# HG changeset patch
# User jackcurragh
# Date 1647867231 0
# Node ID b300c15426f55300f4aa95f2278e8d9f9827873a
# Parent  01ca7075c109e7c9bc7c520fdc0bccc00992a24b
Uploaded

diff -r 01ca7075c109 -r b300c15426f5 bowtie_rRNA_removal_wrapper/bowtie_rRNA_removal_wrapper.py
--- a/bowtie_rRNA_removal_wrapper/bowtie_rRNA_removal_wrapper.py	Tue Mar 15 10:27:46 2022 +0000
+++ b/bowtie_rRNA_removal_wrapper/bowtie_rRNA_removal_wrapper.py	Mon Mar 21 12:53:51 2022 +0000
@@ -414,7 +414,7 @@
             if options.paired == 'paired':
                 cmd2 = 'bowtie %s %s -1 %s -2 %s > %s' % ( aligning_cmds, ref_file_name, options.input1, options.input2, options.output )
             else:
-                cmd2 = 'echo "bowtie %s %s %s > %s" > ~/galaxy_test.txt' % ( aligning_cmds, ref_file_name, options.input1, options.output )
+                cmd2 = 'bowtie %s %s %s > %s' % ( aligning_cmds, ref_file_name, options.input1, options.output )
             # align
             tmp = tempfile.NamedTemporaryFile( dir=tmp_index_dir ).name
             with open(tmp, 'w') as tmp_stderr:
diff -r 01ca7075c109 -r b300c15426f5 bowtie_rRNA_removal_wrapper/bowtie_rRNA_removal_wrapper.xml
--- a/bowtie_rRNA_removal_wrapper/bowtie_rRNA_removal_wrapper.xml	Tue Mar 15 10:27:46 2022 +0000
+++ b/bowtie_rRNA_removal_wrapper/bowtie_rRNA_removal_wrapper.xml	Mon Mar 21 12:53:51 2022 +0000
@@ -1,4 +1,4 @@
-<tool id="bowtie_remove_rrna_wrapper" name="Remove rRNA using Bowtie" version="1.3">
+<tool id="bowtie_rRNA_removal_wrapper" name="Remove rRNA using Bowtie" version="1.4.0">
   <description></description>
   <requirements>
     <requirement type="package" version="1.2.0">bowtie</requirement>
@@ -156,7 +156,7 @@
     <conditional name="refGenomeSource">
       <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options">
         <option value="indexed">Use a built-in index</option>
-        <option value="history">Use one from the history</option>
+        <option value="history" selected="True">Use one from the history</option>
       </param>
       <when value="indexed">
         <param name="index" type="select" label="Select a reference genome" help="if your genome of interest is not listed - contact Galaxy team">
@@ -248,6 +248,7 @@
               </when>
               <when value="vMode">
                 <param name="maxMismatches" type="integer" value="3" min="0" max="3" label="Maximum number of mismatches (-v)" help="May be 0, 1, 2, or 3" />
+                <param name="sSeedLen" type="integer" value="25" min="5" label="Seed length (-l)" help="Minimum value is 5" />
               </when>
             </conditional>
             <param name="sForwardAlign" type="select" label="Choose whether or not to attempt to align against the forward reference strand (--nofw)">
@@ -256,7 +257,7 @@
             </param>
             <param name="sReverseAlign" type="select" label="Choose whether or not to attempt to align against the reverse-complement reference strand (--norc)">
               <option value="reverse">Align against the reverse-complement reference strand</option>
-              <option value="noReverse">Do not align against the reverse-complement reference strand</option>
+              <option value="noReverse" selected="true">Do not align against the reverse-complement reference strand</option>
             </param>
             <conditional name="sBestOption">
               <param name="sBest" type="select" label="Whether or not to make Bowtie guarantee that reported singleton alignments are 'best' in terms of stratum and in terms of the quality values at the mismatched positions (--best)" help="Removes all strand bias. Only affects which alignments are reported by Bowtie. Runs slower with best option">
@@ -295,7 +296,7 @@
             <conditional name="sAllValAlignsOption">
               <param name="sAllValAligns" type="select" label="Whether or not to report all valid alignments per read (-a)">
                 <option value="noAllValAligns">Do not report all valid alignments</option>
-                <option value="doAllValAligns">Report all valid alignments</option>
+                <option value="doAllValAligns" selected="true">Report all valid alignments</option>
               </param>
               <when value="noAllValAligns">
                 <param name="sValAlign" type="integer" value="1" min="1" label="Report up to n valid alignments per read (-k)" />
@@ -304,7 +305,7 @@
             </conditional>
             <param name="sSuppressAlign" type="integer" value="-1" label="Suppress all alignments for a read if more than n reportable alignments exist (-m)" help="-1 for no limit" />
             <param name="sMaxFile" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write all reads with a number of valid alignments exceeding the limit set with the -m option to a file (--max)" />
-            <param name="sUnmappedFile" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write all reads that could not be aligned to a file (--un)" />
+            <param name="sUnmappedFile" type="boolean" truevalue="true" falsevalue="false" checked="True" label="Write all reads that could not be aligned to a file (--un)" />
             <param name="sOffrate" type="integer" value="-1" label="Override the offrate of the index to n (-o)" help="-1 for default" />
             <param name="sSeed" type="integer" value="-1" label="Seed for pseudo-random number generator (--seed)" help="-1 for default" />
           </when> <!-- full -->
@@ -339,7 +340,7 @@
             <conditional name="alignModeOption">
               <param name="alignMode" type="select" label="Alignment mode">
                 <option value="nMode">Maq-like: quality-aware, limit mismatches in seed (-n)</option>
-                <option value="vMode">ignore qualities, limit end-to-end mismatches (-v)</option>
+                <option value="vMode" selected="true">ignore qualities, limit end-to-end mismatches (-v)</option>
               </param>
               <when value="nMode">
                 <param name="pMismatchSeed" type="integer" value="2" min="0" max="3" label="Maximum number of mismatches permitted in the seed (-n)" help="May be 0, 1, 2, or 3" />
@@ -352,6 +353,7 @@
               </when>
               <when value="vMode">
                 <param name="maxMismatches" type="integer" value="" min="0" max="3" label="Maximum number of mismatches (-v)" help="May be 0, 1, 2, or 3" />
+                <param name="pSeedLen" type="integer" value="25" min="5" label="Seed length (-l)" help="Minimum value is 5" />
               </when>
             </conditional>
             <param name="pMinInsert" type="integer" value="0" label="Minimum insert size for valid paired-end alignments (-I)" />
@@ -361,7 +363,7 @@
             </param>
             <param name="pReverseAlign" type="select" label="Choose whether or not to attempt to align against the reverse-complement reference strand (--norc)">
               <option value="reverse">Align against the reverse-complement reference strand</option>
-              <option value="noReverse">Do not align against the reverse-complement reference strand</option>
+              <option value="noReverse" selected="true">Do not align against the reverse-complement reference strand</option>
             </param>
             <conditional name="pBestOption">
               <param name="pBest" type="select" label="Whether or not to make Bowtie guarantee that reported singleton alignments are 'best' in terms of stratum and in terms of the quality values at the mismatched positions (--best)" help="Removes all strand bias. Only affects which alignments are reported by Bowtie. Runs slower with best option">
@@ -402,7 +404,7 @@
             <conditional name="pAllValAlignsOption">
               <param name="pAllValAligns" type="select" label="Whether or not to report all valid alignments per pair (-a)">
                 <option value="noAllValAligns">Do not report all valid alignments</option>
-                <option value="doAllValAligns">Report all valid alignments</option>
+                <option value="doAllValAligns" selected="True">Report all valid alignments</option>
               </param>
               <when value="noAllValAligns">
                 <param name="pValAlign" type="integer" value="1" min="1" label="Report up to n valid alignments per pair (-k)" />
@@ -418,7 +420,7 @@
         </conditional> <!-- pParams -->
       </when> <!-- paired -->
     </conditional> <!-- singlePaired -->
-    <param name="save_mapping_stats" type="boolean" checked="False" label="Save the bowtie mapping statistics to the history" />
+    <param name="save_mapping_stats" type="boolean" checked="True" label="Save the bowtie mapping statistics to the history" />
     <param name="suppressHeader" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Suppress the header in the output SAM file (--sam-nohead)" help="Bowtie produces SAM with several lines of header information by default" />
   </inputs>
   <outputs>
diff -r 01ca7075c109 -r b300c15426f5 bowtie_rRNA_removal_wrapper/test-data/bowtie_in2.fastqsanger
--- a/bowtie_rRNA_removal_wrapper/test-data/bowtie_in2.fastqsanger	Tue Mar 15 10:27:46 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,104 +0,0 @@
-@HWI-EAS91_1_30788AAXX:1:1:1513:715/1
-GTTTTTTGGGCATAGATGTTTAGTTGTGGTAGTCAG
-+
-IIIIIII""IIIIIIIIIIIIIIIIIIIDI?II-+I
-@HWI-EAS91_1_30788AAXX:1:1:1698:516/1
-GTTGTTAGGGAGAGGAGTTGAACCTCTGAGTGTAAA
-+
-IIIIIII""IIIIIIIIIIIIIIIIIII5IIIII9I
-@HWI-EAS91_1_30788AAXX:1:1:1491:637/1
-GCTAGCAGGATGGATCCGGCAATTGGGGCTTCTACA
-+
-IIIIIII""IIIIIIIIIIIIFIIIIIIIIIIIABD
-@HWI-EAS91_1_30788AAXX:1:1:1711:249/1
-GGAAGTAGGGGCCTGCGTTCAGGCGTTCTGTTTGGT
-+
-IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII
-@HWI-EAS91_1_30788AAXX:1:1:1634:211/1
-GAAGCAGGGGCTTGATACTGACACTTCGTCGACGTA
-+
-IIIIIII""IIIIIIIIIIIIIIIIIIIIII9IIDF
-@HWI-EAS91_1_30788AAXX:1:1:1218:141/1
-GTTAAATATTGGGAGTGGGGGGGGGGGGGAGTTTTG
-+
-IIIIIII""IIIIIIIIIIIIIIIIIIII1IIII+I
-@HWI-EAS91_1_30788AAXX:1:1:1398:854/1
-GTGAAGAGGAGGGGATTTATTAGTACGGGAAGGGTG
-+
-IIIIIII""IIIIIBIIIIIIIIIIIIIIA=IIIII
-@HWI-EAS91_1_30788AAXX:1:1:1310:991/1
-GAATAGTGGTAGTATTATTCCTTCTAGGCATAGGAG
-+
-IIIIIII""IIIIIIIIII4IIIIIIDII:IEI2:I
-@HWI-EAS91_1_30788AAXX:1:1:1716:413/1
-GATCCAAGGCTTTATCAACACCTATTCTGATTCTTC
-+
-IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII
-@HWI-EAS91_1_30788AAXX:1:1:1630:59/1
-GGAGCGGGGGGTTGGTAAGGTTGGGGTCGAGTATGA
-+
-IIIIIII""IIIIIIIIIIIIIIIIIIII;IIHIIF
-@HWI-EAS91_1_30788AAXX:1:1:1601:805/1
-GAAAACAGGAAAACAATCCAGTCACTTACCCTATGC
-+
-IIIIIII""IIIIIIIIIIIIIIIIIIIIIII@III
-@HWI-EAS91_1_30788AAXX:1:1:1663:724/1
-GTTTGCCGGCGCCATCCTACGCTCCATTCCCAACAA
-+
-IIIIIII""IIII8IIIIIIHIIII6IIIII1CI=3
-@HWI-EAS91_1_30788AAXX:1:1:1454:975/1
-GCTAGGCGGGAGTGGTAAAAGGCTCAGAAGAAGCCA
-+
-IIIIIII""IIIIIIIIIIIIIIIIEIG;IIIIIII
-@HWI-EAS91_1_30788AAXX:1:1:1461:255/1
-GTACACCGGCGCCTGAGCCCTACTAATAACTCTCAT
-+
-IIIIIII""IIIIII9IIIIIIEI(II9.I4III,I
-@HWI-EAS91_1_30788AAXX:1:1:1775:764/1
-GCATCCCGGTAGATCTAATTTTCTAAATCTGTCAAC
-+
-IIIIIII""III@IIII+IIIIII8H8IIIIIIICI
-@HWI-EAS91_1_30788AAXX:1:1:1269:520/1
-GGAGTATGGAATAAGTGATTTTAGATCGGTTTGTCG
-+
-IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII
-@HWI-EAS91_1_30788AAXX:1:1:1303:1162/1
-GAGCAAGGGCAGGAGGAGGAGTCCTAGGATGTCTTT
-+
-IIIIIII""IIIIFII4*IGIAI(IAII49',3I6I
-@HWI-EAS91_1_30788AAXX:1:1:1090:409/1
-GTTTGTTGGGAATGGAGCGTAGGATGGCGTAGGCAA
-+
-IIIIIII""IIIIIIIIIIIIIIIIIIIII:IIA8I
-@HWI-EAS91_1_30788AAXX:1:1:1336:1000/1
-GGTAAATGGGAAATATTAAGTTTCTGTTTCTAGATC
-+
-IIIIIII""IIIIIIIIIIIIIIIIIIIIIIII9II
-@HWI-EAS91_1_30788AAXX:1:1:1199:1376/1
-GTTTTCTGGAAAACCTTCACCTATTTATGGGGGTTT
-+
-IIIIIII""IIIIIIIIIIIII;III3IIG&:/III
-@HWI-EAS91_1_30788AAXX:1:1:1598:1148/1
-GATCAATGGTTTGGATCAATAAGTGATTATATATTT
-+
-IIIIIII""IIIIIDIIIIII?IIICII=IHIIIII
-@HWI-EAS91_1_30788AAXX:1:1:1723:1459/1
-GAAACCCGGACGTTTGGATGGGCCCGGAGCGAGGAT
-+
-IIIIIII""IIIIIIIIDIIIIIIIII9HII-II=I
-@HWI-EAS91_1_30788AAXX:1:1:1442:1346/1
-TATCAAGGGGCTGCTTCGAATCCGAAGTGGTGGCTG
-+
-IIIIIII""IIIIIDIIIII1I(I4II<?<-II*,&
-@HWI-EAS91_1_30788AAXX:1:1:850:117/1
-GTATGACGGTAAAGAAAATTATTACGAATGCATGGG
-+
-IIIIIII""IIIIIIEIEIIIIIIIIEBIDD9I;:?
-@HWI-EAS91_1_30788AAXX:1:1:795:325/1
-GGGTACTGGGAAGTGGAATGGTGTGAGTCCAAGTTT
-+
-IIIIIII""IIIIIIIIIIIIIIIIIIIII65IIII
-@HWI-EAS91_1_30788AAXX:1:1:873:453/1
-GAGTAGGGGGATTGCTAGAGTTACTTCGTATGAGAT
-+
-IIIIIII""IIIIIIIIIIIIIIIII@IIIIIII=I
diff -r 01ca7075c109 -r b300c15426f5 bowtie_rRNA_removal_wrapper/test-data/bowtie_in5.fastqillumina
--- a/bowtie_rRNA_removal_wrapper/test-data/bowtie_in5.fastqillumina	Tue Mar 15 10:27:46 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,72 +0,0 @@
-@Dummy:1:1:1761:343/1
-TTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGA
-+
-hhhhhhhAAhhhhhhhhhhh^hOhhhhghhhfhhhhhOhh^hAAhhhhhh
-@Dummy:1:1:1578:331/1
-TGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGC
-+
-hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhhAhhhhhhhOOOhhhh
-@Dummy:1:1:1647:512/1
-TACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCA
-+
-hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhhAhhhhhhhOOOhhhh
-@Dummy:1:1:1570:620/1
-GAGTAACAAAGTaaaGTTTGGAccGTTTTTGTCTCGTGCTCGTCGCTGCG
-+
-hhhhhhhAAhhhhhhhhhhhhhahhhhhhhhhhhhAhhhhhhhOOOhhhh
-@Dummy:1:1:1599:330/1
-AGAAGAAAACGTGCGTCAAAAATTACGTGCaGAAGGAGTGATGTAATGTC
-+
-hhhhhhhAAhhhhhhhhhhhhhhhhhhh[hhh_hhAhhhhhhhOOOhhhh
-@Dummy:1:1:1652:270/1
-AGCGTAAAGGCGCTCGTCTTTGGTATGTAGGacTTTGCATTGTTTAATTG
-+
-hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhUhhAhhhhhhhOOOhhhh
-@Dummy:1:1:1746:351/1
-CTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGT
-+
-hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhhAhhhhhhhOOOhhhh
-@Dummy:1:1:1582:633/1
-CCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCAC
-+
-hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhhAhhhhhhhOOOhhhh
-@Dummy:1:1:1598:534/1
-GCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAA
-+
-hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhhAhhhhhhhOOOhhhh
-@Dummy:1:1:1572:324/1
-AAGGTGCTTaaaTTCgtGGGTCCTGAGCTGGCGACCCTGTTTTGTATGGC
-+
-hhhhhhhAAhhhhhhhhhhhhhhhhhhhhJVhOThAhhhhhhhOOOhhhh
-@Dummy:1:1:1749:466/1
-TTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCT
-+
-hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhhAhhhhhhhOOOhhhh
-@Dummy:1:1:1629:446/1
-AGGTTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGT
-+
-hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhhAhhhhhhhOOOhhhh
-@Dummy:1:1:1763:587/1
-AAGCTACATCGTCAACGTTATATTTTGATAGTTTGACGGTTAATGCTGGT
-+
-hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhhAhhhhhhhOOOhhhh
-@Dummy:1:1:1616:363/1
-TGTTTATCCTTTGAATGGTCGCCATGATGGTGGTTATTATACCGTCAAGG
-+
-hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhchhhAhhhhhhhOOOhhhh
-@Dummy:1:1:1768:715/1
-ACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGCTAAAGCT
-+
-hhhhhhhAAhhhhhhhhhhhhhchhhhhhhhhhhhAhhhhhhhOOOhhhh
-@Dummy:1:1:1572:270/1
-TGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTA
-+
-hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhhAhhhhhhhOOOhhhh
-@Dummy:1:1:1673:514/1
-ATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATTGAGGCT
-+
-hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhPAhhhhhhhOOOhhhh
-@Dummy:1:1:1634:330/1
-GGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATG
-+
-hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhWhhAhhhhhhhOOOhhhh
diff -r 01ca7075c109 -r b300c15426f5 bowtie_rRNA_removal_wrapper/test-data/bowtie_in5.fastqsanger
--- a/bowtie_rRNA_removal_wrapper/test-data/bowtie_in5.fastqsanger	Tue Mar 15 10:27:46 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,72 +0,0 @@
-@Dummy:1:1:1761:343/1
-TTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGA
-+
-IIIIIII""IIIIIIIIIII?I0IIIIHIIIGIIIII0II?I""IIIIII
-@Dummy:1:1:1578:331/1
-TGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGC
-+
-IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII
-@Dummy:1:1:1647:512/1
-TACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCA
-+
-IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII
-@Dummy:1:1:1570:620/1
-GAGTAACAAAGTaaaGTTTGGAccGTTTTTGTCTCGTGCTCGTCGCTGCG
-+
-IIIIIII""IIIIIIIIIIIIIBIIIIIIIIIIII"IIIIIII000IIII
-@Dummy:1:1:1599:330/1
-AGAAGAAAACGTGCGTCAAAAATTACGTGCaGAAGGAGTGATGTAATGTC
-+
-IIIIIII""IIIIIIIIIIIIIIIIIII<III@II"IIIIIII000IIII
-@Dummy:1:1:1652:270/1
-AGCGTAAAGGCGCTCGTCTTTGGTATGTAGGacTTTGCATTGTTTAATTG
-+
-IIIIIII""IIIIIIIIIIIIIIIIIIIIIII6II"IIIIIII000IIII
-@Dummy:1:1:1746:351/1
-CTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGT
-+
-IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII
-@Dummy:1:1:1582:633/1
-CCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCAC
-+
-IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII
-@Dummy:1:1:1598:534/1
-GCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAA
-+
-IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII
-@Dummy:1:1:1572:324/1
-AAGGTGCTTaaaTTCgtGGGTCCTGAGCTGGCGACCCTGTTTTGTATGGC
-+
-IIIIIII""IIIIIIIIIIIIIIIIIIII+7I05I"IIIIIII000IIII
-@Dummy:1:1:1749:466/1
-TTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCT
-+
-IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII
-@Dummy:1:1:1629:446/1
-AGGTTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGT
-+
-IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII
-@Dummy:1:1:1763:587/1
-AAGCTACATCGTCAACGTTATATTTTGATAGTTTGACGGTTAATGCTGGT
-+
-IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII
-@Dummy:1:1:1616:363/1
-TGTTTATCCTTTGAATGGTCGCCATGATGGTGGTTATTATACCGTCAAGG
-+
-IIIIIII""IIIIIIIIIIIIIIIIIIIIIIDIII"IIIIIII000IIII
-@Dummy:1:1:1768:715/1
-ACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGCTAAAGCT
-+
-IIIIIII""IIIIIIIIIIIIIDIIIIIIIIIIII"IIIIIII000IIII
-@Dummy:1:1:1572:270/1
-TGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTA
-+
-IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII
-@Dummy:1:1:1673:514/1
-ATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATTGAGGCT
-+
-IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIII1"IIIIIII000IIII
-@Dummy:1:1:1634:330/1
-GGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATG
-+
-IIIIIII""IIIIIIIIIIIIIIIIIIIIIII8II"IIIIIII000IIII
diff -r 01ca7075c109 -r b300c15426f5 bowtie_rRNA_removal_wrapper/test-data/bowtie_in5.fastqsolexa
--- a/bowtie_rRNA_removal_wrapper/test-data/bowtie_in5.fastqsolexa	Tue Mar 15 10:27:46 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,72 +0,0 @@
-@Dummy:1:1:1761:343/1
-TTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGA
-+
-hhhhhhh;;hhhhhhhhhhh^hOhhhhghhhfhhhhhOhh^h;;hhhhhh
-@Dummy:1:1:1578:331/1
-TGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGC
-+
-hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhh;hhhhhhhOOOhhhh
-@Dummy:1:1:1647:512/1
-TACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCA
-+
-hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhh;hhhhhhhOOOhhhh
-@Dummy:1:1:1570:620/1
-GAGTAACAAAGTaaaGTTTGGAccGTTTTTGTCTCGTGCTCGTCGCTGCG
-+
-hhhhhhh;;hhhhhhhhhhhhhahhhhhhhhhhhh;hhhhhhhOOOhhhh
-@Dummy:1:1:1599:330/1
-AGAAGAAAACGTGCGTCAAAAATTACGTGCaGAAGGAGTGATGTAATGTC
-+
-hhhhhhh;;hhhhhhhhhhhhhhhhhhh[hhh_hh;hhhhhhhOOOhhhh
-@Dummy:1:1:1652:270/1
-AGCGTAAAGGCGCTCGTCTTTGGTATGTAGGacTTTGCATTGTTTAATTG
-+
-hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhUhh;hhhhhhhOOOhhhh
-@Dummy:1:1:1746:351/1
-CTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGT
-+
-hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhh;hhhhhhhOOOhhhh
-@Dummy:1:1:1582:633/1
-CCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCAC
-+
-hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhh;hhhhhhhOOOhhhh
-@Dummy:1:1:1598:534/1
-GCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAA
-+
-hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhh;hhhhhhhOOOhhhh
-@Dummy:1:1:1572:324/1
-AAGGTGCTTaaaTTCgtGGGTCCTGAGCTGGCGACCCTGTTTTGTATGGC
-+
-hhhhhhh;;hhhhhhhhhhhhhhhhhhhhJVhOTh;hhhhhhhOOOhhhh
-@Dummy:1:1:1749:466/1
-TTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCT
-+
-hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhh;hhhhhhhOOOhhhh
-@Dummy:1:1:1629:446/1
-AGGTTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGT
-+
-hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhh;hhhhhhhOOOhhhh
-@Dummy:1:1:1763:587/1
-AAGCTACATCGTCAACGTTATATTTTGATAGTTTGACGGTTAATGCTGGT
-+
-hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhh;hhhhhhhOOOhhhh
-@Dummy:1:1:1616:363/1
-TGTTTATCCTTTGAATGGTCGCCATGATGGTGGTTATTATACCGTCAAGG
-+
-hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhchhh;hhhhhhhOOOhhhh
-@Dummy:1:1:1768:715/1
-ACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGCTAAAGCT
-+
-hhhhhhh;;hhhhhhhhhhhhhchhhhhhhhhhhh;hhhhhhhOOOhhhh
-@Dummy:1:1:1572:270/1
-TGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTA
-+
-hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhh;hhhhhhhOOOhhhh
-@Dummy:1:1:1673:514/1
-ATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATTGAGGCT
-+
-hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhP;hhhhhhhOOOhhhh
-@Dummy:1:1:1634:330/1
-GGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATG
-+
-hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhWhh;hhhhhhhOOOhhhh
diff -r 01ca7075c109 -r b300c15426f5 bowtie_rRNA_removal_wrapper/test-data/bowtie_in6.fastqillumina
--- a/bowtie_rRNA_removal_wrapper/test-data/bowtie_in6.fastqillumina	Tue Mar 15 10:27:46 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,72 +0,0 @@
-@Dummy:1:1:1761:343/2
-TTGATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGG
-+
-hhhhhhhAAhhhhhhhOhh^hAAhhhhhhhhhhhh^hOhhhhghhhfhhh
-@Dummy:1:1:1578:331/2
-AAGGACTGGTTTAGATATGAGTCACATTTTGTTCATGGTAGAGATTCTCT
-+
-hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhh
-@Dummy:1:1:1647:512/2
-TTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTTCGATTTTCTG
-+
-hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhh
-@Dummy:1:1:1570:620/2
-CTTGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCT
-+
-hhhhhhhAAhhhhhhhhhhhhhahhhhhhhhhhhh^hOhhhhghhhfhhh
-@Dummy:1:1:1599:330/2
-TTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACTAAAGGCA
-+
-hhhhhhhAAhhhhhhhhhhhhhhhhhhh[hhh_hh^hOhhhhghhhfhhh
-@Dummy:1:1:1652:270/2
-GCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCG
-+
-hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhUhh^hOhhhhghhhfhhh
-@Dummy:1:1:1746:351/2
-CCACTCCTCTCCCGACTGTGTGTGTGTGTGTTTATATTGACCATGCCGCT
-+
-hhhhhhhAAhhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhhhhhhhhhh
-@Dummy:1:1:1582:633/2
-TCTATTGACATTATGGGTCTGCAAGCTGCTTTTTTTTTTTTTTTTTTTTT
-+
-hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhh
-@Dummy:1:1:1598:534/2
-TTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCC
-+
-hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhh
-@Dummy:1:1:1572:324/2
-GCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGT
-+
-hhhhhhhAAhhhhhhhhhhhhhhhhhhhhJVhOTh^hOhhhhghhhfhhh
-@Dummy:1:1:1749:466/2
-GCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTG
-+
-hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhh
-@Dummy:1:1:1629:446/2
-CAAGCGAAGCGCGGTAGGTTTTCTGCTTAGGAGTTTAATCATGTTTCAGA
-+
-hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhh
-@Dummy:1:1:1763:587/2
-CATTGCATTCAGATGGATACATCTGTCAACGCCGCTAATCAGGTTGTTTC
-+
-hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhh
-@Dummy:1:1:1616:363/2
-GTGACTATTGACGTCCTTCCCCGTACGCCGGGCAATAAtGTTTATGTTGG
-+
-hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhchhh^hOhhhhghhhfhhh
-@Dummy:1:1:1768:715/2
-AGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGATA
-+
-hhhhhhhAAhhhhhhhhhhhhhchhhhhhhhhhhh^hOhhhhghhhfhhh
-@Dummy:1:1:1572:270/2
-ACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATG
-+
-hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhh
-@Dummy:1:1:1673:514/2
-GCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATG
-+
-hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhP^hOhhhhghhhfhhh
-@Dummy:1:1:1634:330/2
-TCAAGATTGCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTaCTAT
-+
-hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhWhh^hOhhhhghhhfhhh
diff -r 01ca7075c109 -r b300c15426f5 bowtie_rRNA_removal_wrapper/test-data/bowtie_in6.fastqsanger
--- a/bowtie_rRNA_removal_wrapper/test-data/bowtie_in6.fastqsanger	Tue Mar 15 10:27:46 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,72 +0,0 @@
-@Dummy:1:1:1761:343/2
-TTGATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGG
-+
-IIIIIII""IIIIIII0II?I""IIIIIIIIIIII?I0IIIIHIIIGIII
-@Dummy:1:1:1578:331/2
-AAGGACTGGTTTAGATATGAGTCACATTTTGTTCATGGTAGAGATTCTCT
-+
-IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII
-@Dummy:1:1:1647:512/2
-TTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTTCGATTTTCTG
-+
-IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII
-@Dummy:1:1:1570:620/2
-CTTGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCT
-+
-IIIIIII""IIIIIIIIIIIIIBIIIIIIIIIIII?I0IIIIHIIIGIII
-@Dummy:1:1:1599:330/2
-TTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACTAAAGGCA
-+
-IIIIIII""IIIIIIIIIIIIIIIIIII<III@II?I0IIIIHIIIGIII
-@Dummy:1:1:1652:270/2
-GCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCG
-+
-IIIIIII""IIIIIIIIIIIIIIIIIIIIIII6II?I0IIIIHIIIGIII
-@Dummy:1:1:1746:351/2
-CCACTCCTCTCCCGACTGTGTGTGTGTGTGTTTATATTGACCATGCCGCT
-+
-IIIIIII""IIIIIIIIIIIIIIIIII?I0IIIIHIIIGIIIIIIIIIII
-@Dummy:1:1:1582:633/2
-TCTATTGACATTATGGGTCTGCAAGCTGCTTTTTTTTTTTTTTTTTTTTT
-+
-IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII
-@Dummy:1:1:1598:534/2
-TTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCC
-+
-IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII
-@Dummy:1:1:1572:324/2
-GCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGT
-+
-IIIIIII""IIIIIIIIIIIIIIIIIIII+7I05I?I0IIIIHIIIGIII
-@Dummy:1:1:1749:466/2
-GCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTG
-+
-IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII
-@Dummy:1:1:1629:446/2
-CAAGCGAAGCGCGGTAGGTTTTCTGCTTAGGAGTTTAATCATGTTTCAGA
-+
-IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII
-@Dummy:1:1:1763:587/2
-CATTGCATTCAGATGGATACATCTGTCAACGCCGCTAATCAGGTTGTTTC
-+
-IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII
-@Dummy:1:1:1616:363/2
-GTGACTATTGACGTCCTTCCCCGTACGCCGGGCAATAAtGTTTATGTTGG
-+
-IIIIIII""IIIIIIIIIIIIIIIIIIIIIIDIII?I0IIIIHIIIGIII
-@Dummy:1:1:1768:715/2
-AGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGATA
-+
-IIIIIII""IIIIIIIIIIIIIDIIIIIIIIIIII?I0IIIIHIIIGIII
-@Dummy:1:1:1572:270/2
-ACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATG
-+
-IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII
-@Dummy:1:1:1673:514/2
-GCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATG
-+
-IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIII1?I0IIIIHIIIGIII
-@Dummy:1:1:1634:330/2
-TCAAGATTGCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTaCTAT
-+
-IIIIIII""IIIIIIIIIIIIIIIIIIIIIII8II?I0IIIIHIIIGIII
diff -r 01ca7075c109 -r b300c15426f5 bowtie_rRNA_removal_wrapper/test-data/bowtie_in6.fastqsolexa
--- a/bowtie_rRNA_removal_wrapper/test-data/bowtie_in6.fastqsolexa	Tue Mar 15 10:27:46 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,72 +0,0 @@
-@Dummy:1:1:1761:343/2
-TTGATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGG
-+
-hhhhhhh;;hhhhhhhOhh^h;;hhhhhhhhhhhh^hOhhhhghhhfhhh
-@Dummy:1:1:1578:331/2
-AAGGACTGGTTTAGATATGAGTCACATTTTGTTCATGGTAGAGATTCTCT
-+
-hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhh
-@Dummy:1:1:1647:512/2
-TTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTTCGATTTTCTG
-+
-hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhh
-@Dummy:1:1:1570:620/2
-CTTGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCT
-+
-hhhhhhh;;hhhhhhhhhhhhhahhhhhhhhhhhh^hOhhhhghhhfhhh
-@Dummy:1:1:1599:330/2
-TTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACTAAAGGCA
-+
-hhhhhhh;;hhhhhhhhhhhhhhhhhhh[hhh_hh^hOhhhhghhhfhhh
-@Dummy:1:1:1652:270/2
-GCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCG
-+
-hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhUhh^hOhhhhghhhfhhh
-@Dummy:1:1:1746:351/2
-CCACTCCTCTCCCGACTGTGTGTGTGTGTGTTTATATTGACCATGCCGCT
-+
-hhhhhhh;;hhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhhhhhhhhhh
-@Dummy:1:1:1582:633/2
-TCTATTGACATTATGGGTCTGCAAGCTGCTTTTTTTTTTTTTTTTTTTTT
-+
-hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhh
-@Dummy:1:1:1598:534/2
-TTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCC
-+
-hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhh
-@Dummy:1:1:1572:324/2
-GCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGT
-+
-hhhhhhh;;hhhhhhhhhhhhhhhhhhhhJVhOTh^hOhhhhghhhfhhh
-@Dummy:1:1:1749:466/2
-GCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTG
-+
-hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhh
-@Dummy:1:1:1629:446/2
-CAAGCGAAGCGCGGTAGGTTTTCTGCTTAGGAGTTTAATCATGTTTCAGA
-+
-hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhh
-@Dummy:1:1:1763:587/2
-CATTGCATTCAGATGGATACATCTGTCAACGCCGCTAATCAGGTTGTTTC
-+
-hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhh
-@Dummy:1:1:1616:363/2
-GTGACTATTGACGTCCTTCCCCGTACGCCGGGCAATAAtGTTTATGTTGG
-+
-hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhchhh^hOhhhhghhhfhhh
-@Dummy:1:1:1768:715/2
-AGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGATA
-+
-hhhhhhh;;hhhhhhhhhhhhhchhhhhhhhhhhh^hOhhhhghhhfhhh
-@Dummy:1:1:1572:270/2
-ACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATG
-+
-hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhh
-@Dummy:1:1:1673:514/2
-GCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATG
-+
-hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhP^hOhhhhghhhfhhh
-@Dummy:1:1:1634:330/2
-TCAAGATTGCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTaCTAT
-+
-hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhWhh^hOhhhhghhhfhhh
diff -r 01ca7075c109 -r b300c15426f5 bowtie_rRNA_removal_wrapper/test-data/bowtie_indices.loc
--- a/bowtie_rRNA_removal_wrapper/test-data/bowtie_indices.loc	Tue Mar 15 10:27:46 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-equCab2chrM	equCab2	Horse (Equus caballus): equCab2 chrM	${__HERE__}/indexes/equCab2chrM/equCab2chrM
diff -r 01ca7075c109 -r b300c15426f5 bowtie_rRNA_removal_wrapper/test-data/bowtie_out10.sam
--- a/bowtie_rRNA_removal_wrapper/test-data/bowtie_out10.sam	Tue Mar 15 10:27:46 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,36 +0,0 @@
-Dummy:1:1:1570:620	141	*	0	0	*	*	0	0	CTTGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCT	IIIIIII""IIIIIIIIIIIIIBIIIIIIIIIIII?I0IIIIHIIIGIII	XM:i:0
-Dummy:1:1:1570:620	77	*	0	0	*	*	0	0	GAGTAACAAAGTAAAGTTTGGACCGTTTTTGTCTCGTGCTCGTCGCTGCG	IIIIIII""IIIIIIIIIIIIIBIIIIIIIIIIII"IIIIIII000IIII	XM:i:0
-Dummy:1:1:1572:270	131	phiX174	3577	255	50M	=	3518	-109	ACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATG	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1572:270	67	phiX174	3518	255	50M	=	3577	109	TGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTA	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1572:324	141	*	0	0	*	*	0	0	GCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGT	IIIIIII""IIIIIIIIIIIIIIIIIIII+7I05I?I0IIIIHIIIGIII	XM:i:0
-Dummy:1:1:1572:324	77	*	0	0	*	*	0	0	AAGGTGCTTAAATTCGTGGGTCCTGAGCTGGCGACCCTGTTTTGTATGGC	IIIIIII""IIIIIIIIIIIIIIIIIIII+7I05I"IIIIIII000IIII	XM:i:0
-Dummy:1:1:1578:331	131	phiX174	268	255	50M	=	209	-109	AAGGACTGGTTTAGATATGAGTCACATTTTGTTCATGGTAGAGATTCTCT	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1578:331	67	phiX174	209	255	50M	=	268	109	TGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGC	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1582:633	141	*	0	0	*	*	0	0	TCTATTGACATTATGGGTCTGCAAGCTGCTTTTTTTTTTTTTTTTTTTTT	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII	XM:i:0
-Dummy:1:1:1582:633	77	*	0	0	*	*	0	0	CCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCAC	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII	XM:i:0
-Dummy:1:1:1598:534	131	phiX174	1772	255	50M	=	1717	-105	TTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCC	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1598:534	67	phiX174	1717	255	50M	=	1772	105	GCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAA	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1599:330	131	phiX174	868	255	50M	=	803	-115	TTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACTAAAGGCA	IIIIIII""IIIIIIIIIIIIIIIIIII<III@II?I0IIIIHIIIGIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1599:330	67	phiX174	803	255	50M	=	868	115	AGAAGAAAACGTGCGTCAAAAATTACGTGCAGAAGGAGTGATGTAATGTC	IIIIIII""IIIIIIIIIIIIIIIIIII<III@II"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1616:363	131	phiX174	2773	255	50M	=	2718	-105	GTGACTATTGACGTCCTTCCCCGTACGCCGGGCAATAATGTTTATGTTGG	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIDIII?I0IIIIHIIIGIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1616:363	67	phiX174	2718	255	50M	=	2773	105	TGTTTATCCTTTGAATGGTCGCCATGATGGTGGTTATTATACCGTCAAGG	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIDIII"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1629:446	131	phiX174	2355	255	50M	=	2301	-104	CAAGCGAAGCGCGGTAGGTTTTCTGCTTAGGAGTTTAATCATGTTTCAGA	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1629:446	67	phiX174	2301	255	50M	=	2355	104	AGGTTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGT	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1634:330	131	phiX174	4473	255	50M	=	4418	-105	TCAAGATTGCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTACTAT	IIIIIII""IIIIIIIIIIIIIIIIIIIIIII8II?I0IIIIHIIIGIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1634:330	67	phiX174	4418	255	50M	=	4473	105	GGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATG	IIIIIII""IIIIIIIIIIIIIIIIIIIIIII8II"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1647:512	131	phiX174	451	255	50M	=	401	-100	TTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTTCGATTTTCTG	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1647:512	67	phiX174	401	255	50M	=	451	100	TACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCA	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1652:270	141	*	0	0	*	*	0	0	GCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCG	IIIIIII""IIIIIIIIIIIIIIIIIIIIIII6II?I0IIIIHIIIGIII	XM:i:0
-Dummy:1:1:1652:270	77	*	0	0	*	*	0	0	AGCGTAAAGGCGCTCGTCTTTGGTATGTAGGACTTTGCATTGTTTAATTG	IIIIIII""IIIIIIIIIIIIIIIIIIIIIII6II"IIIIIII000IIII	XM:i:0
-Dummy:1:1:1673:514	131	phiX174	4072	255	50M	=	4018	-104	GCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATG	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIII1?I0IIIIHIIIGIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1673:514	67	phiX174	4018	255	50M	=	4072	104	ATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATTGAGGCT	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIII1"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1746:351	141	*	0	0	*	*	0	0	CCACTCCTCTCCCGACTGTGTGTGTGTGTGTTTATATTGACCATGCCGCT	IIIIIII""IIIIIIIIIIIIIIIIII?I0IIIIHIIIGIIIIIIIIIII	XM:i:0
-Dummy:1:1:1746:351	77	*	0	0	*	*	0	0	CTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGT	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII	XM:i:0
-Dummy:1:1:1749:466	131	phiX174	2251	255	50M	=	2201	-100	GCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTG	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1749:466	67	phiX174	2201	255	50M	=	2251	100	TTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCT	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1761:343	131	phiX174	69	255	50M	=	5	-114	TTGATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGG	IIIIIII""IIIIIII0II?I""IIIIIIIIIIII?I0IIIIHIIIGIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1761:343	67	phiX174	5	255	50M	=	69	114	TTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGA	IIIIIII""IIIIIIIIIII?I0IIIIHIIIGIIIII0II?I""IIIIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1763:587	131	phiX174	2566	255	50M	=	2501	-115	CATTGCATTCAGATGGATACATCTGTCAACGCCGCTAATCAGGTTGTTTC	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1763:587	67	phiX174	2501	255	50M	=	2566	115	AAGCTACATCGTCAACGTTATATTTTGATAGTTTGACGGTTAATGCTGGT	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1768:715	131	phiX174	3173	255	50M	=	3118	-105	AGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGATA	IIIIIII""IIIIIIIIIIIIIDIIIIIIIIIIII?I0IIIIHIIIGIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1768:715	67	phiX174	3118	255	50M	=	3173	105	ACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGCTAAAGCT	IIIIIII""IIIIIIIIIIIIIDIIIIIIIIIIII"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
diff -r 01ca7075c109 -r b300c15426f5 bowtie_rRNA_removal_wrapper/test-data/bowtie_out11.txt
--- a/bowtie_rRNA_removal_wrapper/test-data/bowtie_out11.txt	Tue Mar 15 10:27:46 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-# reads processed: 18
-# reads with at least one reported alignment: 13 (72.22%)
-# reads that failed to align: 5 (27.78%)
-Reported 13 paired-end alignments to 1 output stream(s)
diff -r 01ca7075c109 -r b300c15426f5 bowtie_rRNA_removal_wrapper/test-data/bowtie_out6.sam
--- a/bowtie_rRNA_removal_wrapper/test-data/bowtie_out6.sam	Tue Mar 15 10:27:46 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,26 +0,0 @@
-HWI-EAS91_1_30788AAXX:1:1:1090:409/1	16	chrM	15014	255	36M	*	0	0	TTGCCTACGCCATCCTACGCTCCATTCCCAACAAAC	I8AII:IIIIIIIIIIIIIIIIIIIII""IIIIIII	XA:i:0	MD:Z:36	NM:i:0
-HWI-EAS91_1_30788AAXX:1:1:1199:1376/1	16	chrM	14023	255	36M	*	0	0	AAACCCCCATAAATAGGTGAAGGTTTTCCAGAAAAC	III/:&GII3III;IIIIIIIIIIIII""IIIIIII	XA:i:2	MD:Z:27G0A7	NM:i:2
-HWI-EAS91_1_30788AAXX:1:1:1218:141/1	4	*	0	0	*	*	0	0	GTTAAATATTGGGAGTGGGGGGGGGGGGGAGTTTTG	IIIIIII""IIIIIIIIIIIIIIIIIIII1IIII+I	XM:i:0
-HWI-EAS91_1_30788AAXX:1:1:1269:520/1	16	chrM	11036	255	36M	*	0	0	CGACAAACCGATCTAAAATCACTTATTCCATACTCC	IIIIIIIIIIIIIIIIIIIIIIIIIII""IIIIIII	XA:i:1	MD:Z:27G8	NM:i:1
-HWI-EAS91_1_30788AAXX:1:1:1303:1162/1	16	chrM	14866	255	36M	*	0	0	AAAGACATCCTAGGACTCCTCCTCCTGCCCTTGCTC	I6I3,'94IIAI(IAIGI*4IIFIIII""IIIIIII	XA:i:2	MD:Z:27A0T7	NM:i:2
-HWI-EAS91_1_30788AAXX:1:1:1310:991/1	16	chrM	10002	255	36M	*	0	0	CTCCTATGCCTAGAAGGAATAATACTACCACTATTC	I:2IEI:IIDIIIIII4IIIIIIIIII""IIIIIII	XA:i:1	MD:Z:27T8	NM:i:1
-HWI-EAS91_1_30788AAXX:1:1:1336:1000/1	16	chrM	11616	255	36M	*	0	0	GATCTAGAAACAGAAACTTAATATTTCCCATTTACC	II9IIIIIIIIIIIIIIIIIIIIIIII""IIIIIII	XA:i:2	MD:Z:27T0T7	NM:i:2
-HWI-EAS91_1_30788AAXX:1:1:1398:854/1	16	chrM	3921	255	36M	*	0	0	CACCCTTCCCGTACTAATAAATCCCCTCCTCTTCAC	IIIII=AIIIIIIIIIIIIIIBIIIII""IIIIIII	XA:i:2	MD:Z:27T0A7	NM:i:2
-HWI-EAS91_1_30788AAXX:1:1:1442:1346/1	16	chrM	9331	255	36M	*	0	0	CAGCCACCACTTCGGATTCGAAGCAGCCCCTTGATA	&,*II-<?<II4I(I1IIIIIDIIIII""IIIIIII	XA:i:1	MD:Z:28G7	NM:i:1
-HWI-EAS91_1_30788AAXX:1:1:1454:975/1	16	chrM	8929	255	36M	*	0	0	TGGCTTCTTCTGAGCCTTTTACCACTCCCGCCTAGC	IIIIIII;GIEIIIIIIIIIIIIIIII""IIIIIII	XA:i:2	MD:Z:27A0A7	NM:i:2
-HWI-EAS91_1_30788AAXX:1:1:1461:255/1	0	chrM	12988	255	36M	*	0	0	GTACACCGGCGCCTGAGCCCTACTAATAACTCTCAT	IIIIIII""IIIIII9IIIIIIEI(II9.I4III,I	XA:i:2	MD:Z:7A0A27	NM:i:2
-HWI-EAS91_1_30788AAXX:1:1:1491:637/1	16	chrM	10864	255	36M	*	0	0	TGTAGAAGCCCCAATTGCCGGATCCATCCTGCTAGC	DBAIIIIIIIIIIIFIIIIIIIIIIII""IIIIIII	XA:i:2	MD:Z:27A0G7	NM:i:2
-HWI-EAS91_1_30788AAXX:1:1:1513:715/1	16	chrM	9563	255	36M	*	0	0	CTGACTACCACAACTAAACATCTATGCCCAAAAAAC	I+-II?IDIIIIIIIIIIIIIIIIIII""IIIIIII	XA:i:2	MD:Z:27A0G7	NM:i:2
-HWI-EAS91_1_30788AAXX:1:1:1598:1148/1	16	chrM	2334	255	36M	*	0	0	AAATATATAATCACTTATTGATCCAAACCATTGATC	IIIIIHI=IICIII?IIIIIIDIIIII""IIIIIII	XA:i:0	MD:Z:36	NM:i:0
-HWI-EAS91_1_30788AAXX:1:1:1601:805/1	0	chrM	12584	255	36M	*	0	0	GAAAACAGGAAAACAATCCAGTCACTTACCCTATGC	IIIIIII""IIIIIIIIIIIIIIIIIIIIIII@III	XA:i:2	MD:Z:7A0C27	NM:i:2
-HWI-EAS91_1_30788AAXX:1:1:1630:59/1	16	chrM	12387	255	36M	*	0	0	TCATACTCGACCCCAACCTTACCAACCCCCCGCTCC	FIIHII;IIIIIIIIIIIIIIIIIIII""IIIIIII	XA:i:1	MD:Z:27T8	NM:i:1
-HWI-EAS91_1_30788AAXX:1:1:1634:211/1	0	chrM	9350	255	36M	*	0	0	GAAGCAGGGGCTTGATACTGACACTTCGTCGACGTA	IIIIIII""IIIIIIIIIIIIIIIIIIIIII9IIDF	XA:i:2	MD:Z:7C0C27	NM:i:2
-HWI-EAS91_1_30788AAXX:1:1:1663:724/1	0	chrM	15012	255	36M	*	0	0	GTTTGCCGGCGCCATCCTACGCTCCATTCCCAACAA	IIIIIII""IIII8IIIIIIHIIII6IIIII1CI=3	XA:i:2	MD:Z:7T0A27	NM:i:2
-HWI-EAS91_1_30788AAXX:1:1:1698:516/1	16	chrM	2735	255	36M	*	0	0	TTTACACTCAGAGGTTCAACTCCTCTCCCTAACAAC	I9IIIII5IIIIIIIIIIIIIIIIIII""IIIIIII	XA:i:0	MD:Z:36	NM:i:0
-HWI-EAS91_1_30788AAXX:1:1:1711:249/1	16	chrM	10617	255	36M	*	0	0	ACCAAACAGAACGCCTGAACGCAGGCCCCTACTTCC	IIIIIIIIIIIIIIIIIIIIIIIIIII""IIIIIII	XA:i:1	MD:Z:27T8	NM:i:1
-HWI-EAS91_1_30788AAXX:1:1:1716:413/1	0	chrM	6040	255	36M	*	0	0	GATCCAAGGCTTTATCAACACCTATTCTGATTCTTC	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII	XA:i:2	MD:Z:7T0C27	NM:i:2
-HWI-EAS91_1_30788AAXX:1:1:1723:1459/1	16	chrM	15787	255	36M	*	0	0	ATCCTCGCTCCGGGCCCATCCAAACGTCCGGGTTTC	I=II-IIH9IIIIIIIIIDIIIIIIII""IIIIIII	XA:i:2	MD:Z:27G0G7	NM:i:2
-HWI-EAS91_1_30788AAXX:1:1:1775:764/1	0	chrM	16613	255	36M	*	0	0	GCATCCCGGTAGATCTAATTTTCTAAATCTGTCAAC	IIIIIII""III@IIII+IIIIII8H8IIIIIIICI	XA:i:2	MD:Z:7C0C27	NM:i:2
-HWI-EAS91_1_30788AAXX:1:1:795:325/1	16	chrM	4249	255	36M	*	0	0	AAACTTGGACTCACACCATTCCACTTCCCAGTACCC	IIII56IIIIIIIIIIIIIIIIIIIII""IIIIIII	XA:i:2	MD:Z:27T0G7	NM:i:2
-HWI-EAS91_1_30788AAXX:1:1:850:117/1	16	chrM	5540	255	36M	*	0	0	CCCATGCATTCGTAATAATTTTCTTTACCGTCATAC	?:;I9DDIBEIIIIIIIIEIEIIIIII""IIIIIII	XA:i:2	MD:Z:27T0G7	NM:i:2
-HWI-EAS91_1_30788AAXX:1:1:873:453/1	16	chrM	3188	255	36M	*	0	0	ATCTCATACGAAGTAACTCTAGCAATCCCCCTACTC	I=IIIIIII@IIIIIIIIIIIIIIIII""IIIIIII	XA:i:2	MD:Z:27A0T7	NM:i:2
diff -r 01ca7075c109 -r b300c15426f5 bowtie_rRNA_removal_wrapper/test-data/bowtie_out7.sam
--- a/bowtie_rRNA_removal_wrapper/test-data/bowtie_out7.sam	Tue Mar 15 10:27:46 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,36 +0,0 @@
-Dummy:1:1:1570:620	141	*	0	0	*	*	0	0	CTTGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCT	IIIIIII""IIIIIIIIIIIIIBIIIIIIIIIIII?I0IIIIHIIIGIII	XM:i:0
-Dummy:1:1:1570:620	77	*	0	0	*	*	0	0	GAGTAACAAAGTAAAGTTTGGACCGTTTTTGTCTCGTGCTCGTCGCTGCG	IIIIIII""IIIIIIIIIIIIIBIIIIIIIIIIII"IIIIIII000IIII	XM:i:0
-Dummy:1:1:1572:270	131	phiX174	3577	255	50M	=	3518	-109	ACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATG	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1572:270	67	phiX174	3518	255	50M	=	3577	109	TGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTA	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1572:324	141	*	0	0	*	*	0	0	GCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGT	IIIIIII""IIIIIIIIIIIIIIIIIIII+7I05I?I0IIIIHIIIGIII	XM:i:0
-Dummy:1:1:1572:324	77	*	0	0	*	*	0	0	AAGGTGCTTAAATTCGTGGGTCCTGAGCTGGCGACCCTGTTTTGTATGGC	IIIIIII""IIIIIIIIIIIIIIIIIIII+7I05I"IIIIIII000IIII	XM:i:0
-Dummy:1:1:1578:331	131	phiX174	268	255	50M	=	209	-109	AAGGACTGGTTTAGATATGAGTCACATTTTGTTCATGGTAGAGATTCTCT	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1578:331	67	phiX174	209	255	50M	=	268	109	TGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGC	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1582:633	141	*	0	0	*	*	0	0	TCTATTGACATTATGGGTCTGCAAGCTGCTTTTTTTTTTTTTTTTTTTTT	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII	XM:i:0
-Dummy:1:1:1582:633	77	*	0	0	*	*	0	0	CCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCAC	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII	XM:i:0
-Dummy:1:1:1598:534	131	phiX174	1772	255	50M	=	1717	-105	TTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCC	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1598:534	67	phiX174	1717	255	50M	=	1772	105	GCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAA	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1599:330	131	phiX174	868	255	50M	=	803	-115	TTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACTAAAGGCA	IIIIIII""IIIIIIIIIIIIIIIIIII<III@II?I0IIIIHIIIGIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1599:330	67	phiX174	803	255	50M	=	868	115	AGAAGAAAACGTGCGTCAAAAATTACGTGCAGAAGGAGTGATGTAATGTC	IIIIIII""IIIIIIIIIIIIIIIIIII<III@II"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1616:363	131	phiX174	2773	255	50M	=	2718	-105	GTGACTATTGACGTCCTTCCCCGTACGCCGGGCAATAATGTTTATGTTGG	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIDIII?I0IIIIHIIIGIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1616:363	67	phiX174	2718	255	50M	=	2773	105	TGTTTATCCTTTGAATGGTCGCCATGATGGTGGTTATTATACCGTCAAGG	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIDIII"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1629:446	131	phiX174	2355	255	50M	=	2301	-104	CAAGCGAAGCGCGGTAGGTTTTCTGCTTAGGAGTTTAATCATGTTTCAGA	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1629:446	67	phiX174	2301	255	50M	=	2355	104	AGGTTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGT	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1634:330	131	phiX174	4473	255	50M	=	4418	-105	TCAAGATTGCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTACTAT	IIIIIII""IIIIIIIIIIIIIIIIIIIIIII8II?I0IIIIHIIIGIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1634:330	67	phiX174	4418	255	50M	=	4473	105	GGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATG	IIIIIII""IIIIIIIIIIIIIIIIIIIIIII8II"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1647:512	131	phiX174	451	255	50M	=	401	-100	TTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTTCGATTTTCTG	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1647:512	67	phiX174	401	255	50M	=	451	100	TACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCA	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1652:270	141	*	0	0	*	*	0	0	GCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCG	IIIIIII""IIIIIIIIIIIIIIIIIIIIIII6II?I0IIIIHIIIGIII	XM:i:0
-Dummy:1:1:1652:270	77	*	0	0	*	*	0	0	AGCGTAAAGGCGCTCGTCTTTGGTATGTAGGACTTTGCATTGTTTAATTG	IIIIIII""IIIIIIIIIIIIIIIIIIIIIII6II"IIIIIII000IIII	XM:i:0
-Dummy:1:1:1673:514	131	phiX174	4072	255	50M	=	4018	-104	GCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATG	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIII1?I0IIIIHIIIGIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1673:514	67	phiX174	4018	255	50M	=	4072	104	ATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATTGAGGCT	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIII1"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1746:351	141	*	0	0	*	*	0	0	CCACTCCTCTCCCGACTGTGTGTGTGTGTGTTTATATTGACCATGCCGCT	IIIIIII""IIIIIIIIIIIIIIIIII?I0IIIIHIIIGIIIIIIIIIII	XM:i:0
-Dummy:1:1:1746:351	77	*	0	0	*	*	0	0	CTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGT	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII	XM:i:0
-Dummy:1:1:1749:466	131	phiX174	2251	255	50M	=	2201	-100	GCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTG	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1749:466	67	phiX174	2201	255	50M	=	2251	100	TTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCT	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1761:343	131	phiX174	69	255	50M	=	5	-114	TTGATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGG	IIIIIII""IIIIIII0II?I""IIIIIIIIIIII?I0IIIIHIIIGIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1761:343	67	phiX174	5	255	50M	=	69	114	TTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGA	IIIIIII""IIIIIIIIIII?I0IIIIHIIIGIIIII0II?I""IIIIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1763:587	131	phiX174	2566	255	50M	=	2501	-115	CATTGCATTCAGATGGATACATCTGTCAACGCCGCTAATCAGGTTGTTTC	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1763:587	67	phiX174	2501	255	50M	=	2566	115	AAGCTACATCGTCAACGTTATATTTTGATAGTTTGACGGTTAATGCTGGT	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1768:715	131	phiX174	3173	255	50M	=	3118	-105	AGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGATA	IIIIIII""IIIIIIIIIIIIIDIIIIIIIIIIII?I0IIIIHIIIGIII	XA:i:0	MD:Z:50	NM:i:0
-Dummy:1:1:1768:715	67	phiX174	3118	255	50M	=	3173	105	ACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGCTAAAGCT	IIIIIII""IIIIIIIIIIIIIDIIIIIIIIIIII"IIIIIII000IIII	XA:i:0	MD:Z:50	NM:i:0
diff -r 01ca7075c109 -r b300c15426f5 bowtie_rRNA_removal_wrapper/test-data/bowtie_out8_1.fastq
--- a/bowtie_rRNA_removal_wrapper/test-data/bowtie_out8_1.fastq	Tue Mar 15 10:27:46 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,20 +0,0 @@
-+
-+
-+
-+
-+
-@Dummy:1:1:1570:620/1
-@Dummy:1:1:1572:324/1
-@Dummy:1:1:1582:633/1
-@Dummy:1:1:1652:270/1
-@Dummy:1:1:1746:351/1
-AAGGTGCTTaaaTTCgtGGGTCCTGAGCTGGCGACCCTGTTTTGTATGGC
-AGCGTAAAGGCGCTCGTCTTTGGTATGTAGGacTTTGCATTGTTTAATTG
-CCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCAC
-CTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGT
-GAGTAACAAAGTaaaGTTTGGAccGTTTTTGTCTCGTGCTCGTCGCTGCG
-IIIIIII""IIIIIIIIIIIIIBIIIIIIIIIIII"IIIIIII000IIII
-IIIIIII""IIIIIIIIIIIIIIIIIIII+7I05I"IIIIIII000IIII
-IIIIIII""IIIIIIIIIIIIIIIIIIIIIII6II"IIIIIII000IIII
-IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII
-IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII
diff -r 01ca7075c109 -r b300c15426f5 bowtie_rRNA_removal_wrapper/test-data/bowtie_out8_1.fastqillumina.sorted
--- a/bowtie_rRNA_removal_wrapper/test-data/bowtie_out8_1.fastqillumina.sorted	Tue Mar 15 10:27:46 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,20 +0,0 @@
-+
-+
-+
-+
-+
-@Dummy:1:1:1570:620/1
-@Dummy:1:1:1572:324/1
-@Dummy:1:1:1582:633/1
-@Dummy:1:1:1652:270/1
-@Dummy:1:1:1746:351/1
-AAGGTGCTTaaaTTCgtGGGTCCTGAGCTGGCGACCCTGTTTTGTATGGC
-AGCGTAAAGGCGCTCGTCTTTGGTATGTAGGacTTTGCATTGTTTAATTG
-CCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCAC
-CTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGT
-GAGTAACAAAGTaaaGTTTGGAccGTTTTTGTCTCGTGCTCGTCGCTGCG
-hhhhhhhAAhhhhhhhhhhhhhahhhhhhhhhhhhAhhhhhhhOOOhhhh
-hhhhhhhAAhhhhhhhhhhhhhhhhhhhhJVhOThAhhhhhhhOOOhhhh
-hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhUhhAhhhhhhhOOOhhhh
-hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhhAhhhhhhhOOOhhhh
-hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhhAhhhhhhhOOOhhhh
diff -r 01ca7075c109 -r b300c15426f5 bowtie_rRNA_removal_wrapper/test-data/bowtie_out8_1.fastqsolexa.sorted
--- a/bowtie_rRNA_removal_wrapper/test-data/bowtie_out8_1.fastqsolexa.sorted	Tue Mar 15 10:27:46 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,20 +0,0 @@
-+
-+
-+
-+
-+
-@Dummy:1:1:1570:620/1
-@Dummy:1:1:1572:324/1
-@Dummy:1:1:1582:633/1
-@Dummy:1:1:1652:270/1
-@Dummy:1:1:1746:351/1
-AAGGTGCTTaaaTTCgtGGGTCCTGAGCTGGCGACCCTGTTTTGTATGGC
-AGCGTAAAGGCGCTCGTCTTTGGTATGTAGGacTTTGCATTGTTTAATTG
-CCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCAC
-CTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGT
-GAGTAACAAAGTaaaGTTTGGAccGTTTTTGTCTCGTGCTCGTCGCTGCG
-hhhhhhh;;hhhhhhhhhhhhhahhhhhhhhhhhh;hhhhhhhOOOhhhh
-hhhhhhh;;hhhhhhhhhhhhhhhhhhhhJVhOTh;hhhhhhhOOOhhhh
-hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhUhh;hhhhhhhOOOhhhh
-hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhh;hhhhhhhOOOhhhh
-hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhh;hhhhhhhOOOhhhh
diff -r 01ca7075c109 -r b300c15426f5 bowtie_rRNA_removal_wrapper/test-data/bowtie_out8_2.fastq
--- a/bowtie_rRNA_removal_wrapper/test-data/bowtie_out8_2.fastq	Tue Mar 15 10:27:46 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,20 +0,0 @@
-+
-+
-+
-+
-+
-@Dummy:1:1:1570:620/2
-@Dummy:1:1:1572:324/2
-@Dummy:1:1:1582:633/2
-@Dummy:1:1:1652:270/2
-@Dummy:1:1:1746:351/2
-CCACTCCTCTCCCGACTGTGTGTGTGTGTGTTTATATTGACCATGCCGCT
-CTTGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCT
-GCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGT
-GCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCG
-IIIIIII""IIIIIIIIIIIIIBIIIIIIIIIIII?I0IIIIHIIIGIII
-IIIIIII""IIIIIIIIIIIIIIIIII?I0IIIIHIIIGIIIIIIIIIII
-IIIIIII""IIIIIIIIIIIIIIIIIIII+7I05I?I0IIIIHIIIGIII
-IIIIIII""IIIIIIIIIIIIIIIIIIIIIII6II?I0IIIIHIIIGIII
-IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII
-TCTATTGACATTATGGGTCTGCAAGCTGCTTTTTTTTTTTTTTTTTTTTT
diff -r 01ca7075c109 -r b300c15426f5 bowtie_rRNA_removal_wrapper/test-data/bowtie_out8_2.fastqillumina.sorted
--- a/bowtie_rRNA_removal_wrapper/test-data/bowtie_out8_2.fastqillumina.sorted	Tue Mar 15 10:27:46 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,20 +0,0 @@
-+
-+
-+
-+
-+
-@Dummy:1:1:1570:620/2
-@Dummy:1:1:1572:324/2
-@Dummy:1:1:1582:633/2
-@Dummy:1:1:1652:270/2
-@Dummy:1:1:1746:351/2
-CCACTCCTCTCCCGACTGTGTGTGTGTGTGTTTATATTGACCATGCCGCT
-CTTGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCT
-GCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGT
-GCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCG
-TCTATTGACATTATGGGTCTGCAAGCTGCTTTTTTTTTTTTTTTTTTTTT
-hhhhhhhAAhhhhhhhhhhhhhahhhhhhhhhhhh^hOhhhhghhhfhhh
-hhhhhhhAAhhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhhhhhhhhhh
-hhhhhhhAAhhhhhhhhhhhhhhhhhhhhJVhOTh^hOhhhhghhhfhhh
-hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhUhh^hOhhhhghhhfhhh
-hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhh
diff -r 01ca7075c109 -r b300c15426f5 bowtie_rRNA_removal_wrapper/test-data/bowtie_out8_2.fastqsolexa.sorted
--- a/bowtie_rRNA_removal_wrapper/test-data/bowtie_out8_2.fastqsolexa.sorted	Tue Mar 15 10:27:46 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,20 +0,0 @@
-+
-+
-+
-+
-+
-@Dummy:1:1:1570:620/2
-@Dummy:1:1:1572:324/2
-@Dummy:1:1:1582:633/2
-@Dummy:1:1:1652:270/2
-@Dummy:1:1:1746:351/2
-CCACTCCTCTCCCGACTGTGTGTGTGTGTGTTTATATTGACCATGCCGCT
-CTTGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCT
-GCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGT
-GCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCG
-TCTATTGACATTATGGGTCTGCAAGCTGCTTTTTTTTTTTTTTTTTTTTT
-hhhhhhh;;hhhhhhhhhhhhhahhhhhhhhhhhh^hOhhhhghhhfhhh
-hhhhhhh;;hhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhhhhhhhhhh
-hhhhhhh;;hhhhhhhhhhhhhhhhhhhhJVhOTh^hOhhhhghhhfhhh
-hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhUhh^hOhhhhghhhfhhh
-hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhh
diff -r 01ca7075c109 -r b300c15426f5 bowtie_rRNA_removal_wrapper/test-data/bowtie_out9.sam
--- a/bowtie_rRNA_removal_wrapper/test-data/bowtie_out9.sam	Tue Mar 15 10:27:46 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,26 +0,0 @@
-HWI-EAS91_1_30788AAXX:1:1:1090:409/1	16	chrM	15014	255	36M	*	0	0	TTGCCTACGCCATCCTACGCTCCATTCCCAACAAAC	I8AII:IIIIIIIIIIIIIIIIIIIII""IIIIIII	XA:i:0	MD:Z:36	NM:i:0
-HWI-EAS91_1_30788AAXX:1:1:1199:1376/1	16	chrM	14023	255	36M	*	0	0	AAACCCCCATAAATAGGTGAAGGTTTTCCAGAAAAC	III/:&GII3III;IIIIIIIIIIIII""IIIIIII	XA:i:2	MD:Z:27G0A7	NM:i:2
-HWI-EAS91_1_30788AAXX:1:1:1218:141/1	4	*	0	0	*	*	0	0	GTTAAATATTGGGAGTGGGGGGGGGGGGGAGTTTTG	IIIIIII""IIIIIIIIIIIIIIIIIIII1IIII+I	XM:i:0
-HWI-EAS91_1_30788AAXX:1:1:1269:520/1	16	chrM	11036	255	36M	*	0	0	CGACAAACCGATCTAAAATCACTTATTCCATACTCC	IIIIIIIIIIIIIIIIIIIIIIIIIII""IIIIIII	XA:i:1	MD:Z:27G8	NM:i:1
-HWI-EAS91_1_30788AAXX:1:1:1303:1162/1	16	chrM	14866	255	36M	*	0	0	AAAGACATCCTAGGACTCCTCCTCCTGCCCTTGCTC	I6I3,'94IIAI(IAIGI*4IIFIIII""IIIIIII	XA:i:2	MD:Z:27A0T7	NM:i:2
-HWI-EAS91_1_30788AAXX:1:1:1310:991/1	16	chrM	10002	255	36M	*	0	0	CTCCTATGCCTAGAAGGAATAATACTACCACTATTC	I:2IEI:IIDIIIIII4IIIIIIIIII""IIIIIII	XA:i:1	MD:Z:27T8	NM:i:1
-HWI-EAS91_1_30788AAXX:1:1:1336:1000/1	16	chrM	11616	255	36M	*	0	0	GATCTAGAAACAGAAACTTAATATTTCCCATTTACC	II9IIIIIIIIIIIIIIIIIIIIIIII""IIIIIII	XA:i:2	MD:Z:27T0T7	NM:i:2
-HWI-EAS91_1_30788AAXX:1:1:1398:854/1	16	chrM	3921	255	36M	*	0	0	CACCCTTCCCGTACTAATAAATCCCCTCCTCTTCAC	IIIII=AIIIIIIIIIIIIIIBIIIII""IIIIIII	XA:i:2	MD:Z:27T0A7	NM:i:2
-HWI-EAS91_1_30788AAXX:1:1:1442:1346/1	16	chrM	9331	255	36M	*	0	0	CAGCCACCACTTCGGATTCGAAGCAGCCCCTTGATA	&,*II-<?<II4I(I1IIIIIDIIIII""IIIIIII	XA:i:1	MD:Z:28G7	NM:i:1
-HWI-EAS91_1_30788AAXX:1:1:1454:975/1	16	chrM	8929	255	36M	*	0	0	TGGCTTCTTCTGAGCCTTTTACCACTCCCGCCTAGC	IIIIIII;GIEIIIIIIIIIIIIIIII""IIIIIII	XA:i:2	MD:Z:27A0A7	NM:i:2
-HWI-EAS91_1_30788AAXX:1:1:1461:255/1	0	chrM	12988	255	36M	*	0	0	GTACACCGGCGCCTGAGCCCTACTAATAACTCTCAT	IIIIIII""IIIIII9IIIIIIEI(II9.I4III,I	XA:i:2	MD:Z:7A0A27	NM:i:2
-HWI-EAS91_1_30788AAXX:1:1:1491:637/1	16	chrM	10864	255	36M	*	0	0	TGTAGAAGCCCCAATTGCCGGATCCATCCTGCTAGC	DBAIIIIIIIIIIIFIIIIIIIIIIII""IIIIIII	XA:i:2	MD:Z:27A0G7	NM:i:2
-HWI-EAS91_1_30788AAXX:1:1:1513:715/1	16	chrM	9563	255	36M	*	0	0	CTGACTACCACAACTAAACATCTATGCCCAAAAAAC	I+-II?IDIIIIIIIIIIIIIIIIIII""IIIIIII	XA:i:2	MD:Z:27A0G7	NM:i:2
-HWI-EAS91_1_30788AAXX:1:1:1598:1148/1	16	chrM	2334	255	36M	*	0	0	AAATATATAATCACTTATTGATCCAAACCATTGATC	IIIIIHI=IICIII?IIIIIIDIIIII""IIIIIII	XA:i:0	MD:Z:36	NM:i:0
-HWI-EAS91_1_30788AAXX:1:1:1601:805/1	0	chrM	12584	255	36M	*	0	0	GAAAACAGGAAAACAATCCAGTCACTTACCCTATGC	IIIIIII""IIIIIIIIIIIIIIIIIIIIIII@III	XA:i:2	MD:Z:7A0C27	NM:i:2
-HWI-EAS91_1_30788AAXX:1:1:1630:59/1	16	chrM	12387	255	36M	*	0	0	TCATACTCGACCCCAACCTTACCAACCCCCCGCTCC	FIIHII;IIIIIIIIIIIIIIIIIIII""IIIIIII	XA:i:1	MD:Z:27T8	NM:i:1
-HWI-EAS91_1_30788AAXX:1:1:1634:211/1	0	chrM	9350	255	36M	*	0	0	GAAGCAGGGGCTTGATACTGACACTTCGTCGACGTA	IIIIIII""IIIIIIIIIIIIIIIIIIIIII9IIDF	XA:i:2	MD:Z:7C0C27	NM:i:2
-HWI-EAS91_1_30788AAXX:1:1:1663:724/1	0	chrM	15012	255	36M	*	0	0	GTTTGCCGGCGCCATCCTACGCTCCATTCCCAACAA	IIIIIII""IIII8IIIIIIHIIII6IIIII1CI=3	XA:i:2	MD:Z:7T0A27	NM:i:2
-HWI-EAS91_1_30788AAXX:1:1:1698:516/1	16	chrM	2735	255	36M	*	0	0	TTTACACTCAGAGGTTCAACTCCTCTCCCTAACAAC	I9IIIII5IIIIIIIIIIIIIIIIIII""IIIIIII	XA:i:0	MD:Z:36	NM:i:0
-HWI-EAS91_1_30788AAXX:1:1:1711:249/1	16	chrM	10617	255	36M	*	0	0	ACCAAACAGAACGCCTGAACGCAGGCCCCTACTTCC	IIIIIIIIIIIIIIIIIIIIIIIIIII""IIIIIII	XA:i:1	MD:Z:27T8	NM:i:1
-HWI-EAS91_1_30788AAXX:1:1:1716:413/1	0	chrM	6040	255	36M	*	0	0	GATCCAAGGCTTTATCAACACCTATTCTGATTCTTC	IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII	XA:i:2	MD:Z:7T0C27	NM:i:2
-HWI-EAS91_1_30788AAXX:1:1:1723:1459/1	16	chrM	15787	255	36M	*	0	0	ATCCTCGCTCCGGGCCCATCCAAACGTCCGGGTTTC	I=II-IIH9IIIIIIIIIDIIIIIIII""IIIIIII	XA:i:2	MD:Z:27G0G7	NM:i:2
-HWI-EAS91_1_30788AAXX:1:1:1775:764/1	0	chrM	16613	255	36M	*	0	0	GCATCCCGGTAGATCTAATTTTCTAAATCTGTCAAC	IIIIIII""III@IIII+IIIIII8H8IIIIIIICI	XA:i:2	MD:Z:7C0C27	NM:i:2
-HWI-EAS91_1_30788AAXX:1:1:795:325/1	16	chrM	4249	255	36M	*	0	0	AAACTTGGACTCACACCATTCCACTTCCCAGTACCC	IIII56IIIIIIIIIIIIIIIIIIIII""IIIIIII	XA:i:2	MD:Z:27T0G7	NM:i:2
-HWI-EAS91_1_30788AAXX:1:1:850:117/1	16	chrM	5540	255	36M	*	0	0	CCCATGCATTCGTAATAATTTTCTTTACCGTCATAC	?:;I9DDIBEIIIIIIIIEIEIIIIII""IIIIIII	XA:i:2	MD:Z:27T0G7	NM:i:2
-HWI-EAS91_1_30788AAXX:1:1:873:453/1	16	chrM	3188	255	36M	*	0	0	ATCTCATACGAAGTAACTCTAGCAATCCCCCTACTC	I=IIIIIII@IIIIIIIIIIIIIIIII""IIIIIII	XA:i:2	MD:Z:27A0T7	NM:i:2
diff -r 01ca7075c109 -r b300c15426f5 bowtie_rRNA_removal_wrapper/test-data/phiX.fasta
--- a/bowtie_rRNA_removal_wrapper/test-data/phiX.fasta	Tue Mar 15 10:27:46 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,79 +0,0 @@
->phiX174
-GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTT
-GATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAA
-ATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTG
-TCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTA
-GATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATC
-TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTT
-TCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTT
-CGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCT
-TGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCG
-TCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTAC
-GGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTA
-CGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCAGAAGGAG
-TGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACT
-AAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGC
-CCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCA
-TCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGAC
-TCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA
-CTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAA
-GGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTT
-GGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACA
-ACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGC
-TCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTT
-TCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGC
-ATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCGTGATGTTATTTCTTCATTTGGAGGTAAAAC
-CTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTT
-GATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGC
-CGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGAC
-TAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTG
-TATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGT
-TTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGA
-AGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGAT
-TATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTT
-ATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAAC
-GCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGC
-TTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGT
-TCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTA
-TATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTG
-TCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGC
-CTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTG
-AATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGC
-CGGGCAATAATGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGT
-TTCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTG
-CTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAA
-AGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCT
-GGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTG
-GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGA
-TAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTAT
-CTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGG
-TTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGA
-GATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGAC
-CAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTA
-TGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCA
-AACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGAC
-TTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTT
-CTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGA
-TACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCG
-TCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTT
-CTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTAT
-TGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGC
-ATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATG
-TTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGA
-ATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGG
-GACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCC
-CTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATT
-GCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTACTATTCAGCGTTTGATGAATGCAATGCGACAG
-GCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTT
-ATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCG
-CAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGC
-CGTCTTCATTTCCATGCGGTGCATTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTC
-GTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCAT
-CGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAG
-CCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATA
-TGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACT
-TCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTG
-TCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGC
-AGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACC
-TGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA
-
diff -r 01ca7075c109 -r b300c15426f5 bowtie_rRNA_removal_wrapper/tool-data/bowtie_indices.loc.sample
--- a/bowtie_rRNA_removal_wrapper/tool-data/bowtie_indices.loc.sample	Tue Mar 15 10:27:46 2022 +0000
+++ b/bowtie_rRNA_removal_wrapper/tool-data/bowtie_indices.loc.sample	Mon Mar 21 12:53:51 2022 +0000
@@ -1,37 +1,1 @@
-#This is a sample file distributed with Galaxy that enables tools
-#to use a directory of Bowtie indexed sequences data files. You will
-#need to create these data files and then create a bowtie_indices.loc
-#file similar to this one (store it in this directory) that points to
-#the directories in which those files are stored. The bowtie_indices.loc
-#file has this format (longer white space characters are TAB characters):
-#
-#<unique_build_id>   <dbkey>   <display_name>   <file_base_path>
-#
-#So, for example, if you had hg18 indexed stored in
-#/depot/data2/galaxy/bowtie/hg18/,
-#then the bowtie_indices.loc entry would look like this:
-#
-#hg18	hg18	hg18	/depot/data2/galaxy/bowtie/hg18/hg18
-#
-#and your /depot/data2/galaxy/bowtie/hg18/ directory
-#would contain hg18.*.ebwt files:
-#
-#-rw-r--r--  1 james    universe 830134 2005-09-13 10:12 hg18.1.ebwt
-#-rw-r--r--  1 james    universe 527388 2005-09-13 10:12 hg18.2.ebwt
-#-rw-r--r--  1 james    universe 269808 2005-09-13 10:12 hg18.3.ebwt
-#...etc...
-#
-#Your bowtie_indices.loc file should include an entry per line for each
-#index set you have stored. The "file" in the path does not actually
-#exist, but it is the prefix for the actual index files. For example:
-#
-#hg18canon			hg18	hg18 Canonical	/depot/data2/galaxy/bowtie/hg18/hg18canon
-#hg18full			hg18	hg18 Full		/depot/data2/galaxy/bowtie/hg18/hg18full
-#/orig/path/hg19	hg19	hg19			/depot/data2/galaxy/bowtie/hg19/hg19
-#...etc...
-#
-#Note that for backwards compatibility with workflows, the unique ID of
-#an entry must be the path that was in the original loc file, because that
-#is the value stored in the workflow for that parameter. That is why the
-#hg19 entry above looks odd. New genomes can be better-looking.
-#
+yeast_rRNA  yeast_test  yeast_rRNA  ${__HERE__}/indexes/yeast_rRNA
\ No newline at end of file
diff -r 01ca7075c109 -r b300c15426f5 bowtie_rRNA_removal_wrapper/tool-data/indexes/yeast_rRNA.1.ebwt
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diff -r 01ca7075c109 -r b300c15426f5 bowtie_rRNA_removal_wrapper/tool-data/indexes/yeast_rRNA.2.ebwt
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diff -r 01ca7075c109 -r b300c15426f5 bowtie_rRNA_removal_wrapper/tool-data/indexes/yeast_rRNA.3.ebwt
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diff -r 01ca7075c109 -r b300c15426f5 bowtie_rRNA_removal_wrapper/tool-data/indexes/yeast_rRNA.4.ebwt
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diff -r 01ca7075c109 -r b300c15426f5 bowtie_rRNA_removal_wrapper/tool-data/indexes/yeast_rRNA.rev.1.ebwt
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diff -r 01ca7075c109 -r b300c15426f5 bowtie_rRNA_removal_wrapper/tool-data/indexes/yeast_rRNA.rev.2.ebwt
Binary file bowtie_rRNA_removal_wrapper/tool-data/indexes/yeast_rRNA.rev.2.ebwt has changed
diff -r 01ca7075c109 -r b300c15426f5 bowtie_rRNA_removal_wrapper/tool_data_table_conf.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bowtie_rRNA_removal_wrapper/tool_data_table_conf.xml	Mon Mar 21 12:53:51 2022 +0000
@@ -0,0 +1,8 @@
+<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc-->
+<tables>
+    <!-- Locations of indexes in the Bowtie mapper format -->
+    <table name="bowtie_indexes" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="${__HERE__}/tool-data/bowtie_indices.loc.sample" />
+    </table>
+</tables>
diff -r 01ca7075c109 -r b300c15426f5 bowtie_rRNA_removal_wrapper/tool_data_table_conf.xml.sample
--- a/bowtie_rRNA_removal_wrapper/tool_data_table_conf.xml.sample	Tue Mar 15 10:27:46 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,8 +0,0 @@
-<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc-->
-<tables>
-    <!-- Locations of indexes in the Bowtie mapper format -->
-    <table name="bowtie_indexes" comment_char="#">
-        <columns>value, dbkey, name, path</columns>
-        <file path="tool-data/bowtie_indices.loc" />
-    </table>
-</tables>
diff -r 01ca7075c109 -r b300c15426f5 bowtie_rRNA_removal_wrapper/tool_data_table_conf.xml.test
--- a/bowtie_rRNA_removal_wrapper/tool_data_table_conf.xml.test	Tue Mar 15 10:27:46 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,8 +0,0 @@
-<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc-->
-<tables>
-    <!-- Locations of indexes in the Bowtie mapper format -->
-    <table name="bowtie_indexes" comment_char="#">
-        <columns>value, dbkey, name, path</columns>
-        <file path="${__HERE__}/test-data/bowtie_indices.loc" />
-    </table>
-</tables>