="user">
+                <param name="adapter" type="text" value="AGATCGGAAGAGC" label="Adapter sequence to be trimmed off">
+                    <validator type="regex" message="Adapter sequence must contain DNA characters only (A,C,T,G or N)">^[ACTGNactgn]*$</validator>
+                </param>
+                <yield/>
+            </when>
+        </conditional>
+    </xml>
+    <xml name="paired_adapter_trimming">
+        <expand macro="adapter_trimming">
+            <param name="adapter2" type="text" optional="True" value="" label="Adapter sequence to be trimmed off read 2">
+                <validator type="regex" message="Adapter sequence must contain DNA characters only (A,C,T,G or N)">^[ACTGNactgn]*$</validator>
+            </param>
+        </expand>
+        <param name="trim1" type="boolean" truevalue="--trim1" falsevalue="" checked="False" label="Trims 1 bp off every read from its 3' end." help="" />
+        <param name="three_prime_clip_R1" type="integer" value="" optional="True" label="Remove N bp from the 3' end of read 1">
+            <help>Instructs Trim Galore! to remove N bp from the 3' end of read 1 after adapter/quality trimming has been performed.
+                This may remove some unwanted bias from the 3' end that is not directly related to adapter sequence or basecall quality.
+                (--three_prime_clip_R1)</help>
+        </param>
+        <param name="three_prime_clip_R2" type="integer" value="" optional="True" label="Remove N bp from the 3' end of read 2">
+            <help>Instructs Trim Galore! to remove N bp from the 3' end of read 2 after
+                adapter/quality trimming has been performed. This may remove some unwanted bias from
+                the 3' end that is not directly related to adapter sequence or basecall quality.</help>
+        </param>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="bibtex">
+                @misc{githubTrim_Galore,
+                author = {Krueger, Felix},
+                year = {2021},
+                title = {Trim Galore},
+                publisher = {GitHub},
+                journal = {GitHub repository},
+                url = {https://https://github.com/FelixKrueger/TrimGalore.com/fenderglass/Flye}}
+            </citation>
+        </citations>
+    </xml>
+</macros>

diff -r 084bbd8ba7b8 -r cd7e644cae1d test-data/mec_reads_pair1.fastqsanger
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mec_reads_pair1.fastqsanger Fri Oct 08 09:57:52 2021 +0000

b'@@ -0,0 +1,396 @@\n+@M01368:8:000000000-A3GHV:1:1101:6911:8255/1:R1:ATCTGGTT:R2:TCGCCTTA:F1:CCTA:F2:CCGC\n+TTCAGGGCCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATT\n++\n+GGGGGGGGGGHHHHGHGHHHHHHHHHGGGGGGHHHHGHHHHHHHHHHGHHHHHHGGHGGHHHGHHHHFHHGHHHHHHHHHGHEHEFFGHHEGGCEFGGFHHHBGHHGHHHHGHFHHHGHGHGHGGCDFDDACGGGGGGGAAFFFFFFFFFBAFFFFFB;FFFFFFADDFFFFFFFFFFEFFFFFFFFFFBFFFFFFFFFFFFFFEFFFFFFFFBFEFFFFEFE;DFFFDFBFF/9BFB\n+@M01368:8:000000000-A3GHV:1:1101:14518:9998/1:R1:GTTATTAT:R2:CATCACGA:F1:TATG:F2:TGGA\n+CCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGGGATAGACCTGTGATCCATCGTGAT\n++\n+GGGGGGGGGHGGHHHHGHHHHHHHGCGHHHHHHHHHHHHHHHGGGGGHHHHHHHHHGHHGFHFE5BGEEHFGGGHHHHHHHHFBHHGGGGFHGHHFGHHHHGHHHHHHGEGGGGFHFHGEGHHGGCDGDGHGGGDGGHGGCGGGHGHHH/ACDG?.1FGCDCCGCA.CC@CDCHFHGFFGGGEBFGAB//CEFBFGG.:;D;;A0AFFFFFB..:@ABFF//;BFFFFFBF/9D:A//\n+@M01368:8:000000000-A3GHV:1:1101:18422:19051/1:R1:GTATCCGA:R2:CTACAAGC:F1:CATC:F2:ATTA\n+GGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACG\n++\n+GGGGGGGGGHHHHHHHHHHHHHHHHGHHHHHHFHHHHGGGGHHHHHHHHHGHHHHHHHHHHHHGGHGGHHHHHHHHHHHHHHHHHHHHHHHHHHHGHHHHHGCGGGHHHHHHHHHHHHHHHHHHHHHHGFDHGFHCFGGGGFGGFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF;FFFFFFFFFFFFFFFFFFFFFFFFFFFFEFBFFFFFFFFFF:FFF.\n+@M01368:8:000000000-A3GHV:1:1101:25545:21098/1:R1:ATTAATTA:R2:GCCCATAA:F1:ACAC:F2:CACT\n+CTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATAAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGGCTTATTTAAGGGGAACGGGTGGGG\n++\n+GGFEBDGEGHEGHGEGHCEGGHHCHGHHFFHHGFGAGE53FF2FAFFGDE5FFFE5GFBFGAEE1GHHHGHHHEHE3FGHF@GEGEGGHHGG3FAGFFDE?EEE3GFEGFGFGGCG?GHHHFHGGGC@DHFFHD/A<C@EGFDCGGGHFHHHEGFGHBFHG0:CEHFCHGGED.;0CEF.F99B0CFFEEFGGG0FBFBBF0F/FFBDE?/9//9B.FFBFFFFFFBF..A..;@B--\n+@M01368:8:000000000-A3GHV:1:1101:5446:12248/1:R1:AATTAACA:R2:ATCCGACA:F1:CACT:F2:TCTG\n+TAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTAT\n++\n+GGGGGGGFGHHHHHGGGGHHHHHHHHHHHHHHHHGBGHGGHGGHHHHHHHHHHGHGHGGGGGHHHHHHHHGHHHHHHHHHGGGGGHHHHFFGHHHGGGGGGHHHGFGGHHGGGGHHHHHHGGGGGGHGHHGGGGGGGHGGGGGGHHHHHHHHHHHHHFHGGGHHHHGGGGGG:FE;EGEGGGGG/;?FGGGGGGGFFFFGGFFFFFFFFFBFFFFFFFFFFBFFFFFFEFFFFFEFFF\n+@M01368:8:000000000-A3GHV:1:1101:5861:6452/1:R1:ATTATGTC:R2:TTATCCGA:F1:CTAC:F2:CATC\n+AGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTT\n++\n+GGGGGGGGGHHHHHHHHHHHGHHHHGHHHHHHHHHHHGGGGHHHHHHHHFHHHHHHGGHGHGGHGGHHHHHHHGGHFHHHGGGGGHHHHHHHHHHHHHHHHHHGGGGGHHHHHEGGHHGGGGGGHHHGGGGHGGGGGHHHHHHGGGDCGHHHHGGGGGGGHEFGGGGHGHHHGHGGGFGGGGGGGEGGGGGGG?E0CEFGGGGGFEE9EEFFFFFBFFFFFFFBFFBD.AFFFFFFF0\n+@M01368:8:000000000-A3GHV:1:1102:10403:6021/1:R1:CGCTCCGG:R2:GGATGAGG:F1:GCCC:F2:CAGG\n+TAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTG\n++\n+FGGGGGFGGHA?EAEFBEAGHFABFGG5FDF5DB1EEGAFDFB53FF5FH@G5FFEHGHEFHFFHBE333GF43GCGGGGE@0?BFGGB0B?FHGFDGGHHHBFFDEGGHGFFFDFE@<1>@FFFGHHHHFHEFGDABFFGG/@DCE<CG1<GF0/DD000=<DHGBDFDCECE/:AC?-;-;9B/ABBB-AD9BFB99AB?BDFBAD-.9..@;=;;..9..9/9;BEF'..b';///\n+@M01368:8:000000000-A3GHV:1:1113:25528:14016/1:R1:CCTACAAG:R2:GTATCCGA:F1:CATT:F2:CATC\n+ATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGG\n++\n+GGGGGGGGGHHFHGHHHHGHHHHHHHHHHHGGGGHHHHFHHHHFHGHHHHGAFFEFHEGHHHHHHHHGHEHHGGFGGGHHHHHHFHHHHHGGHHHHGGGGGHFHHFF?HHGGFECEFFGHFFGFHGECDGHGBGFHGDF@@?CGFHCEGGGFD.CCC?EGHBHHHFHHFBCFFGEB/CEGGGGDAA.90C9CEBFGGBBF/9.9FBFFFBBFF//99FFFFEABF//99FFEFFFBFF\n+@M01368:8:000000000-A3GHV:1:1113:5741:16959/1:R1:TAGTAAGT:R2:GTATCCGA:F1:ATGT:F2:CATC\n+CGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGA\n++\n+GGFGGGGGGHHHGHHGGHBGHGAGFFCAFGHGFFGHHGFHHHHHGGGGGHGHHHHHHHHE3BFFHHHGG0EDF@GHFFGGGHGGGGGGGGGGGGGHHGGEEFHGFHHDDG@DGGGHHGDGGGGGHGG?CF?HHGHHHGHGHHHFFHGGGHHHHGGCD.;0<C;CGGGGEFF/.;0;FFFBF/0;0CFGFFB..9B/;0CBFFBBFFFFBAC?DED9;B9AD;.FFFB/B/;FBA/B//\n+@M01368:8:000000000-A3GHV:1:1114:10130:11959/1:R1:CGTTCCCC:R2:ATCAGAGA:F1:TTAA:F2:CAGA\n+TAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTCTGATCTGTCTCTTATACACATCTCCGAGCCCACGAGACTAAGGCGAATCTCGTATGCCGTCTTCTGCTTGCAACAAACACACATCCAGA\n++\n+FFGGGGFGGD4EGGGGGHHGFFGHFGGHHHFEFHECFHHHEHGAGBCCGCCEGGHGHEGFBFHFHHHHGGGHFHGHEGGGFEGEGG??@DBGHGGC-@FFGHFHFHB-??DA-DD@9:BEBG@B?E?A.ABBFBFA??F.FF/BFFB/B9B/9;BF9FF9FFFFFFFFFFFFFF?BB?;9EE;-;DDB9//;B-B@;ABFFEFFFF/-.9A.;//9/BF./B/..9.9:...//////\n+@M01368:8:000000000-A3GHV:1:1114:14540:5315/1:R1:CTTTAGTA:R2:CACTTGGG:F1:AGTA:F2:GGTA\n+GTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGGGGGCTATTTAGGTTTTT\n++\n+GGGGGGGGGHHHHHHHFHHHHGHHGHHGGGHGGHHHHHHHGHHHHHHGGGGGHHFHHHFGHHGGFHHHHHGGGGGHHHGHGGHHHGGGGGGHGHGGGGHHGGGGHHHHHEGDDFGFFFHHGGGGGCDAFCFGFDHHHHGGHGHHHHHHBCGEHHHHGGHG.ACGEHGG0CBFFF:A;BB0;09CGF00CFFFE0AA?//CFFFFFFFFFFFFFFFBEF;A.-=A--:BBFB90;;FE.\n+@M01368:8:000000000-A3GHV:1:1114:15066:16302/1:R1:TAAATAAG:R2:TTATTATT:F1:ACAT:F2:ATGT\n+ACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAACGGTTGTTAATTAATTATTGCTTGTAGGACA\n++\n+GGGGGFGGGBGFFFHGFHHGFFFHGHHHGHHHHFFHHHGHGC?AEFFHEFBFFFGHHHHH1FDGFFHGHGHFEGCGC-<<AHHHGGGGGGGFHH0GHFCCCADGGG?.9/A-???DGGFFF.9F9/EE-;;BBBFFBFFFFFFFFFEFFFFBFFBBFFFFF/BFFBFFFFF-DBFFF;/BFF//BB//9/BEA---9:BFFFFFF/F/.;.:@9.BBFF/;BFF/;/////9/////.\n+@M01368:8:000000000-A3GHV:1:1114:16639:15258/1:R1:CCTAAATA:R2:TTATTATT:F1:GCCC:F2:ATGT\n+CACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGCGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTCCAATATTACAGGCGAACATACTTACTAAATTGTGT\n++\n+GCGC1BBF1GHHHBHHHHGFHGH1A100AA/GGEHGFBAA1FFD2FHHHHECG2F1BB/E0FC/A>EE/FGGFGEF1EGBBEHHCGGGHBGEHFHE0B?E--;C?CCGGG@A@GBFBBBB09?@??A-AB--ABE@=-=-9AE9A;FFFFFE=9-//;//;9FF/////;;///9B///;/B////9FFBB;--A@-;/9;9-:-/;;FFFE9BF?@;-9-99/B9F/://///99/;\n+@M01368:8:000000000-A3GHV:1:1114:2404:13066/1:R1:TCCTACAA:R2:ATGGATCA:F1:GCAT:F2:CAGG\n+AATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCTGTCTATTATACACATC\n++\n+GGGGGGGGGHHHHHGHHHHHHHHHFFHHHHHGGGGHHHHHHHHFHHHHHHFGGHHGGHGGHHHHHHGHHFHHHHGGGGGGHHHHHHGHHHHHHHHHHGGGGGGGHH?FGHHHGGGGGGHHGGFGGHHGGGGHHHHHFGGGGFGHGHHGGGGGGGHGGGEGGHHGHHHHHHHHHGFBFFDA0FGGGFFGG0:EFGGGGGGGG;AEBF0B0BFFBFFFFFFFFFFFFFFFFFFFFFEFF0\n'

diff -r 084bbd8ba7b8 -r cd7e644cae1d test-data/mec_reads_pair2.fastqsanger
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mec_reads_pair2.fastqsanger Fri Oct 08 09:57:52 2021 +0000

b'@@ -0,0 +1,396 @@\n+@M01368:8:000000000-A3GHV:1:1101:6911:8255/2:R1:ATCTGGTT:R2:TCGCCTTA:F1:CCTA:F2:CCGC\n+ACTCACCCACGGCGGCCATCAGCCGATACTAAGTTTGGGGTATGGTGGGGGGGATAATGAATTAGGTTGTGGGGGAGGGTTTGTGGTTGAGAGAAACACAAAAAACAATCTTATATATGGGTAGTCGTTTTGTATTGGTTTTTTGTTTTGTTTGTGTTTTGAGTGTCGGTTTAGTTCGGTGTACTAGGGGGGGTGGATGGGGTCGGCTGGTGAGGGGGTCTTAGTGTATTGAGTGTGG\n++\n+A111A100000000////011110//>>/12@1@22B/////1@>21/>>/-----9/;////9////--;-;-;-----;--------9/-/-///9-;-------9//////9/////-//-/9-;-;9--/////99-;--9-:-;----/---/-----////---9-/////--;A-//////---------9/-----;-----/-/-----;--;//////////9;///-\n+@M01368:8:000000000-A3GHV:1:1101:14518:9998/2:R1:GTTATTAT:R2:CATCACGA:F1:TATG:F2:TGGA\n+CACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTAATTAATTAATGCTTGTAGGACATAATAATAA\n++\n+GGGGGGGGGHHHHHHHHHHHHHHHHGFHHHHGGGGGHGFHHHHHHHHHHHHHHHHHHHGHGGEHGGGGCGGGHHGGCGGGGGHHGHHHGGGGGGGG.BFFFGAGADFGAFDGFGGCFFF;DDFFFFFFFFFFFFFFFFFFEFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFF09FFFE00;BE@;DABBFFFFFBBFB00;F:9;FFBFFF9BFFFFFFFFFFFFF90/::BFFFBF0\n+@M01368:8:000000000-A3GHV:1:1101:18422:19051/2:R1:GTATCCGA:R2:CTACAAGC:F1:CATC:F2:ATTA\n+TTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGGGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGG\n++\n+GGGGGGGGGHHHGHHHHHHHHHHHHHHHHGGGGHHHHHHHHEHHHHHHHGGHHGGHGGHHHHHHHGHGGHHHGGGGGHGHHHHGGGHFHFHHHHHGGGGGHBFFCGDHHHGGGGGGHGGGGGGHHGCGGGFGHHBGGGGGFFFHEGGGGGCDCCE@EFGHHHHFHEGHGFFHHGB;ECBFGGGEFEFFGF0AFGFGFFG.;;DFFFFFFFFFF090BFFFE?FEFBBFBFFFB990BF\n+@M01368:8:000000000-A3GHV:1:1101:25545:21098/2:R1:ATTAATTA:R2:GCCCATAA:F1:ACAC:F2:CACT\n+GGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTTCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCAACCTATGTCGCAGTATCTGTCTTTGAT\n++\n+CGGCGGGCGHHHGHHHHCGHFGHFHGFGGCDGGBD5FGFFFHFHGGGHAEBFGHHHEHGGFHBGGFHHHGGGEEFHHHFHFFHDHGHGHHHHFFHHGGFAEGFFFFFBGHHHFFHHHHHHHFHFHHFHGFHGHGA/<@EFHEHH1GGHFFFHG1>=FGHFHGF.GE//-<BB?9.9BFFFB==AA/FFFFFA-@BA.;;D?F9FAB;---./99BFFFBBAE-.9B/BFB9F/9BFBB\n+@M01368:8:000000000-A3GHV:1:1101:5446:12248/2:R1:AATTAACA:R2:ATCCGACA:F1:CACT:F2:TCTG\n+TTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTT\n++\n+GGGGGGGGGHHHHHGHHHHHHHHGHHHHHHGHHHHGGGGHHHHHHHHHHHHHHHHHHHHHHGGGGGHHHHHHHGFGHHHHHHHHHHHHHHHHHGHHHHHGGGGGHHHHHHHHHHHHHHHGHHHHHHGHGHGHHGGGGGGGGGGGFFFFFFFFFFFFFFAFFFFFFFFFFFFFBFC?.EAFFFFFFFFAFFFFFFFFFFFFFFFEFFFF0FFFFFFF0BFFFFFFFFF?.BDCFFEDA/\n+@M01368:8:000000000-A3GHV:1:1101:5861:6452/2:R1:ATTATGTC:R2:TTATCCGA:F1:CTAC:F2:CATC\n+GGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACG\n++\n+GGGGGGGGGHHHHHHHHHHHHHHHHGHHHHHHHHHHHGGGGHHHHHHHHGHHHHHHHHHHHHHGGHGGHHHHHHHGHHHHHHHHHHHHHHHHHHHGGHHHHGGGGGGEHGHHHHHHHHHHHGHHHHHHGHGHGHGGGGCGGGGGFFFFFFFFFFFFFFFFFFFFFFFF?FFEAF:DAEF9DEFFFFFFF-A.BFFFFFEFFFFEFFFFFFFF0FFEB0FFFFBFFFFFFADEFCF0/.\n+@M01368:8:000000000-A3GHV:1:1102:10403:6021/2:R1:CGCTCCGG:R2:GGATGAGG:F1:GCCC:F2:CAGG\n+ATCAAAGACAGATACTGCGACATAGGGGGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGGGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGAGGTTAATAGGGGGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACGCTGAAGTAGGAACCAGATGTCGGATACAGTTGACTTTAGGTAACCCA\n++\n+BGGGGFFCGGHHA5DFGAE?AAEDFHG2AEE1FBE00A1BGE0?E1FFGEEEGB4F43?EE/>///F??//@BCBAC<<BAGHB?11F/FGFGGBFBGBD.11><.<<<C0<A</<<=0GFHC@-.;FF09BFFGB00B0;FE.C/:CCF0;0C0;BBBFF@.9AF.:9EFF.;.BFF/FF/;/./BFB/..;;ABF/9FF//.;AAF9BBBA;-A.B/9///9/BF///'..b':.00\n+@M01368:8:000000000-A3GHV:1:1113:25528:14016/2:R1:CCTACAAG:R2:GTATCCGA:F1:CATT:F2:CATC\n+GGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACG\n++\n+GGGGGGGGGHHHHHHHHHHHHHHHHGHGHHHHHHHHHGGGGHHHHHHHHHFHHHHHHHHHHHHGGGGGHHHHHHHGHHHHHHHHHHGGHHHHGHHGGHHHEGGGGGHHHHHHHHHGHHHHHGHHHHHGGHGHGHHGGGGGGGGGFEACFFFFFFFFFFFFFFFDFFFAFFFFBFAB@EFAAEFFFFF.ACF.BBFFEBFFFEB;FFFFFFFA/BFBFBBBFFFBFFFFFED.>DFFF.\n+@M01368:8:000000000-A3GHV:1:1113:5741:16959/2:R1:TAGTAAGT:R2:GTATCCGA:F1:ATGT:F2:CATC\n+GGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACG\n++\n+GGGGGGGGGHHHHHHHGHHHHHHHHGHHHHGHDGHHHGGGGHHHHHHHHHHHHHHHGHHHHHGGGEGGHHHHFHHHHHHHHHHHHHHHHHHHHHHGHHGHHGGGGGHHHHHHHHHHHGHHHFHHHHHHGHGHGHGGGGCGGFGGFFFFFFFFFFFFFBFFFFFFFFFFFFFFAFFFFEAEFFFFFFFFFFF9BFFBFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFADAB-/BF.\n+@M01368:8:000000000-A3GHV:1:1114:10130:11959/2:R1:CGTTCCCC:R2:ATCAGAGA:F1:TTAA:F2:CAGA\n+ACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGCTGTCTCTTATACACATCTGACGCTGCCGACGAGCGATCTAGTGGAGAGTTCTGTGGGGCCGGGGATCCTTATAAAAAAAATAGA\n++\n+GGGGGGGGGGHHHHHGGHHHGGGCGGHGHGGGGHHGGGGHHHHHHGGGEGGHHHFGGGGG?E1FE?/EEHHHHHGHHGHHHHGHFHGHGHHGDGGFG2FF2?GHHHHHGCCCFHGHGHHHHGHHFEHHFGHHGHH<1=DGHHHGHHGHGAGAEEDG.CGCGHC0CGBFHGFBBF0ABDDEFF@?--:BB@.;:BF;0.0:0.0:000:BF.-.------.9/;000::0;0:--.000\n+@M01368:8:000000000-A3GHV:1:1114:14540:5315/2:R1:CTTTAGTA:R2:CACTTGGG:F1:AGTA:F2:GGTA\n+CTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCC\n++\n+GGGGGGGGGHHHHHHHHHGGGGGHHHHHHHHHHHHHHHHHHHGHHHHHHHGHHHHFHFHHHGGGGGHHHHHHHHHHHHHGHHHHHHHHGGGGGGHHHFHHHGHHHHHHHHHHHHHHHHHHGHGHHHGGGFGHHHHHHHHFHHHHHF?1FHHGHGHGHGHHGGFFFFDBFBE;BCC.:BFFFFFFFFFFFFFF;AFFFFF-=-.AEDEFFFFF..9A;9FFFF0FFFFE00FFF0:BA.\n+@M01368:8:000000000-A3GHV:1:1114:15066:16302/2:R1:TAAATAAG:R2:TTATTATT:F1:ACAT:F2:ATGT\n+CTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGGGATAGACCTGTGATCCATCGTGTGG\n++\n+GGGGGGGGGHHHHHHHHHHHHHHHDGHHHHFHHGHHGHHHHHGGGGEHHHHFHHFF5FHHFEGHHHGDHGGHGHGFGGGEHFGHHGGGGGHGHHHGHHFHHB3FGHHFGGGG?GFFHCCEBGFFECCDFEGFCFGCHHGFDDHHHGHHCFGGGGGFBFDGFG?-:..AFG.-C0C009;:00;00:9/:CEFFF?AE::9;9?0:FEF0;0..--./00::B/090000000;A....\n+@M01368:8:000000000-A3GHV:1:1114:16639:15258/2:R1:CCTAAATA:R2:TTATTATT:F1:GCCC:F2:ATGT\n+CTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCGCACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGGGATAGACCTGTGATCCATCGTGATG\n++\n+GGGGGGGGGHHHHHHHHHHHHHHHHGHHHHHHHHGHHHHHHGGGGGHGIHHHIH5DEGHHHF?FGHGGHGGHEGGHFHHGHGEHHGGGGGFFFGHFBG2GHEBGHHGHGGEG/GFGABEDFGHEED?GGHHFFGGGCFEGD/GFHFFGEFGCGG?CC??D-EF@EEEFGCDDBBFGGGEBBFFF09090A.BFGA.9CCA0;EBAB00BBFF.@-./;BB;BFFF0:00099AAFFF0\n+@M01368:8:000000000-A3GHV:1:1114:2404:13066/2:R1:TCCTACAA:R2:ATGGATCA:F1:GCAT:F2:CAGG\n+CTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGACCATACTTACTAAAGTGTGTTAATTAATTAATGCTTGTAGGACTGTCTCTTATACACATT\n++\n+GGGGGGGGGHHHHHHHHHFFHHHHGGGGGHFFFHHFHHHHHHHHHHHHHHHGFEGGGHGEDFCDFHGHFG@@DGGHHHHHHGGGGCGGGGGEHGGCGBB?CF99EGFGGFGG?D9CFFFF/BBFFFFFEF9BFFAFFFFEFFFFFFFFFFFFFFFFFFFFF.FFBBFFFFFFFFFFFF-9;;;BFFFFFB9BFBFBFABFFEFFFFFFFFFF::BFFBFFFF.9//;FFFFF/BFFB/\n'

diff -r 084bbd8ba7b8 -r cd7e644cae1d test-data/paired_collection_example_pair1_results3.fastq.gz

Binary file test-data/paired_collection_example_pair1_results3.fastq.gz has changed

diff -r 084bbd8ba7b8 -r cd7e644cae1d test-data/paired_collection_example_pair2_results3.fastq.gz

Binary file test-data/paired_collection_example_pair2_results3.fastq.gz has changed

diff -r 084bbd8ba7b8 -r cd7e644cae1d test-data/paired_collection_example_results3.txt
--- a/test-data/paired_collection_example_results3.txt Tue Jul 30 06:26:49 2019 -0400
+++ b/test-data/paired_collection_example_results3.txt Fri Oct 08 09:57:52 2021 +0000

@@ -3,11 +3,13 @@
==========================
Input filename: input_1.fastq
Trimming mode: paired-end
-Trim Galore version: 0.6.3
-Cutadapt version: 2.4
-Number of cores used for trimming: 1
+Trim Galore version: 0.6.7
+Cutadapt version: 3.4
+Python version: could not detect
+Number of cores used for trimming: 4
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
+Using Nextera adapter for trimming (count: 29). Second best hit was Illumina (count: 0)
Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
@@ -16,10 +18,10 @@
Length cut-off for read 2: 35 bp (default)

-This is cutadapt 2.4 with Python 3.7.3
-Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_1.fastq
-Processing reads on 1 core in single-end mode ...
-Finished in 0.01 s (72 us/read; 0.83 M reads/minute).
+This is cutadapt 3.4 with Python 3.9.6
+Command line parameters: -j 4 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_1.fastq
+Processing reads on 4 cores in single-end mode ...
+Finished in 0.01 s (115 µs/read; 0.52 M reads/minute).

=== Summary ===

@@ -33,10 +35,10 @@

=== Adapter 1 ===

-Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 52 times.
+Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 52 times

No. of allowed errors:
-0-9 bp: 0; 10-12 bp: 1
+1-9 bp: 0; 10-12 bp: 1

Bases preceding removed adapters:
A: 9.6%
@@ -85,11 +87,13 @@
==========================
Input filename: input_2.fastq
Trimming mode: paired-end
-Trim Galore version: 0.6.3
-Cutadapt version: 2.4
-Number of cores used for trimming: 1
+Trim Galore version: 0.6.7
+Cutadapt version: 3.4
+Python version: could not detect
+Number of cores used for trimming: 4
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
+Using Nextera adapter for trimming (count: 29). Second best hit was Illumina (count: 0)
Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
@@ -98,10 +102,10 @@
Length cut-off for read 2: 35 bp (default)

-This is cutadapt 2.4 with Python 3.7.3
-Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_2.fastq
-Processing reads on 1 core in single-end mode ...
-Finished in 0.01 s (55 us/read; 1.08 M reads/minute).
+This is cutadapt 3.4 with Python 3.9.6
+Command line parameters: -j 4 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_2.fastq
+Processing reads on 4 cores in single-end mode ...
+Finished in 0.02 s (159 µs/read; 0.38 M reads/minute).

=== Summary ===

@@ -115,10 +119,10 @@

=== Adapter 1 ===

-Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 58 times.
+Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 58 times

No. of allowed errors:
-0-9 bp: 0; 10-12 bp: 1
+1-9 bp: 0; 10-12 bp: 1

Bases preceding removed adapters:
A: 12.1%

diff -r 084bbd8ba7b8 -r cd7e644cae1d test-data/paired_collection_example_results3gz.txt
--- a/test-data/paired_collection_example_results3gz.txt Tue Jul 30 06:26:49 2019 -0400
+++ b/test-data/paired_collection_example_results3gz.txt Fri Oct 08 09:57:52 2021 +0000

@@ -3,11 +3,13 @@
==========================
Input filename: input_1.fastq.gz
Trimming mode: paired-end
-Trim Galore version: 0.6.3
-Cutadapt version: 2.4
-Number of cores used for trimming: 1
+Trim Galore version: 0.6.7
+Cutadapt version: 3.4
+Python version: could not detect
+Number of cores used for trimming: 4
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
+Using Nextera adapter for trimming (count: 29). Second best hit was smallRNA (count: 0)
Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
@@ -17,10 +19,10 @@
Output file will be GZIP compressed

-This is cutadapt 2.4 with Python 3.7.3
-Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_1.fastq.gz
-Processing reads on 1 core in single-end mode ...
-Finished in 0.02 s (176 us/read; 0.34 M reads/minute).
+This is cutadapt 3.4 with Python 3.9.6
+Command line parameters: -j 4 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_1.fastq.gz
+Processing reads on 4 cores in single-end mode ...
+Finished in 0.01 s (129 µs/read; 0.47 M reads/minute).

=== Summary ===

@@ -34,10 +36,10 @@

=== Adapter 1 ===

-Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 52 times.
+Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 52 times

No. of allowed errors:
-0-9 bp: 0; 10-12 bp: 1
+1-9 bp: 0; 10-12 bp: 1

Bases preceding removed adapters:
A: 9.6%
@@ -86,11 +88,13 @@
==========================
Input filename: input_2.fastq.gz
Trimming mode: paired-end
-Trim Galore version: 0.6.3
-Cutadapt version: 2.4
-Number of cores used for trimming: 1
+Trim Galore version: 0.6.7
+Cutadapt version: 3.4
+Python version: could not detect
+Number of cores used for trimming: 4
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
+Using Nextera adapter for trimming (count: 29). Second best hit was smallRNA (count: 0)
Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
@@ -100,10 +104,10 @@
Output file will be GZIP compressed

-This is cutadapt 2.4 with Python 3.7.3
-Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_2.fastq.gz
-Processing reads on 1 core in single-end mode ...
-Finished in 0.02 s (169 us/read; 0.36 M reads/minute).
+This is cutadapt 3.4 with Python 3.9.6
+Command line parameters: -j 4 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_2.fastq.gz
+Processing reads on 4 cores in single-end mode ...
+Finished in 0.04 s (395 µs/read; 0.15 M reads/minute).

=== Summary ===

@@ -117,10 +121,10 @@

=== Adapter 1 ===

-Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 58 times.
+Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 58 times

No. of allowed errors:
-0-9 bp: 0; 10-12 bp: 1
+1-9 bp: 0; 10-12 bp: 1

Bases preceding removed adapters:
A: 12.1%

diff -r 084bbd8ba7b8 -r cd7e644cae1d test-data/paired_collection_example_unpair1_results3.fastq.gz

Binary file test-data/paired_collection_example_unpair1_results3.fastq.gz has changed

diff -r 084bbd8ba7b8 -r cd7e644cae1d test-data/paired_collection_example_unpair2_results3.fastq.gz

Binary file test-data/paired_collection_example_unpair2_results3.fastq.gz has changed

diff -r 084bbd8ba7b8 -r cd7e644cae1d test-data/paired_example_pair1_results2.fastq.gz

Binary file test-data/paired_example_pair1_results2.fastq.gz has changed

diff -r 084bbd8ba7b8 -r cd7e644cae1d test-data/paired_example_pair2_results2.fastq.gz

Binary file test-data/paired_example_pair2_results2.fastq.gz has changed

diff -r 084bbd8ba7b8 -r cd7e644cae1d test-data/paired_example_results2.txt
--- a/test-data/paired_example_results2.txt Tue Jul 30 06:26:49 2019 -0400
+++ b/test-data/paired_example_results2.txt Fri Oct 08 09:57:52 2021 +0000

@@ -3,21 +3,23 @@
==========================
Input filename: input_1.fastq
Trimming mode: paired-end
-Trim Galore version: 0.6.3
-Cutadapt version: 2.4
-Number of cores used for trimming: 1
+Trim Galore version: 0.6.7
+Cutadapt version: 3.4
+Python version: could not detect
+Number of cores used for trimming: 4
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
+Using Nextera adapter for trimming (count: 29). Second best hit was smallRNA (count: 0)
Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp

-This is cutadapt 2.4 with Python 3.7.3
-Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_1.fastq
-Processing reads on 1 core in single-end mode ...
-Finished in 0.01 s (75 us/read; 0.80 M reads/minute).
+This is cutadapt 3.4 with Python 3.9.6
+Command line parameters: -j 4 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_1.fastq
+Processing reads on 4 cores in single-end mode ...
+Finished in 0.01 s (117 µs/read; 0.51 M reads/minute).

=== Summary ===

@@ -31,10 +33,10 @@

=== Adapter 1 ===

-Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 52 times.
+Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 52 times

No. of allowed errors:
-0-9 bp: 0; 10-12 bp: 1
+1-9 bp: 0; 10-12 bp: 1

Bases preceding removed adapters:
A: 9.6%
@@ -83,21 +85,23 @@
==========================
Input filename: input_2.fastq
Trimming mode: paired-end
-Trim Galore version: 0.6.3
-Cutadapt version: 2.4
-Number of cores used for trimming: 1
+Trim Galore version: 0.6.7
+Cutadapt version: 3.4
+Python version: could not detect
+Number of cores used for trimming: 4
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
+Using Nextera adapter for trimming (count: 29). Second best hit was smallRNA (count: 0)
Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp

-This is cutadapt 2.4 with Python 3.7.3
-Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_2.fastq
-Processing reads on 1 core in single-end mode ...
-Finished in 0.00 s (50 us/read; 1.19 M reads/minute).
+This is cutadapt 3.4 with Python 3.9.6
+Command line parameters: -j 4 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_2.fastq
+Processing reads on 4 cores in single-end mode ...
+Finished in 0.03 s (256 µs/read; 0.23 M reads/minute).

=== Summary ===

@@ -111,10 +115,10 @@

=== Adapter 1 ===

-Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 58 times.
+Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 58 times

No. of allowed errors:
-0-9 bp: 0; 10-12 bp: 1
+1-9 bp: 0; 10-12 bp: 1

Bases preceding removed adapters:
A: 12.1%

diff -r 084bbd8ba7b8 -r cd7e644cae1d test-data/paired_example_results2gz.txt
--- a/test-data/paired_example_results2gz.txt Tue Jul 30 06:26:49 2019 -0400
+++ b/test-data/paired_example_results2gz.txt Fri Oct 08 09:57:52 2021 +0000

@@ -3,11 +3,13 @@
==========================
Input filename: input_1.fastq.gz
Trimming mode: paired-end
-Trim Galore version: 0.6.3
-Cutadapt version: 2.4
-Number of cores used for trimming: 1
+Trim Galore version: 0.6.7
+Cutadapt version: 3.4
+Python version: could not detect
+Number of cores used for trimming: 4
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
+Using Nextera adapter for trimming (count: 29). Second best hit was Illumina (count: 0)
Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
@@ -15,10 +17,10 @@
Output file will be GZIP compressed

-This is cutadapt 2.4 with Python 3.7.3
-Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_1.fastq.gz
-Processing reads on 1 core in single-end mode ...
-Finished in 0.03 s (287 us/read; 0.21 M reads/minute).
+This is cutadapt 3.4 with Python 3.9.6
+Command line parameters: -j 4 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_1.fastq.gz
+Processing reads on 4 cores in single-end mode ...
+Finished in 0.01 s (114 µs/read; 0.53 M reads/minute).

=== Summary ===

@@ -32,10 +34,10 @@

=== Adapter 1 ===

-Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 52 times.
+Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 52 times

No. of allowed errors:
-0-9 bp: 0; 10-12 bp: 1
+1-9 bp: 0; 10-12 bp: 1

Bases preceding removed adapters:
A: 9.6%
@@ -84,11 +86,13 @@
==========================
Input filename: input_2.fastq.gz
Trimming mode: paired-end
-Trim Galore version: 0.6.3
-Cutadapt version: 2.4
-Number of cores used for trimming: 1
+Trim Galore version: 0.6.7
+Cutadapt version: 3.4
+Python version: could not detect
+Number of cores used for trimming: 4
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
+Using Nextera adapter for trimming (count: 29). Second best hit was Illumina (count: 0)
Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
@@ -96,10 +100,10 @@
Output file will be GZIP compressed

-This is cutadapt 2.4 with Python 3.7.3
-Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_2.fastq.gz
-Processing reads on 1 core in single-end mode ...
-Finished in 0.02 s (170 us/read; 0.35 M reads/minute).
+This is cutadapt 3.4 with Python 3.9.6
+Command line parameters: -j 4 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_2.fastq.gz
+Processing reads on 4 cores in single-end mode ...
+Finished in 0.02 s (232 µs/read; 0.26 M reads/minute).

=== Summary ===

@@ -113,10 +117,10 @@

=== Adapter 1 ===

-Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 58 times.
+Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 58 times

No. of allowed errors:
-0-9 bp: 0; 10-12 bp: 1
+1-9 bp: 0; 10-12 bp: 1

Bases preceding removed adapters:
A: 12.1%

diff -r 084bbd8ba7b8 -r cd7e644cae1d test-data/paired_hardtrimmed3_pair1_.fastqsanger
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/paired_hardtrimmed3_pair1_.fastqsanger Fri Oct 08 09:57:52 2021 +0000

b'@@ -0,0 +1,396 @@\n+@M01368:8:000000000-A3GHV:1:1101:6911:8255/1\n+TCGCACCTACGTTCAATATT\n++\n+FFEFE;DFFFDFBFF/9BFB\n+@M01368:8:000000000-A3GHV:1:1101:14518:9998/1\n+GACCTGTGATCCATCGTGAT\n++\n+FF//;BFFFFFBF/9D:A//\n+@M01368:8:000000000-A3GHV:1:1101:18422:19051/1\n+TATTATTTATCGCACCTACG\n++\n+FFEFBFFFFFFFFFF:FFF.\n+@M01368:8:000000000-A3GHV:1:1101:25545:21098/1\n+TTTAAGGGGAACGGGTGGGG\n++\n+FBFFFFFFBF..A..;@B--\n+@M01368:8:000000000-A3GHV:1:1101:5446:12248/1\n+AAGGGGAACGTGTGGGCTAT\n++\n+FFFBFFFFFFEFFFFFEFFF\n+@M01368:8:000000000-A3GHV:1:1101:5861:6452/1\n+TGATCCATCGTGATGTCTTT\n++\n+FFFFFBFFBD.AFFFFFFF0\n+@M01368:8:000000000-A3GHV:1:1102:10403:6021/1\n+ACCCTATGTCGCAGTATCTG\n++\n+..9..9/9;BEF;A:9/BFF\n+@M01368:8:000000000-A3GHV:1:1102:10677:23253/1\n+AATTCTGTCTCTTATACACA\n++\n+F0FFFFFFFFFFFFFFFFF:\n+@M01368:8:000000000-A3GHV:1:1102:13809:1733/1\n+GTCTCTTATACACATCTCCG\n++\n+FBBBFFFFFBFF0BFBF9F.\n+@M01368:8:000000000-A3GHV:1:1102:17584:10050/1\n+AATCTCGTATGCCGTCTTCT\n++\n+FF;.BF9ADF/9;A;DFFF0\n+@M01368:8:000000000-A3GHV:1:1102:18842:24844/1\n+TCTGTCTTTGATTCCTGCCT\n++\n+BBBFBFBFFF//BFB/BFF/\n+@M01368:8:000000000-A3GHV:1:1102:21788:11027/1\n+ACTAAAGTGTGTTAATTCTG\n++\n+FBFF0FFBBBBFBFBFFFF0\n+@M01368:8:000000000-A3GHV:1:1102:5728:8777/1\n+CCTGAAGTAGGAACCAGATG\n++\n+FFFFBBFFFFF/FFEFFFBB\n+@M01368:8:000000000-A3GHV:1:1102:5983:21093/1\n+TATTATTTATCGCACCTACG\n++\n+F0BFFFBBFF0EFFFFFFFA\n+@M01368:8:000000000-A3GHV:1:1102:7765:18353/1\n+CCTATGTCGCAGTATCTGTC\n++\n+.::FBFBFFE-A9:BFFFF0\n+@M01368:8:000000000-A3GHV:1:1103:10405:17879/1\n+TATTATTTATCGCACCTACG\n++\n+FBFFFFFFFFFFFFFFFFF?\n+@M01368:8:000000000-A3GHV:1:1103:13493:8205/1\n+GATTCCTGCCTCATCCTATT\n++\n+FFFFFFFFBFBBBFFFFEFF\n+@M01368:8:000000000-A3GHV:1:1103:14060:21273/1\n+TATTACTGTCTCTTATACAC\n++\n+:FFFBB/BFFFFFBFFFFB/\n+@M01368:8:000000000-A3GHV:1:1103:14528:12993/1\n+TCGCAGTATCTGTCTTTGAT\n++\n+BFEA-A.B//9F9F//;BBB\n+@M01368:8:000000000-A3GHV:1:1103:17657:20856/1\n+TGCCTCATCCTATTATTTAT\n++\n+FFFFFFFFFFF/FFFFBFF9\n+@M01368:8:000000000-A3GHV:1:1103:23099:3794/1\n+GCGAATCTCGGATGCCGTCT\n++\n+FFFF@;.9BF..;-./-A=F\n+@M01368:8:000000000-A3GHV:1:1103:25465:20010/1\n+AAAAAAAAAAAACAACAGAC\n++\n+.B/;:>---;--..;.../9\n+@M01368:8:000000000-A3GHV:1:1103:25519:6301/1\n+GAGACTAAGGCGAATTTCGT\n++\n+-B?DFFF/B/B?---.//;.\n+@M01368:8:000000000-A3GHV:1:1103:6074:6549/1\n+GTATCTGTCTTTGATTCCTG\n++\n+A./FFFFFFFFFFFF/BFF/\n+@M01368:8:000000000-A3GHV:1:1104:11572:8264/1\n+TATTATTTATCGCACCTACG\n++\n+B/BFFFF/BFFE?EFAFEF9\n+@M01368:8:000000000-A3GHV:1:1104:11928:24197/1\n+TAGGAACCAGATGTCGGATA\n++\n+FFFFFFFFFFFFFFFFF@D9\n+@M01368:8:000000000-A3GHV:1:1104:12288:20635/1\n+TCTGTCTTTGATTCCTGCCT\n++\n+;FBBFBFB///;99999BA9\n+@M01368:8:000000000-A3GHV:1:1104:13832:4398/1\n+ACCCAGTAGACTAGTGCGTC\n++\n+9...:.9//9////;/9-.-\n+@M01368:8:000000000-A3GHV:1:1104:23670:4161/1\n+GGGTGATAGACCTGTGATCC\n++\n+BF./AAF/BFFBBF/F/BFB\n+@M01368:8:000000000-A3GHV:1:1104:24927:22253/1\n+TTCCTGCCTCATCCTATTAT\n++\n+//;/;9/A/;/9BFFFBFBB\n+@M01368:8:000000000-A3GHV:1:1104:4705:7727/1\n+CGTGATGTCTTATTTAAGGG\n++\n+F?.AFFF/BFFEFFFFFEFF\n+@M01368:8:000000000-A3GHV:1:1104:7756:4776/1\n+GTCGCAGTATCTGTCTTTGA\n++\n+FFBEFFF:9FFFFBBFFFF/\n+@M01368:8:000000000-A3GHV:1:1105:11310:21761/1\n+TGTCGGATACAGTTCACTTT\n++\n+FFBFFFFFFFFFFFFEFFF0\n+@M01368:8:000000000-A3GHV:1:1105:11578:14676/1\n+TGAAGTAGGAACCAGATGTC\n++\n+FF/FFFFFFFFFFFFFFFF0\n+@M01368:8:000000000-A3GHV:1:1105:13575:19255/1\n+TGGGCTATTTAGGTTTTATG\n++\n+FF?B---;B99//9/;A//9\n+@M01368:8:000000000-A3GHV:1:1105:15502:11453/1\n+CTGTCTCTTATACACATCTC\n++\n+FFFFEFFFFFFFFBFFFBFF\n+@M01368:8:000000000-A3GHV:1:1105:16787:9771/1\n+GACCTGTGATCCATCGTGAT\n++\n+FFFFFFBFFFFFFFFFEFF/\n+@M01368:8:000000000-A3GHV:1:1105:17564:15723/1\n+TTAGGTTTTATGACCCTGAA\n++\n+FFBBFBBFFFFFE1:BFFB0\n+@M01368:8:000000000-A3GHV:1:1105:18108:12091/1\n+GATACCTGTCTCTTATACAC\n++\n+F-A.B//;BFFEF//BB///\n+@M01368:8:000000000-A3GHV:1:1105:18331:16683/1\n+CGCACCTACGTTCAATATTA\n++\n+B.DABFFFFFFB.//:FB//\n+@M01368:8:000000000-A3GHV:1:1105:20577:18421/1\n+CTTTGATTCCTGCCTCATCC\n++\n+FBB/:FF9BF/BF.BBFF/:\n+@M01368:8:000000000-A3GHV:1:1105:21099:2895/1\n+ATTCCTGCCTCATCCTATTT\n++\n+BFBFFBFF.0:000BFFBF0\n+@M01368:8:000000'..b'ACC\n++\n+FFFFFFFFFFF/BFBEFFC-\n+@M01368:8:000000000-A3GHV:1:1107:26478:23602/1\n+CTGTCTCTTATACACCTCTC\n++\n+BFFFBBFFF//B/////-;9\n+@M01368:8:000000000-A3GHV:1:1108:11059:23181/1\n+GACCTGTGATCCATCGTGAT\n++\n+FFFFBF;BBFFBFFFFE?F/\n+@M01368:8:000000000-A3GHV:1:1108:12233:13498/1\n+GAACCCTGTCTCTTATACAC\n++\n+EFF?EFFFF0BFFFFBBB00\n+@M01368:8:000000000-A3GHV:1:1108:14328:14751/1\n+GGATACCTGTCTCTTATACA\n++\n+EFFFBF/BF/FFEFFBFFF/\n+@M01368:8:000000000-A3GHV:1:1108:16350:22621/1\n+TGGGCTATTTAGGTTTTATG\n++\n+BE.99FAFFFFFFF/;EFF/\n+@M01368:8:000000000-A3GHV:1:1108:21791:23272/1\n+TGTGGGCTATTTAGGTTTTA\n++\n+EEFEFFFBFBFBBFFFFF./\n+@M01368:8:000000000-A3GHV:1:1108:23314:26089/1\n+TGAAGTAGGAACCAGATGTG\n++\n+BB./:BFFF/F;AA?F////\n+@M01368:8:000000000-A3GHV:1:1108:25084:18127/1\n+TGTGATCCATCGTGATGTCT\n++\n+FF9FBFFB/F/.;FFFF/BB\n+@M01368:8:000000000-A3GHV:1:1108:7626:10048/1\n+TATGCCGTCTTCTGCTTGAA\n++\n+AAFFFFFFAFABBFFFB/;;\n+@M01368:8:000000000-A3GHV:1:1109:11270:12255/1\n+AGACTAAGGCGAATCTCGTT\n++\n+-@DBFFFFBFD---.;BAA.\n+@M01368:8:000000000-A3GHV:1:1109:19224:11655/1\n+CTTATACACATCTCCGAGCC\n++\n+FFB/;F/99/FBFFBDCF;B\n+@M01368:8:000000000-A3GHV:1:1109:21978:9490/1\n+GGCGAATCTCGTATGCAGTT\n++\n+FFFFA;;;FF..9//;/;;/\n+@M01368:8:000000000-A3GHV:1:1109:22910:4079/1\n+GATACAGTCCACTTTAGCTA\n++\n+CCDFFFFFFF0BFFFFFFF0\n+@M01368:8:000000000-A3GHV:1:1109:24217:19077/1\n+TGCCTCATCCTATTACTGTC\n++\n+9;F./B//BBFB9////99/\n+@M01368:8:000000000-A3GHV:1:1109:25237:11722/1\n+AGGCGAATATCGTATGCCGT\n++\n+BF/99D-;.//.../9;B-.\n+@M01368:8:000000000-A3GHV:1:1109:27103:7153/1\n+GACCCTGAAGTAGCTGTCTC\n++\n+BBFFBFFFF///;/9B;///\n+@M01368:8:000000000-A3GHV:1:1109:8763:7859/1\n+GGGCTATTTAGGCTTTATGC\n++\n+EDAA.A/BFFFFFFFFFEB/\n+@M01368:8:000000000-A3GHV:1:1110:12808:18367/1\n+AAGGGGAACGTGTGGGCCTG\n++\n+BFBFFB9..AF?FFFFFFF9\n+@M01368:8:000000000-A3GHV:1:1110:14751:26540/1\n+GTATCTGTCTTTGATTCCTG\n++\n+9-/;B9BF/9BB//B/;///\n+@M01368:8:000000000-A3GHV:1:1110:15519:10008/1\n+ATGACCCTGAAGTAGGAACC\n++\n+FFFFFBFFF.BFFFBFBBA;\n+@M01368:8:000000000-A3GHV:1:1110:16559:7507/1\n+AGGGTGATAGACCTGTGATC\n++\n+/99;;:.//:FFFFBBF//9\n+@M01368:8:000000000-A3GHV:1:1110:16700:6843/1\n+CTTATACACATCTCCGAGCC\n++\n+BFFFFB/BFFBFFF/ADCAD\n+@M01368:8:000000000-A3GHV:1:1110:18014:7856/1\n+TGCTTGCAAAAAAAAAATAG\n++\n+/BBFFF.9/FF?DA=@9./9\n+@M01368:8:000000000-A3GHV:1:1110:23303:11846/1\n+CTGTCTTTGATTCCTGCCTC\n++\n+FBBFFFF/BBFFFFBFF9B;\n+@M01368:8:000000000-A3GHV:1:1111:13195:14562/1\n+ACATCTCCGAGCCCACGAGA\n++\n+FFEFFFFED-DCFF?.:BFA\n+@M01368:8:000000000-A3GHV:1:1111:14287:20817/1\n+ATTAAAGTGTGTTAATTAAT\n++\n+B//B/;/;9//9//;B/:B9\n+@M01368:8:000000000-A3GHV:1:1111:23624:14516/1\n+CATCGTGATGTCTTATTTAG\n++\n+B/FBDE9/;99/B/BFFEF/\n+@M01368:8:000000000-A3GHV:1:1111:7437:24508/1\n+CACATCTCCGAGCCCACGAG\n++\n+FFFFB:FFFFD=CAEEEF>-\n+@M01368:8:000000000-A3GHV:1:1111:8665:25542/1\n+TACGTTCAATATTACAGGCG\n++\n+FFFBA/F//BFFFBF/;/A-\n+@M01368:8:000000000-A3GHV:1:1111:9655:13916/1\n+GTCGCAGTATCTGTCTTTGA\n++\n+F/B?A@F-9BBFF//BB/9/\n+@M01368:8:000000000-A3GHV:1:1112:10272:7828/1\n+CGAATCTCGTATGCCGTCTT\n++\n+FAD--.99;A?////:.9A.\n+@M01368:8:000000000-A3GHV:1:1112:9832:16531/1\n+ATGACCTTGAAGTAGGAACC\n++\n+FFF/BF//9/B//9:B//..\n+@M01368:8:000000000-A3GHV:1:1112:9832:6701/1\n+TTTATGACCCTGAAGTAGGA\n++\n+FFFFFFF/B./FB///;BF/\n+@M01368:8:000000000-A3GHV:1:1113:13532:8618/1\n+AGCTACCTCCAAGTGTTATG\n++\n+FF/BFFB/:.BB//;FBFFF\n+@M01368:8:000000000-A3GHV:1:1113:21679:18011/1\n+AGACTAAGGCGAAGTTCATT\n++\n+;-;AFFE;/99-9--/;///\n+@M01368:8:000000000-A3GHV:1:1113:25528:14016/1\n+TCGTGATGTCTTATTTAAGG\n++\n+FFFEABF//99FFEFFFBFF\n+@M01368:8:000000000-A3GHV:1:1113:5741:16959/1\n+GGGCTATTTAGGTTTTATGA\n++\n+9AD;.FFFB/B/;FBA/B//\n+@M01368:8:000000000-A3GHV:1:1114:10130:11959/1\n+GCAACAAACACACATCCAGA\n++\n+F./B/..9.9:...//////\n+@M01368:8:000000000-A3GHV:1:1114:14540:5315/1\n+TGGGGGCTATTTAGGTTTTT\n++\n+;A.-=A--:BBFB90;;FE.\n+@M01368:8:000000000-A3GHV:1:1114:15066:16302/1\n+TAATTATTGCTTGTAGGACA\n++\n+F/;BFF/;/////9/////.\n+@M01368:8:000000000-A3GHV:1:1114:16639:15258/1\n+ACATACTTACTAAATTGTGT\n++\n+-9-99/B9F/://///99/;\n+@M01368:8:000000000-A3GHV:1:1114:2404:13066/1\n+ATCTGTCTATTATACACATC\n++\n+FFFFFFFFFFFFFFFFEFF0\n'

diff -r 084bbd8ba7b8 -r cd7e644cae1d test-data/paired_hardtrimmed3_pair2_.fastqsanger
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/paired_hardtrimmed3_pair2_.fastqsanger Fri Oct 08 09:57:52 2021 +0000

diff -r 084bbd8ba7b8 -r cd7e644cae1d test-data/paired_hardtrimmed5_pair1_.fastqsanger
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/paired_hardtrimmed5_pair1_.fastqsanger Fri Oct 08 09:57:52 2021 +0000

b'@@ -0,0 +1,396 @@\n+@M01368:8:000000000-A3GHV:1:1101:6911:8255/1\n+ATCTGGTTCCTACTTCAGGG\n++\n+BCCCCFFFFFFFGGGGGGGG\n+@M01368:8:000000000-A3GHV:1:1101:14518:9998/1\n+GTTATTATTATGTCCTACAA\n++\n+AAAAAFFFFFFFGGGGGGGG\n+@M01368:8:000000000-A3GHV:1:1101:18422:19051/1\n+GTATCCGACATCTGGTTCCT\n++\n+CCCCCFDDDDDFGGGGGGGG\n+@M01368:8:000000000-A3GHV:1:1101:25545:21098/1\n+ATTAATTAACACACTTTAGT\n++\n+33AA?DFD5BDFGGGFEBDG\n+@M01368:8:000000000-A3GHV:1:1101:5446:12248/1\n+AATTAACACACTTTAGTAAG\n++\n+CCCCDFFFFCCFGGGGGGGG\n+@M01368:8:000000000-A3GHV:1:1101:5861:6452/1\n+ATTATGTCCTACAAGCATTA\n++\n+ABCCCFFFFFFFGGGGGGGG\n+@M01368:8:000000000-A3GHV:1:1102:10403:6021/1\n+CGCTCCGGGCCCATAACACT\n++\n+>A@AAAAD2ADDFFGGGGGF\n+@M01368:8:000000000-A3GHV:1:1102:10677:23253/1\n+CCTTAAATAAGACATCACGA\n++\n+ABBBBFFFFFFFGGGGGGGC\n+@M01368:8:000000000-A3GHV:1:1102:13809:1733/1\n+ATATTGAACGTAGGTGCGAT\n++\n+BCCBCFFFFFBFGGGGGGGG\n+@M01368:8:000000000-A3GHV:1:1102:17584:10050/1\n+ATCAAAGACAGATACTGCGA\n++\n+CCCCCFFFFFFFGGGGGGGG\n+@M01368:8:000000000-A3GHV:1:1102:18842:24844/1\n+CACTTGGGGGTAGCTAAAGT\n++\n+BBBCBFF@CCBBGGGGGGGG\n+@M01368:8:000000000-A3GHV:1:1102:21788:11027/1\n+GCCCACACGTTCCCCTTAAA\n++\n+ABCCBCCBBFFFGGGGGGGG\n+@M01368:8:000000000-A3GHV:1:1102:5728:8777/1\n+ATATTGAACGTAGGTGCGAT\n++\n+BBBBBFFFFFAFGG5GGGGG\n+@M01368:8:000000000-A3GHV:1:1102:5983:21093/1\n+GTATCCGACATCTGGTTCCT\n++\n+AAABCFCABBCFGGGGGGGG\n+@M01368:8:000000000-A3GHV:1:1102:7765:18353/1\n+CTCCGGGCCCATAACACTTG\n++\n+CCDCCCCCCBCFGGGGGGGG\n+@M01368:8:000000000-A3GHV:1:1103:10405:17879/1\n+GTATCCGACATCTGGTTCCT\n++\n+CBCCCFCCCCCFGGGGGGGG\n+@M01368:8:000000000-A3GHV:1:1103:13493:8205/1\n+GTAGCTAAAGTGAACTGTAT\n++\n+CCCCCFFFFFFFGGGGGGGG\n+@M01368:8:000000000-A3GHV:1:1103:14060:21273/1\n+GTATCCGACATCTGGTTCCT\n++\n+AAABAFCCCCCFGGGGGGGG\n+@M01368:8:000000000-A3GHV:1:1103:14528:12993/1\n+GCCCATAACACTTGGGGGTA\n++\n+BBBBBFFFBDFFGFBCG2EG\n+@M01368:8:000000000-A3GHV:1:1103:17657:20856/1\n+AAAGCGAACTGTATCCGACA\n++\n+ABB?AABBBBFFGGGGGGGG\n+@M01368:8:000000000-A3GHV:1:1103:23099:3794/1\n+AAGACAGATACTGCGACATA\n++\n+BBBBBFFFFFFFGGEEGGFG\n+@M01368:8:000000000-A3GHV:1:1103:25465:20010/1\n+GACATAGGGTGCTCCGGCTC\n++\n+ABBBBFFFFBAAGGGFEFGG\n+@M01368:8:000000000-A3GHV:1:1103:25519:6301/1\n+AAATAAGACATCACGATGGA\n++\n+3A3AAFFFFBFFGGG2CF?4\n+@M01368:8:000000000-A3GHV:1:1103:6074:6549/1\n+TAACACTTGGGGGTAGCTAA\n++\n+CCCBCFFFFFCCGGGGGGGG\n+@M01368:8:000000000-A3GHV:1:1104:11572:8264/1\n+GTATCCGACATCTGGTTCCT\n++\n+BABCBFBACCCFGGGGGGGG\n+@M01368:8:000000000-A3GHV:1:1104:11928:24197/1\n+ACGTAGGTGCGATAAATAAT\n++\n+CDDCCFCFFFBCGGGGGGGG\n+@M01368:8:000000000-A3GHV:1:1104:12288:20635/1\n+CACTTGGGGGTAGCTAAAGT\n++\n+ABA?AFBAB2>AFGGGGFFG\n+@M01368:8:000000000-A3GHV:1:1104:13832:4398/1\n+CACGATGGATCACAGGTCTA\n++\n+AAABABCAFFFFGGGGGGGG\n+@M01368:8:000000000-A3GHV:1:1104:23670:4161/1\n+ATTCAATTGTTATTATTATG\n++\n+AAAABFFFFFFFGGGGGGGC\n+@M01368:8:000000000-A3GHV:1:1104:24927:22253/1\n+AGCTAAAGTGAACTGTATCC\n++\n+AAA?AFFF3DFFFGGBGFF3\n+@M01368:8:000000000-A3GHV:1:1104:4705:7727/1\n+CTACAAGCATTAATTAATTA\n++\n+BBBBBFFBFFFFGGGGGGGG\n+@M01368:8:000000000-A3GHV:1:1104:7756:4776/1\n+GGCCCATAACACTTGGGGGT\n++\n+CCCCCCFFFFFFGGGGGGGE\n+@M01368:8:000000000-A3GHV:1:1105:11310:21761/1\n+ATAAATAATAGGATGAGGCA\n++\n+CCCCBFFFFFFFGGGGGGGG\n+@M01368:8:000000000-A3GHV:1:1105:11578:14676/1\n+ATTGAACGTAGGTGCGATAA\n++\n+CDDDDFFFBFFCGGGGGGGG\n+@M01368:8:000000000-A3GHV:1:1105:13575:19255/1\n+TTAGTAAGTATGTTCGCCTG\n++\n+AA1A1DFFFFFBGG3A111F\n+@M01368:8:000000000-A3GHV:1:1105:15502:11453/1\n+GTCCTACAAGCATTAATTAA\n++\n+A3AAAFFFFFCFGGGGGGGG\n+@M01368:8:000000000-A3GHV:1:1105:16787:9771/1\n+GTTATTATTATGTCCTACAA\n++\n+AABCCFFFFFFFGGGGGGGG\n+@M01368:8:000000000-A3GHV:1:1105:17564:15723/1\n+TATGCTCGCCTGTAATATTG\n++\n+EDCCDFFCEEDCGGGGGGGG\n+@M01368:8:000000000-A3GHV:1:1105:18108:12091/1\n+TAATAGGATGAGGCAGGAAT\n++\n+CCCCCFBFFFFFGGGGGGGG\n+@M01368:8:000000000-A3GHV:1:1105:18331:16683/1\n+TCTGGTTCCTACTTCAGGGT\n++\n+BABA?DFFFFFFGGGGGGGG\n+@M01368:8:000000000-A3GHV:1:1105:20577:18421/1\n+GGGGGTAGCTAAAGTGAACT\n++\n+ABB@3>AAFFFFFEAGGGFG\n+@M01368:8:000000000-A3GHV:1:1105:21099:2895/1\n+TAGCTAAAGTGAACTGTATC\n++\n+CBCBBFFFFFFFGGGGGGGG\n+@M01368:8:000000'..b'GGT\n++\n+ABBBA@FFFFBBGGGGGGGG\n+@M01368:8:000000000-A3GHV:1:1107:26478:23602/1\n+GCTAAAGTGAACTGTATCCG\n++\n+1AAAAF1B13BBBEGGGFGG\n+@M01368:8:000000000-A3GHV:1:1108:11059:23181/1\n+GTTATTATTATGTCCTACAA\n++\n+CCCCCFFFFFFFGGGGGGGG\n+@M01368:8:000000000-A3GHV:1:1108:12233:13498/1\n+TAGGTGCGATAAATAATAGG\n++\n+BCCBAFFBCCCCGGGGGGGG\n+@M01368:8:000000000-A3GHV:1:1108:14328:14751/1\n+ATAATAGGATGAGGCAGGAA\n++\n+BCCCBFFFFFFFGGGGGGGG\n+@M01368:8:000000000-A3GHV:1:1108:16350:22621/1\n+TTAGTAAGTATGTTCGCCTG\n++\n+AAAACFFFFFFFGGGFGGGG\n+@M01368:8:000000000-A3GHV:1:1108:21791:23272/1\n+CTTTAGTAAGTATGTTCGCC\n++\n+3ABBBFFFFF@FGGGGGGGC\n+@M01368:8:000000000-A3GHV:1:1108:23314:26089/1\n+ATTGAACGTAGGTGCGATAA\n++\n+BBBBBFFF?FFAGFBFGGEG\n+@M01368:8:000000000-A3GHV:1:1108:25084:18127/1\n+TTATTATGTCCTACAAGCAT\n++\n+CCBBCFFFFFFFGGGGGGGG\n+@M01368:8:000000000-A3GHV:1:1108:7626:10048/1\n+ATCAAAGACAGATACTGCGA\n++\n+CCCCCFFFFFFFGGGGGGGG\n+@M01368:8:000000000-A3GHV:1:1109:11270:12255/1\n+AATCAAAGACAGATACTGCG\n++\n+CCCCCFFFFFFFGGGGGGGG\n+@M01368:8:000000000-A3GHV:1:1109:19224:11655/1\n+AAATAGCCCACACGTTCCCC\n++\n+BBB@A4FFFBBBGGGGGGGG\n+@M01368:8:000000000-A3GHV:1:1109:21978:9490/1\n+GGGTCATAAAACCTAAATAG\n++\n+?A3AA?DFFFFFGGGGGGGF\n+@M01368:8:000000000-A3GHV:1:1109:22910:4079/1\n+TAATAGGATGAGGCAGGAAT\n++\n+CCCCCFFFFFFFGGGGGGGG\n+@M01368:8:000000000-A3GHV:1:1109:24217:19077/1\n+AAAGTGAACTGTATCCGACA\n++\n+>AAA3BDFFFFDGBFFEEGG\n+@M01368:8:000000000-A3GHV:1:1109:25237:11722/1\n+CCTGTAATATTGAACGTAGG\n++\n+AABBBFFFFFBBF5BGGFGA\n+@M01368:8:000000000-A3GHV:1:1109:27103:7153/1\n+GTAATATTGAACGTAGGTGC\n++\n+33>A?FFFDFBFGCG4EGFG\n+@M01368:8:000000000-A3GHV:1:1109:8763:7859/1\n+TAGTAAGTATGTTCGCCTGT\n++\n+BABAADFFFFFFGGGGGGGG\n+@M01368:8:000000000-A3GHV:1:1110:12808:18367/1\n+AATTAACACACTTTAGTAAG\n++\n+BBBBBFFFFBBFGGGGGGGG\n+@M01368:8:000000000-A3GHV:1:1110:14751:26540/1\n+TAACACTTGGGGGTAGCTAA\n++\n+AAA?1CFFFFADGEEGFGB1\n+@M01368:8:000000000-A3GHV:1:1110:15519:10008/1\n+CTGTAATATTGAACGTAGGT\n++\n+BBBBBFFFFFFFGGGGGGCB\n+@M01368:8:000000000-A3GHV:1:1110:16559:7507/1\n+CATTCAATTGTTATTATTAT\n++\n+ABBBAFFFFFFFFGGGGGGG\n+@M01368:8:000000000-A3GHV:1:1110:16700:6843/1\n+AAATAATAGGATGAGGCAGG\n++\n+BBBBBFFFFFFFGGGGGGGG\n+@M01368:8:000000000-A3GHV:1:1110:18014:7856/1\n+ATAAATAATAGGATGAGGCA\n++\n+AABBBFFFFFFFCGGGCGGG\n+@M01368:8:000000000-A3GHV:1:1110:23303:11846/1\n+ACTTGGGGGTAGCTAAAGTG\n++\n+3ABB?FAB?DAAGGGFBGGB\n+@M01368:8:000000000-A3GHV:1:1111:13195:14562/1\n+ATCAAAGACAGATACTGCGA\n++\n+ABAAAFFFFFFFGGGGGGGG\n+@M01368:8:000000000-A3GHV:1:1111:14287:20817/1\n+GCCAACACGTTCCCCTTAAA\n++\n+>>A3>AAAACFFFGFGFGGG\n+@M01368:8:000000000-A3GHV:1:1111:23624:14516/1\n+GTCCTACAAGCATTAATTAA\n++\n+3>3AAFFFFFAFGGGGGGGG\n+@M01368:8:000000000-A3GHV:1:1111:7437:24508/1\n+ACACACTTTAGTAAGTATGT\n++\n+CBCCDCFFFFFFGGGGGGGG\n+@M01368:8:000000000-A3GHV:1:1111:8665:25542/1\n+TCCTACTTCAGGGTCATAAA\n++\n+AA3AAFFFFFFFGGGFGFFG\n+@M01368:8:000000000-A3GHV:1:1111:9655:13916/1\n+GGCCCATAACACTTGGGGGT\n++\n+1>>1AAFFFFFBGGFE1EEE\n+@M01368:8:000000000-A3GHV:1:1112:10272:7828/1\n+GTATCCGACATCTGGTTCCT\n++\n+AAABABBBBBBFGGGGGGGG\n+@M01368:8:000000000-A3GHV:1:1112:9832:16531/1\n+CTGTAATATTGAACGTAGGT\n++\n+AABABFFFFFFFF4GGGGEB\n+@M01368:8:000000000-A3GHV:1:1112:9832:6701/1\n+CGCCTGTAATATTGAACGTA\n++\n+AABBBBFFFFFFGGGFGGGG\n+@M01368:8:000000000-A3GHV:1:1113:13532:8618/1\n+GGAATCAAAGACAGATACTG\n++\n+AA?AAFFFFFFFGGGGGFBF\n+@M01368:8:000000000-A3GHV:1:1113:21679:18011/1\n+GATCACAGGTCTATCACCCT\n++\n+AA>1>11F1D1DDFFFFGGG\n+@M01368:8:000000000-A3GHV:1:1113:25528:14016/1\n+CCTACAAGCATTAATTAATT\n++\n+>AAAAFFFBFFFGGGGGGGG\n+@M01368:8:000000000-A3GHV:1:1113:5741:16959/1\n+TAGTAAGTATGTTCGCCTGT\n++\n+ABBBBFFFFFFFGGGFGGGG\n+@M01368:8:000000000-A3GHV:1:1114:10130:11959/1\n+CGTTCCCCTTAAATAAGACA\n++\n+>A33>FFFFFF@FFFGGGGF\n+@M01368:8:000000000-A3GHV:1:1114:14540:5315/1\n+CTTTAGTAAGTATGTTCGCC\n++\n+AABCCFFFFFFFGGGGGGGG\n+@M01368:8:000000000-A3GHV:1:1114:15066:16302/1\n+TAAATAAGACATCACGATGG\n++\n+BBBBAFFBDFBFBGGGGGFG\n+@M01368:8:000000000-A3GHV:1:1114:16639:15258/1\n+CCTAAATAGCCCACACGTTC\n++\n+11>>ABFFFFFFGGCGC1BB\n+@M01368:8:000000000-A3GHV:1:1114:2404:13066/1\n+TCCTACAAGCATTAATTAAT\n++\n+CCCCCFFFFCFFGGGGGGGG\n'

diff -r 084bbd8ba7b8 -r cd7e644cae1d test-data/paired_hardtrimmed5_pair2_.fastqsanger
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/paired_hardtrimmed5_pair2_.fastqsanger Fri Oct 08 09:57:52 2021 +0000

diff -r 084bbd8ba7b8 -r cd7e644cae1d test-data/sanger_full_range_report_results1.txt
--- a/test-data/sanger_full_range_report_results1.txt Tue Jul 30 06:26:49 2019 -0400
+++ b/test-data/sanger_full_range_report_results1.txt Fri Oct 08 09:57:52 2021 +0000

@@ -3,21 +3,24 @@
==========================
Input filename: input_1.fastq
Trimming mode: single-end
-Trim Galore version: 0.6.3
-Cutadapt version: 2.4
-Number of cores used for trimming: 1
+Trim Galore version: 0.6.7
+Cutadapt version: 3.4
+Python version: could not detect
+Number of cores used for trimming: 4
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
+Unable to auto-detect most prominent adapter from the first specified file (count Nextera: 0, count smallRNA: 0, count Illumina: 0)
+Defaulting to Illumina universal adapter ( AGATCGGAAGAGC ). Specify -a SEQUENCE to avoid this behavior).
Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; default (inconclusive auto-detection))
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length before a sequence gets removed: 20 bp

-This is cutadapt 2.4 with Python 3.7.3
-Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC input_1.fastq
-Processing reads on 1 core in single-end mode ...
-Finished in 0.00 s (1608 us/read; 0.04 M reads/minute).
+This is cutadapt 3.4 with Python 3.9.6
+Command line parameters: -j 4 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC input_1.fastq
+Processing reads on 4 cores in single-end mode ...
+Finished in 0.01 s (5282 µs/read; 0.01 M reads/minute).

=== Summary ===

@@ -31,10 +34,10 @@

=== Adapter 1 ===

-Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 1 times.
+Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 1 times

No. of allowed errors:
-0-9 bp: 0; 10-13 bp: 1
+1-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
A: 0.0%

diff -r 084bbd8ba7b8 -r cd7e644cae1d test-data/sanger_full_range_report_results1gz.txt
--- a/test-data/sanger_full_range_report_results1gz.txt Tue Jul 30 06:26:49 2019 -0400
+++ b/test-data/sanger_full_range_report_results1gz.txt Fri Oct 08 09:57:52 2021 +0000

@@ -3,11 +3,14 @@
==========================
Input filename: input_1.fastq.gz
Trimming mode: single-end
-Trim Galore version: 0.6.3
-Cutadapt version: 2.4
-Number of cores used for trimming: 1
+Trim Galore version: 0.6.7
+Cutadapt version: 3.4
+Python version: could not detect
+Number of cores used for trimming: 4
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
+Unable to auto-detect most prominent adapter from the first specified file (count Illumina: 0, count Nextera: 0, count smallRNA: 0)
+Defaulting to Illumina universal adapter ( AGATCGGAAGAGC ). Specify -a SEQUENCE to avoid this behavior).
Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; default (inconclusive auto-detection))
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
@@ -15,10 +18,10 @@
Output file will be GZIP compressed

-This is cutadapt 2.4 with Python 3.7.3
-Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC input_1.fastq.gz
-Processing reads on 1 core in single-end mode ...
-Finished in 0.02 s (7871 us/read; 0.01 M reads/minute).
+This is cutadapt 3.4 with Python 3.9.6
+Command line parameters: -j 4 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC input_1.fastq.gz
+Processing reads on 4 cores in single-end mode ...
+Finished in 0.01 s (5217 µs/read; 0.01 M reads/minute).

=== Summary ===

@@ -32,10 +35,10 @@

=== Adapter 1 ===

-Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 1 times.
+Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 1 times

No. of allowed errors:
-0-9 bp: 0; 10-13 bp: 1
+1-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
A: 0.0%

diff -r 084bbd8ba7b8 -r cd7e644cae1d test-data/sanger_full_range_results1.fastq.gz

Binary file test-data/sanger_full_range_results1.fastq.gz has changed

diff -r 084bbd8ba7b8 -r cd7e644cae1d test-data/sanger_full_range_results2.fastq.gz

Binary file test-data/sanger_full_range_results2.fastq.gz has changed

diff -r 084bbd8ba7b8 -r cd7e644cae1d test-data/sanger_full_range_results3.fastq.gz

Binary file test-data/sanger_full_range_results3.fastq.gz has changed

diff -r 084bbd8ba7b8 -r cd7e644cae1d test-data/trimmed_polyA_reads_pair1.fastqsanger
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/trimmed_polyA_reads_pair1.fastqsanger Fri Oct 08 09:57:52 2021 +0000

b'@@ -0,0 +1,396 @@\n+@M01368:8:000000000-A3GHV:1:1101:6911:8255/1\n+ATCTGGTTCCTACTTCAGGGCCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATT\n++\n+BCCCCFFFFFFFGGGGGGGGGGGHHHHGHGHHHHHHHHHGGGGGGHHHHGHHHHHHHHHHGHHHHHHGGHGGHHHGHHHHFHHGHHHHHHHHHGHEHEFFGHHEGGCEFGGFHHHBGHHGHHHHGHFHHHGHGHGHGGCDFDDACGGGGGGGAAFFFFFFFFFBAFFFFFB;FFFFFFADDFFFFFFFFFFEFFFFFFFFFFBFFFFFFFFFFFFFFEFFFFFFFFBFEFFFFEFE;DFFFDFBFF/9BFB\n+@M01368:8:000000000-A3GHV:1:1101:14518:9998/1\n+GTTATTATTATGTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGGGATAGACCTGTGATCCATCGTGAT\n++\n+AAAAAFFFFFFFGGGGGGGGGGHGGHHHHGHHHHHHHGCGHHHHHHHHHHHHHHHGGGGGHHHHHHHHHGHHGFHFE5BGEEHFGGGHHHHHHHHFBHHGGGGFHGHHFGHHHHGHHHHHHGEGGGGFHFHGEGHHGGCDGDGHGGGDGGHGGCGGGHGHHH/ACDG?.1FGCDCCGCA.CC@CDCHFHGFFGGGEBFGAB//CEFBFGG.:;D;;A0AFFFFFB..:@ABFF//;BFFFFFBF/9D:A//\n+@M01368:8:000000000-A3GHV:1:1101:18422:19051/1\n+GTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACG\n++\n+CCCCCFDDDDDFGGGGGGGGGGHHHHHHHHHHHHHHHHGHHHHHHFHHHHGGGGHHHHHHHHHGHHHHHHHHHHHHGGHGGHHHHHHHHHHHHHHHHHHHHHHHHHHHGHHHHHGCGGGHHHHHHHHHHHHHHHHHHHHHHGFDHGFHCFGGGGFGGFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF;FFFFFFFFFFFFFFFFFFFFFFFFFFFFEFBFFFFFFFFFF:FFF.\n+@M01368:8:000000000-A3GHV:1:1101:25545:21098/1\n+ATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATAAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGGCTTATTTAAGGGGAACGGGTGGGG\n++\n+33AA?DFD5BDFGGGFEBDGEGHEGHGEGHCEGGHHCHGHHFFHHGFGAGE53FF2FAFFGDE5FFFE5GFBFGAEE1GHHHGHHHEHE3FGHF@GEGEGGHHGG3FAGFFDE?EEE3GFEGFGFGGCG?GHHHFHGGGC@DHFFHD/A<C@EGFDCGGGHFHHHEGFGHBFHG0:CEHFCHGGED.;0CEF.F99B0CFFEEFGGG0FBFBBF0F/FFBDE?/9//9B.FFBFFFFFFBF..A..;@B--\n+@M01368:8:000000000-A3GHV:1:1101:5446:12248/1\n+AATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTAT\n++\n+CCCCDFFFFCCFGGGGGGGGFGHHHHHGGGGHHHHHHHHHHHHHHHHGBGHGGHGGHHHHHHHHHHGHGHGGGGGHHHHHHHHGHHHHHHHHHGGGGGHHHHFFGHHHGGGGGGHHHGFGGHHGGGGHHHHHHGGGGGGHGHHGGGGGGGHGGGGGGHHHHHHHHHHHHHFHGGGHHHHGGGGGG:FE;EGEGGGGG/;?FGGGGGGGFFFFGGFFFFFFFFFBFFFFFFFFFFBFFFFFFEFFFFFEFFF\n+@M01368:8:000000000-A3GHV:1:1101:5861:6452/1\n+ATTATGTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTT\n++\n+ABCCCFFFFFFFGGGGGGGGGGHHHHHHHHHHHGHHHHGHHHHHHHHHHHGGGGHHHHHHHHFHHHHHHGGHGHGGHGGHHHHHHHGGHFHHHGGGGGHHHHHHHHHHHHHHHHHHGGGGGHHHHHEGGHHGGGGGGHHHGGGGHGGGGGHHHHHHGGGDCGHHHHGGGGGGGHEFGGGGHGHHHGHGGGFGGGGGGGEGGGGGGG?E0CEFGGGGGFEE9EEFFFFFBFFFFFFFBFFBD.AFFFFFFF0\n+@M01368:8:000000000-A3GHV:1:1102:10403:6021/1\n+CGCTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTG\n++\n+>A@AAAAD2ADDFFGGGGGFGGHA?EAEFBEAGHFABFGG5FDF5DB1EEGAFDFB53FF5FH@G5FFEHGHEFHFFHBE333GF43GCGGGGE@0?BFGGB0B?FHGFDGGHHHBFFDEGGHGFFFDFE@<1>@FFFGHHHHFHEFGDABFFGG/@DCE<CG1<GF0/DD000=<DHGBDFDCECE/:AC?-;-;9B/ABBB-AD9BFB99AB?BDFBAD-.9..@;=;;..9..9/9;BEF;A:9/BFF\n+@1:A:M01368:8:000000000-A3GHV:1:1102:10677:23253/1_PolyA:1\n+CCTTAAATAAGACATCACGATGGATCAC'..b'F<0CC/;C-:-;;09;FFBFBBFFBC0FFFGGFC0009C00090/-:--9--;-;AFFE;/99-9--/;///\n+@M01368:8:000000000-A3GHV:1:1113:25528:14016/1\n+CCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGG\n++\n+>AAAAFFFBFFFGGGGGGGGGGHHFHGHHHHGHHHHHHHHHHHGGGGHHHHFHHHHFHGHHHHGAFFEFHEGHHHHHHHHGHEHHGGFGGGHHHHHHFHHHHHGGHHHHGGGGGHFHHFF?HHGGFECEFFGHFFGFHGECDGHGBGFHGDF@@?CGFHCEGGGFD.CCC?EGHBHHHFHHFBCFFGEB/CEGGGGDAA.90C9CEBFGGBBF/9.9FBFFFBBFF//99FFFFEABF//99FFEFFFBFF\n+@1:A:M01368:8:000000000-A3GHV:1:1113:5741:16959/1_PolyA:1\n+TAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATG\n++\n+ABBBBFFFFFFFGGGFGGGGGGHHHGHHGGHBGHGAGFFCAFGHGFFGHHGFHHHHHGGGGGHGHHHHHHHHE3BFFHHHGG0EDF@GHFFGGGHGGGGGGGGGGGGGHHGGEEFHGFHHDDG@DGGGHHGDGGGGGHGG?CF?HHGHHHGHGHHHFFHGGGHHHHGGCD.;0<C;CGGGGEFF/.;0;FFFBF/0;0CFGFFB..9B/;0CBFFBBFFFFBAC?DED9;B9AD;.FFFB/B/;FBA/B/\n+@1:A:M01368:8:000000000-A3GHV:1:1114:10130:11959/1_PolyA:1\n+CGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTCTGATCTGTCTCTTATACACATCTCCGAGCCCACGAGACTAAGGCGAATCTCGTATGCCGTCTTCTGCTTGCAACAAACACACATCCAG\n++\n+>A33>FFFFFF@FFFGGGGFGGD4EGGGGGHHGFFGHFGGHHHFEFHECFHHHEHGAGBCCGCCEGGHGHEGFBFHFHHHHGGGHFHGHEGGGFEGEGG??@DBGHGGC-@FFGHFHFHB-??DA-DD@9:BEBG@B?E?A.ABBFBFA??F.FF/BFFB/B9B/9;BF9FF9FFFFFFFFFFFFFF?BB?;9EE;-;DDB9//;B-B@;ABFFEFFFF/-.9A.;//9/BF./B/..9.9:.../////\n+@M01368:8:000000000-A3GHV:1:1114:14540:5315/1\n+CTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGGGGGCTATTTAGGTTTTT\n++\n+AABCCFFFFFFFGGGGGGGGGGHHHHHHHFHHHHGHHGHHGGGHGGHHHHHHHGHHHHHHGGGGGHHFHHHFGHHGGFHHHHHGGGGGHHHGHGGHHHGGGGGGHGHGGGGHHGGGGHHHHHEGDDFGFFFHHGGGGGCDAFCFGFDHHHHGGHGHHHHHHBCGEHHHHGGHG.ACGEHGG0CBFFF:A;BB0;09CGF00CFFFE0AA?//CFFFFFFFFFFFFFFFBEF;A.-=A--:BBFB90;;FE.\n+@1:A:M01368:8:000000000-A3GHV:1:1114:15066:16302/1_PolyA:1\n+TAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAACGGTTGTTAATTAATTATTGCTTGTAGGAC\n++\n+BBBBAFFBDFBFBGGGGGFGGGBGFFFHGFHHGFFFHGHHHGHHHHFFHHHGHGC?AEFFHEFBFFFGHHHHH1FDGFFHGHGHFEGCGC-<<AHHHGGGGGGGFHH0GHFCCCADGGG?.9/A-???DGGFFF.9F9/EE-;;BBBFFBFFFFFFFFFEFFFFBFFBBFFFFF/BFFBFFFFF-DBFFF;/BFF//BB//9/BEA---9:BFFFFFF/F/.;.:@9.BBFF/;BFF/;/////9/////\n+@M01368:8:000000000-A3GHV:1:1114:16639:15258/1\n+CCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGCGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTCCAATATTACAGGCGAACATACTTACTAAATTGTGT\n++\n+11>>ABFFFFFFGGCGC1BBF1GHHHBHHHHGFHGH1A100AA/GGEHGFBAA1FFD2FHHHHECG2F1BB/E0FC/A>EE/FGGFGEF1EGBBEHHCGGGHBGEHFHE0B?E--;C?CCGGG@A@GBFBBBB09?@??A-AB--ABE@=-=-9AE9A;FFFFFE=9-//;//;9FF/////;;///9B///;/B////9FFBB;--A@-;/9;9-:-/;;FFFE9BF?@;-9-99/B9F/://///99/;\n+@M01368:8:000000000-A3GHV:1:1114:2404:13066/1\n+TCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCTGTCTATTATACACATC\n++\n+CCCCCFFFFCFFGGGGGGGGGGHHHHHGHHHHHHHHHFFHHHHHGGGGHHHHHHHHFHHHHHHFGGHHGGHGGHHHHHHGHHFHHHHGGGGGGHHHHHHGHHHHHHHHHHGGGGGGGHH?FGHHHGGGGGGHHGGFGGHHGGGGHHHHHFGGGGFGHGHHGGGGGGGHGGGEGGHHGHHHHHHHHHGFBFFDA0FGGGFFGG0:EFGGGGGGGG;AEBF0B0BFFBFFFFFFFFFFFFFFFFFFFFFEFF0\n'

diff -r 084bbd8ba7b8 -r cd7e644cae1d test-data/trimmed_polyA_reads_pair2.fastqsanger
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/trimmed_polyA_reads_pair2.fastqsanger Fri Oct 08 09:57:52 2021 +0000

diff -r 084bbd8ba7b8 -r cd7e644cae1d trim_galore.xml
--- a/trim_galore.xml Tue Jul 30 06:26:49 2019 -0400
+++ b/trim_galore.xml Fri Oct 08 09:57:52 2021 +0000

[

b'@@ -1,50 +1,10 @@\n-<tool id="trim_galore" name="Trim Galore!" version="0.6.3" profile="17.01">\n- \n+<tool id="trim_galore" name="Trim Galore!" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">\n <description>Quality and adapter trimmer of reads</description>\n <macros>\n- <macro name="adapter_trimming">\n- <conditional name="trimming">\n- <param name="trimming_select" type="select" label="Adapter sequence to be trimmed">\n- <option value="">Automatic detection</option>\n- <option value="--illumina">Illumina universal</option>\n- <option value="--nextera">Nextera transposase</option>\n- <option value="--small_rna">Illumina small RNA adapters</option>\n- <option value="user">User defined adapter sequence</option>\n- </param>\n- <when value=""/>\n- <when value="--illumina"/>\n- <when value="--nextera"/>\n- <when value="--small_rna"/>\n- <when value="user">\n- <param name="adapter" type="text" value="AGATCGGAAGAGC" label="Adapter sequence to be trimmed off">\n- <validator type="regex" message="Adapter sequence must contain DNA characters only (A,C,T,G or N)">^[ACTGNactgn]*$</validator>\n- </param>\n- <yield/>\n- </when>\n- </conditional>\n- </macro>\n- <macro name="paired_adapter_trimming">\n- <expand macro="adapter_trimming">\n- <param name="adapter2" type="text" optional="True" value="" label="Adapter sequence to be trimmed off read 2">\n- <validator type="regex" message="Adapter sequence must contain DNA characters only (A,C,T,G or N)">^[ACTGNactgn]*$</validator>\n- </param>\n- </expand>\n- <param name="trim1" type="boolean" truevalue="--trim1" falsevalue="" checked="False" label="Trims 1 bp off every read from its 3\' end." help="" />\n- <param name="three_prime_clip_R1" type="integer" value="" optional="True" label="Remove N bp from the 3\' end of read 1">\n- <help>Instructs Trim Galore! to remove N bp from the 3\' end of read 1 after adapter/quality trimming has been performed.\n- This may remove some unwanted bias from the 3\' end that is not directly related to adapter sequence or basecall quality.\n- (--three_prime_clip_R1)</help>\n- </param>\n- <param name="three_prime_clip_R2" type="integer" value="" optional="True" label="Remove N bp from the 3\' end of read 2">\n- <help>Instructs Trim Galore! to remove N bp from the 3\' end of read 2 after\n- adapter/quality trimming has been performed. This may remove some unwanted bias from\n- the 3\' end that is not directly related to adapter sequence or basecall quality.</help>\n- </param>\n- </macro>\n+ <import>macros.xml</import>\n </macros>\n- <requirements>\n- <requirement type="package" version="0.6.3">trim-galore</requirement>\n- </requirements>\n+ <expand macro="requirements" />\n+ <expand macro="xrefs"/>\n <version_command>\n trim_galore --version\n </version_command>\n@@ -92,6 +52,9 @@\n \n trim_galore\n \n+ ## according the develpers 4 cores could be a sweet spot, anything above has diminishing returns\n+ --cores \\${GALAXY_SLOTS:-4}\n+\n ## we only support fastqsanger\n --phred33\n \n@@ -177,6 +140,18 @@\n --dont_gzip\n #end if\n \n+ ## Trimming settings\n+ #if $trimming.settingsType == \'custom\'\n+ #if $trimming.hardtrim5\n+ --hardtrim5 $trimming.hardtrim5\n+ #end if\n+ #if $trimming.hardtrim3 \n+ --hardtrim3 $trimming.h'..b'Trim Galore! removes entire sequence pairs if one (or both) of the two reads became shorter than the set length cutoff. Reads of a read-pair that are longer than a given threshold but for which the partner read has become too short can optionally be written out to single-end files. This ensures that the information of a read pair is not lost entirely if only one read is of good quality\n * Trim Galore! can trim paired-end files by 1 additional bp from the 3\' end of all reads to avoid problems with invalid alignments with Bowtie 1\n \n-.. _Trim Galore!: http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/\n \n It is developed by Felix Krueger at the Babraham Institute.\n \n@@ -591,6 +717,54 @@\n | Selecting this option for non-directional RRBS libraries will screen quality-trimmed sequences for \'CAA\' or \'CGA\' at the start of the read and, if found, removes the first two basepairs. Like with the option \'--rrbs\' this avoids using cytosine positions that were filled-in during the end-repair step. \'--non_directional\' requires \'--rrbs\' to be specified as well.\n |\n | *option --non_directional*\n+\n+---- \n+\n+**Trim specific seetings**\n+\n+* **Hard-trimming mode**\n+ \n+ | Instead of performing adapter-/quality trimming, this option will simply hard-trim sequences to N bp at the 5\' or 3\' -end.\n+ |\n+ | *options -hardtrim5 and -hardtrim3*\n+\n+* **Mouse Epigenetic Clock mode**\n+\n+ | In this mode, reads are trimmed in a specific way that is currently used for the Mouse Epigenetic Clock (see here: `Multi-tissue DNA methylation age predictor in mouse`_). Following this, Trim Galore will exit.\n+ | \n+ | In it\'s current implementation, the dual-UMI RRBS reads come in the following format:\n+ |\n+ | Read 1 5\' UUUUUUUU CAGTA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF TACTG UUUUUUUU 3\'\n+ | Read 2 3\' UUUUUUUU GTCAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF ATGAC UUUUUUUU 5\'\n+ |\n+ | Where UUUUUUUU is a random 8-mer unique molecular identifier (UMI), CAGTA is a constant region, and FFFFFFF... is the actual RRBS-Fragment to be sequenced. The UMIs for Read 1 (R1) and Read 2 (R2), as well as the fixed sequences (F1 or F2), are written into the read ID and removed from the actual sequence.\n+ |\n+ | *option --clock*\n+\n+* **PolyA mode**\n+\n+ | This is a new, still experimental, trimming mode to identify and remove poly-A tails from sequences. When selected, Trim Galore attempts to identify from the first supplied sample whether sequences contain more often a stretch of either \'AAAAAAAAAA\' or \'TTTTTTTTTT\'. This determines if Read 1 of a paired-end end file, or single-end files, are trimmed for PolyA or PolyT. In case of paired-end sequencing, Read2 is trimmed for the complementary base from the start of the reads.\n+ | \n+ | PLEASE NOTE: The poly-A trimming mode expects that sequences were both adapter and quality trimmed before looking for Poly-A tails, and it is the user\'s responsibility to carry out an initial round of trimming.\n+ |\n+ | *option --polyA*\n+\n+* **Amplicon mode**\n+\n+ | This is a special mode of operation for paired-end data, such as required for the IMPLICON method, where a UMI sequence is getting transferred from the start of Read 2 to the readID of both reads. Following this, Trim Galore will exit.\n+ | \n+ | In it\'s current implementation, the UMI carrying reads come in the following format:\n+ |\n+ | Read 1 5\' FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF 3\'\n+ | Read 2 3\' UUUUUUUUFFFFFFFFFFFFFFFFFFFFFFFFFFFF 5\'\n+ |\n+ | Where UUUUUUUU is a random 8-mer unique molecular identifier (UMI) and FFFFFFF... is the actual fragment to be sequenced.\n+ |\n+ | *option --amplicon*\n+\n+.. _Trim Galore!: http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/\n+.. _Multi-tissue DNA methylation age predictor in mouse: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1203-5\n+\n ]]></help>\n- <citations></citations>\n+ <expand macro="citations" />\n </tool>\n'