# HG changeset patch
# User iuc
# Date 1724684347 0
# Node ID f7732611d0fc98b2d9d0aacc2bfc5755a52d3992
# Parent  0c5a5e670ac0cc917bfaf5bf47811c69b1158962
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 7632986831e24fcd189a57d824b9e6b1d5dc5c4c

diff -r 0c5a5e670ac0 -r f7732611d0fc fasterq_dump.xml
--- a/fasterq_dump.xml	Fri Jun 23 21:31:47 2023 +0000
+++ b/fasterq_dump.xml	Mon Aug 26 14:59:07 2024 +0000
@@ -13,8 +13,10 @@
     @CONFIGURE_RETRY@
     @SET_ACCESSIONS@
     while [ \$SRA_PREFETCH_ATTEMPT -le \$SRA_PREFETCH_RETRIES ] ; do
-        fasterq-dump "\$acc" -e \${GALAXY_SLOTS:-1}
-        --seq-defline '@\$sn/\$ri'
+        fasterq-dump "\$acc"
+        -e \${GALAXY_SLOTS:-1}
+        -t \${TMPDIR}
+        --seq-defline '$adv.seq_defline'
         --qual-defline '+'
         $adv.split
         #if str( $adv.minlen ) != "":
@@ -71,6 +73,7 @@
     <inputs>
         <expand macro="input_conditional"/>
         <section name="adv" title="Advanced Options" expanded="False">
+            <expand macro="defline" defline_param="--seq-defline" defline_default="@$ac.$sn/$ri"/>
             <param name="minlen" type="integer" label="Minimum read length" optional="true" help="Filter by sequence length. Will dump only reads longer or equal to this value." argument="--min-read-len"/>
             <param name="split" type="select" display="radio" label="Select how to split the spots" help="This option will only be used when there are multiple reads per spot (for example paired-end).">
                 <option value="--split-3">--split-3: write properly paired biological reads into different files and single reads in another file</option>
@@ -186,6 +189,30 @@
                 </element>
             </output_collection>
         </test>
+        <test expect_num_outputs="4">
+            <param name="input_select" value="file_list"/>
+            <param name="file_list" value="sra_manifest.tabular" ftype="sra_manifest.tabular"/>
+            <section name="adv">
+                <param name="seq_defline" value="@$ac.$si/$ri $sn length=$rl"/>
+            </section>
+            <output_collection name="list_paired" type="list:paired" count="1">
+                <element name="SRR11953971">
+                    <element name="forward" ftype="fastqsanger.gz" decompress="True">
+                        <assert_contents>
+                            <!-- TODO replace has_size by has_line -->
+                            <has_size min="56206"/>
+                            <!-- <has_line line="@SRR11953971.2053/1 2053 length=101"/> -->
+                        </assert_contents>
+                    </element>
+                    <element name="reverse" ftype="fastqsanger.gz" decompress="True">
+                        <assert_contents>
+                            <has_size min="59843"/>
+                            <!-- <has_line line="@SRR11953971.2053/2 2053 length=101"/> -->
+                        </assert_contents>
+                    </element>
+                </element>
+            </output_collection>
+        </test>
     </tests>
     <help><![CDATA[
 **What it does?**
diff -r 0c5a5e670ac0 -r f7732611d0fc fastq_dump.xml
--- a/fastq_dump.xml	Fri Jun 23 21:31:47 2023 +0000
+++ b/fastq_dump.xml	Mon Aug 26 14:59:07 2024 +0000
@@ -12,7 +12,7 @@
     @SET_ACCESSIONS@
 
     #if $input.input_select == "sra_file":
-        fastq-dump --log-level fatal --accession '${input.file.name}'
+        fastq-dump --log-level fatal --accession "\$acc"
     #else:
         ## Do not use prefetch if region is specified, to avoid downloading
         ## the complete sra file.
@@ -20,9 +20,9 @@
             prefetch -X 200000000 "\$acc" &&
         #end if
         fastq-dump --accession "\$acc"
-        --split-files
     #end if
-    --defline-seq '@\$sn[_\$rn]/\$ri'
+    --split-files
+    --defline-seq '$adv.defline_seq'
     --defline-qual '+'
 
     $adv.split
@@ -91,6 +91,7 @@
             <option value="fastqsanger.bz2">bzip2 compressed fastq</option>
         </param>
         <section name="adv" title="Advanced Options" expanded="False">
+            <expand macro="defline" defline_param="--defline-seq" defline_default="@$ac.$sn[_$rn]/$ri"/>
             <param name="minID" type="integer" label="Minimum spot ID" optional="true" help="Minimum spot id to be dumped." argument="--minSpotId"/>
             <param name="maxID" type="integer" label="Maximum spot ID" optional="true" help="Maximum spot id to be dumped." argument="--maxSpotId"/>
             <param name="minlen" type="integer" label="Minimum read length" optional="true" help="Filter by sequence length. Will dump only reads longer or equal to this value." argument="--minReadLen"/>
@@ -225,6 +226,64 @@
                 </element>
             </output_collection>
         </test>
+        <test expect_num_outputs="2">
+            <param name="input_select" value="accession_number"/>
+            <param name="outputformat" value="fastqsanger.gz"/>
+            <param name="accession" value="ERR086330, SRR11953971"/>
+            <section name="adv">
+                <param name="defline_seq" value="@$ac.$si/$ri $sn length=$rl"/>
+            </section>
+            <output_collection name="list_paired" type="list:paired" count="2">
+                <element name="ERR086330">
+                    <element name="forward" ftype="fastqsanger.gz" decompress="True">
+                        <assert_contents>
+                            <!-- decompressed content assertions only work from 23.1
+                                 therefore we test for size being at least one byte
+                                 larger than the results of the previous test which
+                                 uses the shorter default deflines
+                                 TODO replace has_size by has_line-->
+                            <has_size min="147"/>
+                            <!-- <has_line line="@ERR086330.1/1 1 length=76"/> -->
+                        </assert_contents>
+                    </element>
+                    <element name="reverse" ftype="fastqsanger.gz" decompress="True">
+                        <assert_contents>
+                            <has_size min="141"/>
+                            <!-- <has_line line="@ERR086330.1/2 1 length=76"/> -->
+                        </assert_contents>
+                    </element>
+                </element>
+                <element name="SRR11953971">
+                    <element name="forward" ftype="fastqsanger.gz" decompress="True">
+                        <assert_contents>
+                            <has_size min="56206"/>
+                            <!-- <has_line line="@SRR11953971.1/1 1 length=101"/> -->
+                        </assert_contents>
+                    </element>
+                    <element name="reverse" ftype="fastqsanger.gz" decompress="True">
+                        <assert_contents>
+                            <has_size min="59843"/>
+                            <!-- <has_line line="@SRR11953971.1/2 1 length=101"/> -->
+                        </assert_contents>
+                    </element>
+                </element>
+            </output_collection>
+        </test>
+        <test expect_num_outputs="2">
+            <param name="input_select" value="sra_file"/>
+            <param name="sra_file" value="SRR522874.sra"/>
+            <param name="split" value="True"/>
+            <param name="skip_technical" value="True"/>
+            <section name="adv">
+                <param name="defline_seq" value="@$sn/$ri"/>
+            </section>
+            <output_collection name="list_paired" type="list:paired" count="1">
+                <element name="SRR522874.sra">
+                    <element name="forward" file="SRR522874.sra_2_1.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
+                    <element name="reverse" file="SRR522874.sra_4_1.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
+                </element>
+            </output_collection>
+        </test>
     </tests>
     <help><![CDATA[
 **What it does?**
diff -r 0c5a5e670ac0 -r f7732611d0fc macros.xml
--- a/macros.xml	Fri Jun 23 21:31:47 2023 +0000
+++ b/macros.xml	Mon Aug 26 14:59:07 2024 +0000
@@ -1,6 +1,6 @@
 <macros>
-    <token name="@TOOL_VERSION@">3.0.5</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@TOOL_VERSION@">3.1.1</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <token name="@PROFILE@">22.01</token>
     <xml name="edam_ontology">
         <edam_topics>
@@ -15,8 +15,8 @@
     <macro name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">sra-tools</requirement>
-            <requirement type="package" version="2.6">pigz</requirement>
-            <requirement type="package" version="1.17">samtools</requirement>
+            <requirement type="package" version="2.8">pigz</requirement>
+            <requirement type="package" version="1.20">samtools</requirement>
             <yield/>
         </requirements>
     </macro>
@@ -36,11 +36,6 @@
     <token name="@COPY_CONFIGFILE@"><![CDATA[
         mkdir -p ~/.ncbi &&
         cp '$user_settings_mkfg' ~/.ncbi/user-settings.mkfg &&
-        vdb-config -s "/repository/user/main/public/root=\$PWD" &&
-        vdb-config -s "/repository/user/ad/public/root=\$PWD" &&
-        vdb-config -s "/repository/user/default-path=\$PWD" &&
-        vdb-config -s "/repository/user/main/public/root=\$PWD" &&
-        vdb-config -s /http/timeout/read=10000 &&
     ]]></token>
     <token name="@SET_ACCESSIONS@"><![CDATA[
         #if $input.input_select == "sra_file":
@@ -69,6 +64,11 @@
 /config/default = "false"
 /libs/temp_cache = "."
 /tools/prefetch/download_to_cache = "false"
+/http/timeout/read = "1000"
+/repository/user/main/public/root = "."
+/repository/user/ad/public/root = "."
+/repository/user/default-path = "."
+/repository/user/main/public/root = "."
             ]]></configfile>
         </configfiles>
     </macro>
@@ -116,13 +116,42 @@
         <param name="minMapq" type="integer" min="0" max="42" label="Minimum mapping quality" optional="true" help="Minimum mapping quality an alignment has to have, to be dumped." argument="--min-mapq"/>
     </macro>
     <macro name="region">
-        <param format="text" name="region" type="text" label="aligned region" optional="true"
+        <param name="region" type="text" label="aligned region" optional="true"
                help="Filter by position on genome. Can be either accession.version (ex: NC_000001.10), chromosome name (ex:chr1 or 1) or 1-based coordinates (ex: chr1:1-101)." argument="--aligned-region"/>
     </macro>
     <macro name="matepairDist">
         <param name="matepairDist" type="text" label="mate-pair distance (from-to|unknown)" optional="true"
                help="Filter by distance between matepairs. Use unknown to find matepairs split between the references. Use from-to (inclusive) to limit matepair distance on the same reference" argument="--matepair-distance"/>
     </macro>
+    <macro name="defline" tokens="defline_param,defline_default">
+        <param argument="@DEFLINE_PARAM@" value="@DEFLINE_DEFAULT@" type="text" label="Defline format specification for sequence">
+            <help>A string of characters and/or variables. The variables can be one of:
+                $ac: accession, $si: spot id, $sn: spot name, $sg: spot group (barcode), $sl: spot length in bases, $ri: read number, $rn: read name, $rl: read length in bases.
+                '[]' could be used for an optional output: if all vars in [] yield empty values whole group is not printed. Empty value is empty string or for numeric variables.
+                Ex: @$sn[_$rn]/$ri '_$rn' is omitted if name is empty"</help>
+            <!-- allow many chars, but quotes and backslash -->
+            <sanitizer>
+                <valid initial="string.ascii_letters,string.digits">
+                    <add value="@" />
+                    <add value="$" />
+                    <add value="[" />
+                    <add value="]" />
+                    <add value="_" />
+                    <add value="-" />
+                    <add value="+" />
+                    <add value="." />
+                    <add value=";" />
+                    <add value=":" />
+                    <add value="/" />
+                    <add value="?" />
+                    <add value=" " />
+                    <add value="=" />
+                </valid>
+            </sanitizer>
+            <validator type="regex" message="Must start with @">^.*</validator>
+
+        </param> 
+    </macro>
     <macro name="citation">
         <citations>
             <citation type="doi">10.1093/nar/gkq1019</citation>
diff -r 0c5a5e670ac0 -r f7732611d0fc test-data/DRR015708_forward.fastqsanger
--- a/test-data/DRR015708_forward.fastqsanger	Fri Jun 23 21:31:47 2023 +0000
+++ b/test-data/DRR015708_forward.fastqsanger	Mon Aug 26 14:59:07 2024 +0000
@@ -1,20 +1,20 @@
-@HWI-ST895_0148_AC1GFWACXX:5:1101:1258:1938/1
+@DRR015708.HWI-ST895_0148_AC1GFWACXX:5:1101:1258:1938/1
 NTATTGTAGCGCACTATGAGGTCGCTCATTANTNTACATCNNCATCCAAATTTCAGCATNANTTTNNNNNTGTTTGATATTCTCAAAGNGATNAACGTTT
 +
 #1=DDFFFHGHHHJIIIIGIJFHIJJJJJJI#0#08DFII##-7@FHIIJJJJGEHEEE#,#,,;#####,,;?DCCDEFEEFCDDDD#+2+#+2<?<CC
-@HWI-ST895_0148_AC1GFWACXX:5:1101:1667:1930/1
+@DRR015708.HWI-ST895_0148_AC1GFWACXX:5:1101:1667:1930/1
 NTTCTAAACTCATTCCAGAAGTAATTGATGCGTCACCAATAATTGCAATATGTTTTCTATTGATTTGATTGATTTTATCTGCTGTTGCCATCCCAACAAT
 +
 #4=DDFFFHHHHHJJJJJJIIHIJJJJJJJJIHJJJJJIJJJJJJJJJJJJJIJJJJJJJJJJJJJJIIIICHHGEHHGIFEHHHHFFDFFFDDCEB@AC
-@HWI-ST895_0148_AC1GFWACXX:5:1101:1833:1936/1
+@DRR015708.HWI-ST895_0148_AC1GFWACXX:5:1101:1833:1936/1
 NTCACCTACAACTCGAATATTCGAATGATATGTGATATTGTTAGATGATTTTGGCATGCTTGCAGAAAGTGCATAAACACCTGTATTGATTCCCGAATTT
 +
 #4=DFFFFHHHHHIJIJJIHIIJIIJJJJIJIHIIGGIIJHIEHGGHGHIIJJJIIJJJJJHHCHGGGE@FHGHIIJIEHHEDCCDCCDEEED@AB/=A#
-@HWI-ST895_0148_AC1GFWACXX:5:1101:2003:1864/1
+@DRR015708.HWI-ST895_0148_AC1GFWACXX:5:1101:2003:1864/1
 NCTTAAAACTTATTAAATGAATCAATTAGATAAAAGACTTTTTTTGTTAGATGCTTATGCCTTAATTTTTAGAGGATATTATGCATTTATCAAAAATCCA
 +
 #4=DFFFFHHHHHJJJIJJJJJJJJJJJJJJJJIHGDGHIJJJJJJGHHJGIJIJJJJJJJIJIJJJJJHFFHGFDDFEEFEECCEEDEEDDCC3<A5>C
-@HWI-ST895_0148_AC1GFWACXX:5:1101:2399:1887/1
+@DRR015708.HWI-ST895_0148_AC1GFWACXX:5:1101:2399:1887/1
 NTAAAGGTTATTGTGCTTCACAGAAAATGCATTATTATGGGTATAAACTTCATGCGGTTTGCTCAGCGGAAGGTGTCTTTCAAAGTTTGGATATTAGTCC
 +
 #1=DDFFEHHHHHGIJJJJGIJJJJJJJJJJJJIJJJJJJJCFGFIIHJIJHIJJJJHIJJJJIJIJIFHBDE;@ACEEEDDCCCCCDDDCCDCCFECCC
diff -r 0c5a5e670ac0 -r f7732611d0fc test-data/DRR015708_reverse.fastqsanger
--- a/test-data/DRR015708_reverse.fastqsanger	Fri Jun 23 21:31:47 2023 +0000
+++ b/test-data/DRR015708_reverse.fastqsanger	Mon Aug 26 14:59:07 2024 +0000
@@ -1,20 +1,20 @@
-@HWI-ST895_0148_AC1GFWACXX:5:1101:1258:1938/2
+@DRR015708.HWI-ST895_0148_AC1GFWACXX:5:1101:1258:1938/2
 CATTANNAGNNANNNTTNNNNGANNNNNTCGANNNNNANTTTTAANCGNNNNNCTCTTNGAGAATATCAAANAGNTNAAAAATTANGCTGANNNTNGNAT
 +
 CCCFF##4<##2###32####22#####11?F#####0#07CHGI#.;#####--;BB#,;?ADDDEEDDD#,8#,#,58<?BD:#+2?@?#########
-@HWI-ST895_0148_AC1GFWACXX:5:1101:1667:1930/2
+@DRR015708.HWI-ST895_0148_AC1GFWACXX:5:1101:1667:1930/2
 GAAAGATGGTATTTCTGGTTTTCCAACGCGTACAGAAAGTGAGTTTGATACATTTGGAACGGGACATTCTTCTACATCTATTTCAGCAATTGTTGGGATG
 +
 BBCFFDFFHCFHHJJJJJIJJJJJJJIJJJJJJJIHGIIDHGIFIIJIIGHIIHIIJDHIIJH=DFFFFFEEEEEDEDDDEDEDDDDDCDDDCDDDBBDB
-@HWI-ST895_0148_AC1GFWACXX:5:1101:1833:1936/2
+@DRR015708.HWI-ST895_0148_AC1GFWACXX:5:1101:1833:1936/2
 AAATATAATTGGAGAATCAACTTTATTTTCGAATACAATTCCAAATCAAAAAGAAGATAAAACACTAGAATTATCTCAAAAGAATTCAACTCAAAAAGAT
 +
 CCCFFFFFHHHHGJIJIJJIJJJJJJJJJJJIJJJJJJJJJJJJEIJJJJHIJJIJJJIJJJIJJIJJJIJIJJJHHHGEHFFDFF>C@C>CEC;A538:
-@HWI-ST895_0148_AC1GFWACXX:5:1101:2003:1864/2
+@DRR015708.HWI-ST895_0148_AC1GFWACXX:5:1101:2003:1864/2
 ATTGAAACCTTTTGAGTTGATTCGTGGATTTTTGATAAATGCATAATATCCTCTAAAAATTAAGGCATAAGCATCTAACAAAAAAAGTCTTTTATCTAAT
 +
 CCCFFFFFHHHHHJEGGHIHIIJJHHJHIJIJJJGJIJJJJJJJJJJJJJIIIJIJJIJIJJIJJJJIGHEHIIHHHHFHFFEDDDDCDEEDDDDDDEDD
-@HWI-ST895_0148_AC1GFWACXX:5:1101:2399:1887/2
+@DRR015708.HWI-ST895_0148_AC1GFWACXX:5:1101:2399:1887/2
 TTGGTATTCTGCGGATAAATATCCTTTATCAGCTAAGAGCGTACAATTTTTAAACTGCTGTTTTATATCTTTCAGATAATGAATGTCATGCACTGAAGCT
 +
 BCCFBDFFHHHHHJJJJJJJJJJJJJJJJJJJJJIJIFIJJHHIIIJJJJGHJJJJJJJJHIIJJIJJHHHHHHGEFFFFFFCDCEEEFDDDDCDD>CDD
diff -r 0c5a5e670ac0 -r f7732611d0fc test-data/ERR027433_forward.fastqsanger
--- a/test-data/ERR027433_forward.fastqsanger	Fri Jun 23 21:31:47 2023 +0000
+++ b/test-data/ERR027433_forward.fastqsanger	Mon Aug 26 14:59:07 2024 +0000
@@ -1,20 +1,20 @@
-@IL4_4847:5:1:1051:7109/1
+@ERR027433.IL4_4847:5:1:1051:7109/1
 GCCGCCAACGTCCGACGGCGCGTCCCGCACGACTTGAACCGATCTCACCGAGACAGAACTAT
 +
 C@CC@@@C2BBCBB:>@8@@5@>>@@@@@>@97@@==<@>>@4<'@8>:35=%&B#######
-@IL4_4847:5:1:1058:16093/1
+@ERR027433.IL4_4847:5:1:1058:16093/1
 AAGGTCGGGCATTCGTTCGAGCCGACGACCGCGAGGAAGCGGTTCGGCCGGGCGTAGAATCC
 +
 ?ABBABB;<@>@=<?@CBBB:@2>BCBB,,?):7@/3$54'818->1-+=+()$6--C8+?1
-@IL4_4847:5:1:1111:15034/1
+@ERR027433.IL4_4847:5:1:1111:15034/1
 TCGATCCGCAGGGCAATCTGTGGATCCCGGCGTTCGACGACGGCGGGCGGGTGGCTCGGCAT
 +
 2524;@@@/4<@6@;9?C@@93@>BAB2>>C@>B>C4BC4@-+B<@525++%=)########
-@IL4_4847:5:1:1122:6048/1
+@ERR027433.IL4_4847:5:1:1122:6048/1
 ATCTCCTCGACGCGCACCAGATAGCGGTCGTAGCAATCGCCGTCCACGCCGACGGGCCCACT
 +
 BBB@@@@@@@AB.<@2)7;B-@==:@>@@@A7@<AA4:A3'@9+4;&00'9+AC5--DA5,?
-@IL4_4847:5:1:1138:20693/1
+@ERR027433.IL4_4847:5:1:1138:20693/1
 CTGCTCGCGCGAGAACGCGCGCAAGCTCGGGGGCGGTGGCGGGGTCGGGCGACACCGATGTA
 +
 CB<C7@>);9@@@@=1B@@@@2@=*:4@@@0%(-$,'3%%'%$%$,44%3&$=$C;CC-C##
diff -r 0c5a5e670ac0 -r f7732611d0fc test-data/ERR027433_reverse.fastqsanger
--- a/test-data/ERR027433_reverse.fastqsanger	Fri Jun 23 21:31:47 2023 +0000
+++ b/test-data/ERR027433_reverse.fastqsanger	Mon Aug 26 14:59:07 2024 +0000
@@ -1,20 +1,20 @@
-@IL4_4847:5:1:1051:7109/3
+@ERR027433.IL4_4847:5:1:1051:7109/3
 AACGCACTGCGCGCGGACTCGCCCCCGCGGCCACTCCGTGGGCCGGCGTACGGA
 +
 )(664;(>>/:1<+/'())0)',8%'*7'+9904)'(+()'''':+4+'.7)'(
-@IL4_4847:5:1:1058:16093/3
+@ERR027433.IL4_4847:5:1:1058:16093/3
 GCATAGCTGCCCTCGCCTTCTACTCGCACCGAACAAGCGGCCCGCCTACGCGGG
 +
 ;=>1(/2(:/=@(:'9/<(*'&.(?.6)(';+.5''-3.&''7(96%0:+($2$
-@IL4_4847:5:1:1111:15034/3
+@ERR027433.IL4_4847:5:1:1111:15034/3
 GAGTGGAGCCGCGGACGGGAGCGCGGCGGCTGCCTCACAGCACCCGGGGGGTCG
 +
 ::3+:2655(*('((3*&&&4+')6'3/2,+++*.+')-/)4((<-+&&'&%<(
-@IL4_4847:5:1:1122:6048/3
+@ERR027433.IL4_4847:5:1:1122:6048/3
 GAGGTCGGCGTTCTGGATGACAGGCGCGAAGCCCCCGCCGTCGGTGCCTTCACG
 +
 =8+(-(,(3.5*=99+;).)8'(,(/(+(-6@'-3<6&,%/4++)')1/)>(.&
-@IL4_4847:5:1:1138:20693/3
+@ERR027433.IL4_4847:5:1:1138:20693/3
 TGGACGTTGTGGTGGTTGTAAGAGATTTCGCTCCCCATGTTGGCGAGCTGCGAT
 +
 ;)?5;=9996@((((097:41=,A((+)5>9,:''''67+9)=(968-(8;8)3
diff -r 0c5a5e670ac0 -r f7732611d0fc test-data/ERR086330_1.fastq.gz
Binary file test-data/ERR086330_1.fastq.gz has changed
diff -r 0c5a5e670ac0 -r f7732611d0fc test-data/ERR086330_2.fastq.gz
Binary file test-data/ERR086330_2.fastq.gz has changed
diff -r 0c5a5e670ac0 -r f7732611d0fc test-data/SRR002702_1.fastq.gz
Binary file test-data/SRR002702_1.fastq.gz has changed
diff -r 0c5a5e670ac0 -r f7732611d0fc test-data/SRR002702_2.fastq.gz
Binary file test-data/SRR002702_2.fastq.gz has changed
diff -r 0c5a5e670ac0 -r f7732611d0fc test-data/SRR11953971_1.fastq.gz
Binary file test-data/SRR11953971_1.fastq.gz has changed
diff -r 0c5a5e670ac0 -r f7732611d0fc test-data/SRR11953971_2.fastq.gz
Binary file test-data/SRR11953971_2.fastq.gz has changed
diff -r 0c5a5e670ac0 -r f7732611d0fc test-data/SRR1993644.fastqsanger
--- a/test-data/SRR1993644.fastqsanger	Fri Jun 23 21:31:47 2023 +0000
+++ b/test-data/SRR1993644.fastqsanger	Mon Aug 26 14:59:07 2024 +0000
@@ -1,20 +1,20 @@
-@1/2
+@SRR1993644.1/2
 TATACTACTGTCATGTTTGCTTTTTTCGTGCTCATTACCTTATCGTATGCTTCCATCCAAAGATCTAGTTGTTTATAATATTCTCCCGGCCTTACTTCAAC
 +
 ?@<DDDADDFAAC@>GG<FDCBHIIGB:8??DEAHGAFEDF<B?F9DBFFCDHF>48BBCF)8877=@=@C7=E??EBD:AADA;>C3;BB6:A@>>@:3>
-@2/2
+@SRR1993644.2/2
 AAAAAAACTTTCTTTACAGGCGTAAAGAAAGTGAAATTGACAGTATTTATACATGAAATAGCAATGTCTTTCCCACTTCCCTACGCTGGCATTAACCAGAT
 +
 <@@DA6DDF42ABGF9F?F@C<EDDDFBGI>04BGC>BFF><?*88BDFDEAFFDGCGEFEEFIFFFEF>EBDBB@@:ACCCAB8@?=;B<@BABBBBB?#
-@3/2
+@SRR1993644.3/2
 GTGCCATCATTTTCTATCCATTATTATGGATTATTGGCTCATCGTTTAATCCGGGTGATAGTTTATCTGGATCAAGTATTATTCCACAAAATGCAACGTTA
 +
 =BBFFFFFHHHHHJJJJJJJJJJJJIJIJEIIGIJJJHGIGGIIGHIDIJGHIIJ?FFHGIIJJJJJJJJHGIHHHCEHFFFFFFFFEAECCDADDDDDDD
-@4/2
+@SRR1993644.4/2
 TTCAAAACACATAAAGCTAATTGCCGCATATGACAATATTGCTAAAATAATTTTTTTACCAGATATCGGTGTTAATCGAAATAATGTACTTTCGGTCATTT
 +
 BBCFFFFFHHHHHJJJJJJJJJJJJJJJJJJJJJJJIJJJJJJIJJJJJJIIJJJJJJJIJJHHHHHFFDDCDEEEDDDDDDDDEDDDFFFEDDDDDDDDE
-@5/2
+@SRR1993644.5/2
 ACTTGCCAATGCGATGCACCAATCTTTTCAGCAATAATCGGCAAAATTGGGTCGACTACTCCTATACCTGAAAAGGCAAGGAAAGTAGCCAACACTGTAAT
 +
 BCCFFFFFHHHHHIJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJIHIIJIJHHHHFFFFFFEEEEEEDDDDDDDDDDDDDCDDDDDDDDDDDDDED
diff -r 0c5a5e670ac0 -r f7732611d0fc test-data/SRR522874.fastq.gz
Binary file test-data/SRR522874.fastq.gz has changed
diff -r 0c5a5e670ac0 -r f7732611d0fc test-data/SRR522874.sra_1.fastq.gz
Binary file test-data/SRR522874.sra_1.fastq.gz has changed
diff -r 0c5a5e670ac0 -r f7732611d0fc test-data/SRR522874.sra_2.fastq.gz
Binary file test-data/SRR522874.sra_2.fastq.gz has changed
diff -r 0c5a5e670ac0 -r f7732611d0fc test-data/SRR522874.sra_2_1.fastq.gz
Binary file test-data/SRR522874.sra_2_1.fastq.gz has changed
diff -r 0c5a5e670ac0 -r f7732611d0fc test-data/SRR522874.sra_3.fastq.gz
Binary file test-data/SRR522874.sra_3.fastq.gz has changed
diff -r 0c5a5e670ac0 -r f7732611d0fc test-data/SRR522874.sra_4.fastq.gz
Binary file test-data/SRR522874.sra_4.fastq.gz has changed
diff -r 0c5a5e670ac0 -r f7732611d0fc test-data/SRR522874.sra_4_1.fastq.gz
Binary file test-data/SRR522874.sra_4_1.fastq.gz has changed
diff -r 0c5a5e670ac0 -r f7732611d0fc test-data/SRR522874_1.fastq.gz
Binary file test-data/SRR522874_1.fastq.gz has changed
diff -r 0c5a5e670ac0 -r f7732611d0fc test-data/SRR522874_2.fastq.gz
Binary file test-data/SRR522874_2.fastq.gz has changed
diff -r 0c5a5e670ac0 -r f7732611d0fc test-data/SRR6982805.fastqsanger.gz
Binary file test-data/SRR6982805.fastqsanger.gz has changed
diff -r 0c5a5e670ac0 -r f7732611d0fc test-data/SRR925743_forward.fastqsanger
--- a/test-data/SRR925743_forward.fastqsanger	Fri Jun 23 21:31:47 2023 +0000
+++ b/test-data/SRR925743_forward.fastqsanger	Mon Aug 26 14:59:07 2024 +0000
@@ -1,20 +1,20 @@
-@1/1
+@SRR925743.1/1
 AGGGATGTGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGT
 +
 EGGEGGGDFGEEEAEECGDEGGFEEGEFGBEEDDECFEFDD@CDD<EDDE?2@?AEEDEED=D+C?5@A=6:>BA8:>@:4+36945&4354445>/B>@
-@2/1
+@SRR925743.2/1
 AGGGATGTGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGGTAGGGTTAGGGT
 +
 HHHHHHEGFHEEFEEHEEHHGGEGGGGEFGFGGGGHHHHFBEEEEEFGGEEAEEEDD0ADDBD9BDBDDA@6?BA;?CD=:-7<<::)1;5,6-6A@?=9
-@3/1
+@SRR925743.3/1
 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCA
 +
 HHHHFHHHHHHHHHHHFHHHHHHHHHHHHHHHHHHHHHHHGEFHGEGGFGGGGGGHHHHEFEIDDEEEEEDD4DD;??:6>6<@.<==@?.@@<?#####
-@4/1
+@SRR925743.4/1
 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACACTAACCCTAACCCTAACCCTAACCCTA
 +
 HHGBHHHHGFHHHHHFDHHFHGEHHHHHEFHHHHEGEGEFFFAFFFDCFGF?@GCDFGFEFHHEFDF*F6DC4DD:A8>@D@CD8->=>=<@CB@#####
-@5/1
+@SRR925743.5/1
 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACACTAACCCTCACACTCACCCTA
 +
 GGGFGFFGGGFBGGEGGFFGGGCFFGGGGGEGFFFFFGFFGFFFDFFB+FGGFEE?FCF::7B5A?+BB###############################
diff -r 0c5a5e670ac0 -r f7732611d0fc test-data/SRR925743_reverse.fastqsanger
--- a/test-data/SRR925743_reverse.fastqsanger	Fri Jun 23 21:31:47 2023 +0000
+++ b/test-data/SRR925743_reverse.fastqsanger	Mon Aug 26 14:59:07 2024 +0000
@@ -1,20 +1,20 @@
-@1/2
+@SRR925743.1/2
 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTA
 +
 GHHHDFDFGFGEGFBGEGGEGEGGGHGFGHFHFHHHHHHHEF?EFEFF?EHGGHHHGHFHEHDEHGHFFEEE9BDDBEBAD.AD:ACBBC=4@>?5>=+?
-@2/2
+@SRR925743.2/2
 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTA
 +
 HHHHHHHHHHHHHGHHHHHHGHHHHHHHHHHHFHHHFHHHHHHHHHHHHHHHHHHHGHHHGHHBHGHHFDBDDED5FCFCEEGF<@>>>@,<5<@@?>;D
-@3/2
+@SRR925743.3/2
 ATGGATGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGT
 +
 HHHHHHHHHFIEGFHFHDHHHHGFFHGEGDIGGEGGHHHAGEGGGDHHHHHHHHHHHFGDGGGEGDFFF>BEEEE3B;BB;>B7C@DA=DFBDD.BEE=9
-@4/2
+@SRR925743.4/2
 ATGGATGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGT
 +
 GFFFHHFFHHHFHHFEFGGBGEEEE?<9?6=>>:=DDDD@DBGDB;DBDBA.ADD8<2<>6A@=A5>550=>>>>BE;EEEDEEE79+336<68=BCEB@
-@5/2
+@SRR925743.5/2
 ATGGATGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGGTAGGGTTAGGGTTAGGGTTAGGGGTAGGGT
 +
 479<.>><:<A7BABBE8@=:<<:@BB?C75:2?;.5<<3FEFGEEC88FEDEE=AB><AA@B<ABDC8.27<9:58.58??6<:@>+?=9@########