Simulate a HiSeq runfolder.
authorDiane Trout <diane@caltech.edu>
Thu, 1 Mar 2012 00:58:39 +0000 (16:58 -0800)
committerDiane Trout <diane@caltech.edu>
Thu, 1 Mar 2012 00:58:39 +0000 (16:58 -0800)
Also man do i need to clean up my simulation code

htsworkflow/pipelines/test/simulate_runfolder.py
htsworkflow/pipelines/test/test_runfolder_rta1_12.py [new file with mode: 0644]
htsworkflow/pipelines/test/testdata/aligned_config_1_12.xml [new file with mode: 0644]
htsworkflow/pipelines/test/testdata/demultiplex_1.12.4.2.xml [new file with mode: 0644]
htsworkflow/pipelines/test/testdata/demultiplexed_bustard_1.12.4.2.xml [new file with mode: 0644]
htsworkflow/pipelines/test/testdata/demultiplexed_summary_1.12.4.2.xml [new file with mode: 0644]
htsworkflow/pipelines/test/testdata/rta_basecalls_config_1.12.4.2.xml [new file with mode: 0755]
htsworkflow/pipelines/test/testdata/rta_intensities_config_1.12.4.2.xml [new file with mode: 0755]
htsworkflow/pipelines/test/testdata/sample_summary_1_12.htm [new file with mode: 0644]

index c07783ef3f8f7323b2e73ea6687d9d4846852eaa..0b57631e58f5cb53696968f0feafe23dc947fbcd 100644 (file)
@@ -1,7 +1,7 @@
 """
 Create simulated solexa/illumina runfolders for testing
 """
-
+import gzip
 import os
 import shutil
 
@@ -55,6 +55,25 @@ def make_bustard_config132(image_dir):
     destination = os.path.join(image_dir, 'config.xml')
     shutil.copy(source, destination)
 
+def make_aligned_config_1_12(aligned_dir):
+    """This is rouglhly equivalent to the old gerald file"""
+    source = os.path.join(TESTDATA_DIR, 'aligned_config_1_12.xml')
+    destination = os.path.join(aligned_dir, 'config.xml')
+    shutil.copy(source, destination)
+
+def make_unaligned_config_1_12(unaligned_dir):
+    demultiplex_pairs = [ # (src,
+      # dest),
+        (os.path.join(TESTDATA_DIR, 'demultiplex_1.12.4.2.xml'),
+         os.path.join(unaligned_dir, 'DemultiplexConfig.xml')),
+        (os.path.join(TESTDATA_DIR, 'demultiplexed_bustard_1.12.4.2.xml'),
+         os.path.join(unaligned_dir, 'DemultiplexConfig.xml')),
+        (os.path.join(TESTDATA_DIR, 'demultiplexed_summary_1.12.4.2.xml'),
+         os.path.join(unaligned_dir, 'DemultiplexConfig.xml')),
+    ]
+    for src, dest in demultiplex_pairs:
+        shutil.copy(src, dest)
+
 def make_rta_intensities_1460(data_dir, version='1.4.6.0'):
     """
     Construct an artificial RTA Intensities parameter file and directory
@@ -107,6 +126,19 @@ def make_rta_intensities_1_10(data_dir, version='1.10.36.0'):
 
     return intensities_dir
 
+def make_rta_intensities_1_12(data_dir, version='1.12.4.2'):
+    """
+    Construct an artificial RTA Intensities parameter file and directory
+    """
+    intensities_dir = os.path.join(data_dir, 'Intensities')
+    if not os.path.exists(intensities_dir):
+      os.mkdir(intensities_dir)
+
+    param_file = os.path.join(TESTDATA_DIR, 'rta_intensities_config_1.12.4.2.xml')
+    shutil.copy(param_file, os.path.join(intensities_dir, 'RTAConfig.xml'))
+
+    return intensities_dir
+
 def make_rta_basecalls_1870(intensities_dir):
     """
     Construct an artificial RTA Intensities parameter file and directory
@@ -134,6 +166,21 @@ def make_rta_basecalls_1_10(intensities_dir):
 
     return basecalls_dir
 
+def make_rta_basecalls_1_12(intensities_dir):
+    """
+    Construct an artificial RTA Intensities parameter file and directory
+    """
+    basecalls_dir = os.path.join(intensities_dir, 'BaseCalls')
+    if not os.path.exists(basecalls_dir):
+        os.mkdir(basecalls_dir)
+
+    make_qseqs(basecalls_dir, basecall_info=ABXX_BASE_CALL_INFO)
+    param_file = os.path.join(TESTDATA_DIR, 'rta_basecalls_config_1.12.4.2.xml')
+    shutil.copy(param_file, os.path.join(basecalls_dir, 'config.xml'))
+
+    return basecalls_dir
+
+
 def make_qseqs(bustard_dir, basecall_info=None):
     """
     Fill gerald directory with qseq files
@@ -234,6 +281,9 @@ def make_matrix_dir_rta160(bustard_dir):
 def make_matrix_dir_rta_1_10(bustard_dir):
     make_matrix_dir_rta160(bustard_dir)
 
+def make_matrix_dir_rta_1_12(bustard_dir):
+    make_matrix_dir_rta160(bustard_dir)
+
 def make_phasing_dir(bustard_dir):
     """
     Create several phasing files in <bustard_dir>/Phasing/
@@ -394,6 +444,200 @@ _bbbbbaaababaabbbbab]D]aaaaaaaaaaaaaa
         f.write(seq)
         f.close()
 
+UNALIGNED_READS = [1,2]
+UNALIGNED_SAMPLES = [ (1, UNALIGNED_READS, '11111', None, None),
+                      (2, UNALIGNED_READS, '11112', None, None),
+                      (3, UNALIGNED_READS, '11113', 1, 'ATCACG'),
+                      (3, UNALIGNED_READS, '11113', 2, 'CGATGT'),
+                      (3, UNALIGNED_READS, '11113', 3, 'TTAGGC'),
+                      (4, UNALIGNED_READS, '11114', 6, 'GCCAAT'),
+                      (5, UNALIGNED_READS, '11115', 1, 'ATCACG'),
+                      (5, UNALIGNED_READS, '11116', 7, 'ACTTGA'),
+                      (5, UNALIGNED_READS, '11117', 9, 'GATCAG'),
+                      (6, UNALIGNED_READS, '11118', 1, 'ATCACG'),
+                      (7, UNALIGNED_READS, '11119', 2, 'CGATGT'),
+                      (8, UNALIGNED_READS, '11120', 3, 'TTAGGC'),
+                      (1, UNALIGNED_READS, None, None, None),
+                      (2, UNALIGNED_READS, None, None, None),
+                      (3, UNALIGNED_READS, None, None, None),
+                      (4, UNALIGNED_READS, None, None, None),
+                      (5, UNALIGNED_READS, None, None, None)]
+
+
+def make_aligned_eland_export(aligned_dir, flowcell_id):
+    summary_source = os.path.join(TESTDATA_DIR, 'sample_summary_1_12.htm')
+    for lane, read, project_id, index_id, index_seq in UNALIGNED_SAMPLES:
+        paths = DemultiplexedPaths(aligned_dir,
+                                   flowcell_id,
+                                   lane,
+                                   project_id,
+                                   index_id,
+                                   index_seq)
+        paths.make_sample_dirs()
+        paths.make_summary_dirs()
+        summary_dest = os.path.join(paths.summary_dir, 'Sample_Summary.htm')
+        shutil.copy(summary_source, summary_dest)
+
+        body = get_unaligned_sample_export(lane, index_seq)
+        for split in ['001','002']:
+            for read in UNALIGNED_READS:
+                suffix = 'R{0}_{1}_export.txt.gz'.format(read, split)
+                pathname = paths.make_test_filename(suffix)
+                stream = gzip.open(pathname, 'w')
+                stream.write(body)
+                stream.close()
+
+
+def make_unaligned_fastqs_1_12(unaligned_dir, flowcell_id):
+    """Create a default mix of unaligned sample files
+    """
+    for lane, read, name, index_id, index in UNALIGNED_SAMPLES:
+        make_unaligned_fastq_sample_1_12(unaligned_dir,
+                                         flowcell_id,
+                                         lane,
+                                         read,
+                                         name,
+                                         index_id,
+                                         index)
+
+def make_unaligned_fastq_sample_1_12(unaligned_dir,
+                                     flowcell_id,
+                                     lane,
+                                     reads,
+                                     project_id,
+                                     index_id=None,
+                                     index_seq=None):
+
+    paths = DemultiplexedPaths(unaligned_dir,
+                               flowcell_id,
+                               lane,
+                               project_id,
+                               index_id,
+                               index_seq)
+    paths.make_sample_dirs()
+
+    sample_seq = get_unaligned_sample_fastq_data(flowcell_id, lane, index_seq)
+    for split in ['001','002']:
+        for read in reads:
+            suffix = 'R{0}_{1}.fastq.gz'.format(read, split)
+            pathname = paths.make_test_filename(suffix)
+            stream = gzip.open(pathname, 'w')
+            stream.write(sample_seq)
+            stream.close()
+
+    sheetname = os.path.join(paths.sample_dir, 'SampleSheet.csv')
+    stream = open(sheetname, 'w')
+    stream.write('FCID,Lane,SampleID,SampleRef,Index,Description,Control,Recipe,Operator,SampleProject'+os.linesep)
+    template = '{flowcell},{lane},{id},mm9,{index},Sample #{id},N,PR_indexing,Operator,{sample_project}'+os.linesep
+    stream.write(template.format(flowcell=flowcell_id,
+                                 lane=lane,
+                                 id=paths.sample_id,
+                                 index=paths.index_seq,
+                                 sample_project=paths.sample_project))
+    stream.close()
+
+
+class DemultiplexedPaths(object):
+    def __init__(self, basedir, flowcell_id, lane, project_id, index_id, index_seq):
+        if lane not in LANE_LIST:
+            raise ValueError("Invalid lane ID: {0}".format(lane))
+        self.basedir = basedir
+        self.flowcell_id = flowcell_id
+        self.lane = lane
+
+        if project_id is None:
+            # undetermined
+            self.index_seq = ''
+            self.sample_id = 'lane{0}'.format(lane)
+            self.sample_project = 'Undetermined_indices'
+            self.rootname = 'lane{lane}_Undetermined_L00{lane}_'.format(
+                lane=lane)
+            self.project_dir = 'Undetermined_indices'
+            self.sample_dir = 'Sample_lane{lane}'.format(lane=lane)
+        elif index_seq is None:
+            self.index_seq = ''
+            self.sample_id = project_id
+            self.sample_project = '{project_id}'.format(project_id=project_id)
+            self.rootname = '{project_id}_NoIndex_L00{lane}_'.format(
+                project_id=project_id,
+                lane=lane)
+            self.project_dir = 'Project_' + self.sample_project
+            self.sample_dir = 'Sample_{project_id}'.format(
+                project_id=project_id)
+        else:
+            self.index_seq = index_seq
+            self.sample_id = project_id
+            self.sample_project = '{project_id}_Index{index_id}'.format(
+                project_id=project_id,
+                index_id=index_id)
+            self.rootname = '{project_id}_{index}_L00{lane}_'.format(
+                project_id=project_id,
+                index=index_seq,
+                lane=lane)
+            self.project_dir = 'Project_' + self.sample_project
+            self.sample_dir = 'Sample_{project_id}'.format(
+                project_id=project_id)
+
+        self.project_dir = os.path.join(self.basedir, self.project_dir)
+        self.sample_dir = os.path.join(self.project_dir, self.sample_dir)
+        self.summary_dir = 'Summary_Stats_{0}'.format(self.flowcell_id)
+        self.summary_dir = os.path.join(self.project_dir, self.summary_dir)
+        print "HI:", self.summary_dir
+
+
+    def make_sample_dirs(self):
+        if not os.path.isdir(self.project_dir):
+            os.mkdir(self.project_dir)
+        if not os.path.isdir(self.sample_dir):
+            os.mkdir(self.sample_dir)
+
+    def make_summary_dirs(self):
+        print "HI:", self.summary_dir
+        if not os.path.isdir(self.summary_dir):
+            os.mkdir(self.summary_dir)
+
+    def make_test_filename(self, suffix):
+        filename = self.rootname + suffix
+        pathname = os.path.join(self.sample_dir, filename)
+        return pathname
+    def dump(self):
+        print ('index seq: {0}'.format(self.index_seq))
+
+        print ('project dir: {0}'.format(self.project_dir))
+        print ('sample dir: {0}'.format(self.sample_dir))
+        print ('rootname: {0}'.format(self.rootname))
+        print ('path: {0}'.format(
+            os.path.join(self.project_dir,
+                         self.sample_dir,
+                         self.rootname+'R1_001.fastq.gz')))
+
+
+def get_unaligned_sample_fastq_data(flowcell_id, lane, index_seq):
+    seq = """@HWI-ST0787:101:{flowcell}:{lane}:1101:2416:3469 1:Y:0:{index}
+TCCTTCATTCCACCGGAGTCTGTGGAATTCTCGGGTGCCAAGGAACTCCA
++
+CCCFFFFFHHHHHJJJJJJJJJIJJJJJJJJJJJJJJJJIIJJIIJJJJJ
+@HWI-ST0787:101:{flowcell}:{lane}:1101:2677:3293 1:Y:0:{index}
+TGGAAATCCATTGGGGTTTCCCCTGGAATTCTCGGGTGCCAAGGAACTCC
++
+@CCFF3BDHHHHHIIIIIHHIIIDIIIGIIIEGIIIIIIIIIIIIIIIHH
+@HWI-ST0787:101:{flowcell}:{lane}:1101:2616:3297 1:Y:0:{index}
+TAATACTGCCGGGTAATGATGGCTGGAATTCTCGGGTGCCAAGGAACTCC
++
+CCCFFFFFHHHHHCGHJJJJJJJJJJJJJJJJJIIJJJJJJJJJIHJJJI
+@HWI-ST0787:101:{flowcell}:{lane}:1101:2545:3319 1:N:0:{index}
+TCCTTCATTCCACCGGAGTCTGCTGGAATTCTCGGGTGCCAAGGAACTCC
++
+CCCFFFFFHHHFHJGIGHIJHIIGHIGIGIGEHFIJJJIHIJHJIIJJIH
+""".format(flowcell=flowcell_id, lane=lane, index=index_seq)
+    return seq
+
+def get_unaligned_sample_export(lane, index_seq):
+    body = """HWI-ST0787\t102\t{lane}\t1101\t1207\t1993\t{index}\t1\tAANGGATTCGATCCGGCTTAAGAGATGAAAACCGAAAGGGCCGACCGAA\taaBS`ccceg[`ae[dRR_[[SPPPP__ececfYYWaegh^\\ZLLY\\X`\tNM\t\t\t\t\t\t
+HWI-ST0787\t102     {lane}       1101    1478    1997    {index}  1       CAAGAACCCCGGGGGGGGGGGGGCAGAGAGGGGGAATTTTTTTTTTGTT       BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB       NM                                                                                      N
+HWI-ST0787      102     {lane}       1101    1625    1994    {index}  1       AANAATGCTACAGAGACAAAACAAAACTGATATGAAAGTTGAGAATAAA       \^BS\cccgegg[Q[QQQ[`egdgffbeggfgh^^YcfgfhXaHY^O^c       chrII.fa
+""".format(lane=lane, index=index_seq)
+    return body
 
 def ls_tree(root):
     for dirpath, dirnames, filenames in os.walk(root):
diff --git a/htsworkflow/pipelines/test/test_runfolder_rta1_12.py b/htsworkflow/pipelines/test/test_runfolder_rta1_12.py
new file mode 100644 (file)
index 0000000..927cf61
--- /dev/null
@@ -0,0 +1,291 @@
+#!/usr/bin/env python
+
+from datetime import datetime, date
+import os
+import tempfile
+import shutil
+import unittest
+
+from htsworkflow.pipelines import eland
+from htsworkflow.pipelines import ipar
+from htsworkflow.pipelines import bustard
+from htsworkflow.pipelines import gerald
+from htsworkflow.pipelines import runfolder
+from htsworkflow.pipelines.runfolder import ElementTree
+
+from htsworkflow.pipelines.test.simulate_runfolder import *
+
+
+def make_runfolder(obj=None):
+    """
+    Make a fake runfolder, attach all the directories to obj if defined
+    """
+    # make a fake runfolder directory
+    flowcell_id = 'D07K6ACXX'
+    temp_dir = tempfile.mkdtemp(prefix='tmp_runfolder_')
+
+    runfolder_dir = os.path.join(temp_dir,
+                                 '110815_SN787_0101_A{0}'.format(flowcell_id))
+    os.mkdir(runfolder_dir)
+
+    data_dir = os.path.join(runfolder_dir, 'Data')
+    os.mkdir(data_dir)
+
+    intensities_dir = make_rta_intensities_1_12(data_dir)
+
+    basecalls_dir = make_rta_basecalls_1_12(intensities_dir)
+    make_matrix_dir_rta_1_12(basecalls_dir)
+
+    unaligned_dir = os.path.join(runfolder_dir, "Unaligned")
+    os.mkdir(unaligned_dir)
+    make_unaligned_fastqs_1_12(unaligned_dir, flowcell_id)
+    make_unaligned_config_1_12(unaligned_dir)
+
+    aligned_dir = os.path.join(runfolder_dir, "Aligned")
+    os.mkdir(aligned_dir)
+    make_aligned_eland_export(aligned_dir, flowcell_id)
+    make_aligned_config_1_12(aligned_dir)
+
+    if obj is not None:
+        obj.temp_dir = temp_dir
+        obj.runfolder_dir = runfolder_dir
+        obj.data_dir = data_dir
+        obj.image_analysis_dir = intensities_dir
+        obj.bustard_dir = unaligned_dir
+        obj.gerald_dir = aligned_dir
+
+
+class RunfolderTests(unittest.TestCase):
+    """
+    Test components of the runfolder processing code
+    which includes firecrest, bustard, and gerald
+    """
+    def setUp(self):
+        # attaches all the directories to the object passed in
+        make_runfolder(self)
+
+    def tearDown(self):
+        shutil.rmtree(self.temp_dir)
+
+    def test_bustard(self):
+        """Construct a bustard object"""
+        b = bustard.bustard(self.bustard_dir)
+        self.failUnlessEqual(b.version, '1.8.70.0')
+        self.failUnlessEqual(b.date,    None)
+        self.failUnlessEqual(b.user,    None)
+        self.failUnlessEqual(len(b.phasing), 0)
+
+        xml = b.get_elements()
+        b2 = bustard.Bustard(xml=xml)
+        self.failUnlessEqual(b.version, b2.version)
+        self.failUnlessEqual(b.date,    b2.date )
+        self.failUnlessEqual(b.user,    b2.user)
+
+    def test_gerald(self):
+        # need to update gerald and make tests for it
+        g = gerald.gerald(self.gerald_dir)
+
+        self.failUnlessEqual(g.version,
+            '@(#) Id: GERALD.pl,v 1.171 2008/05/19 17:36:14 mzerara Exp')
+        self.failUnlessEqual(g.date, datetime(2009,2,22,21,15,59))
+        self.failUnlessEqual(len(g.lanes), len(g.lanes.keys()))
+        self.failUnlessEqual(len(g.lanes), len(g.lanes.items()))
+
+
+        # list of genomes, matches what was defined up in
+        # make_gerald_config.
+        # the first None is to offset the genomes list to be 1..9
+        # instead of pythons default 0..8
+        genomes = [None,
+                   '/g/mm9',
+                   '/g/mm9',
+                   '/g/elegans190',
+                   '/g/arabidopsis01222004',
+                   '/g/mm9',
+                   '/g/mm9',
+                   '/g/mm9',
+                   '/g/mm9', ]
+
+        # test lane specific parameters from gerald config file
+        for i in range(1,9):
+            cur_lane = g.lanes[i]
+            self.failUnlessEqual(cur_lane.analysis, 'eland_extended')
+            self.failUnlessEqual(cur_lane.eland_genome, genomes[i])
+            self.failUnlessEqual(cur_lane.read_length, '37')
+            self.failUnlessEqual(cur_lane.use_bases, 'Y'*37)
+
+        # I want to be able to use a simple iterator
+        for l in g.lanes.values():
+          self.failUnlessEqual(l.analysis, 'eland_extended')
+          self.failUnlessEqual(l.read_length, '37')
+          self.failUnlessEqual(l.use_bases, 'Y'*37)
+
+        # test data extracted from summary file
+        clusters = [None,
+                    (281331, 11169), (203841, 13513),
+                    (220889, 15653), (137294, 14666),
+                    (129388, 14525), (262092, 10751),
+                    (185754, 13503), (233765, 9537),]
+
+        self.failUnlessEqual(len(g.summary), 1)
+        for i in range(1,9):
+            summary_lane = g.summary[0][i]
+            self.failUnlessEqual(summary_lane.cluster, clusters[i])
+            self.failUnlessEqual(summary_lane.lane, i)
+
+        xml = g.get_elements()
+        # just make sure that element tree can serialize the tree
+        xml_str = ElementTree.tostring(xml)
+        g2 = gerald.Gerald(xml=xml)
+        return
+
+        # do it all again after extracting from the xml file
+        self.failUnlessEqual(g.version, g2.version)
+        self.failUnlessEqual(g.date, g2.date)
+        self.failUnlessEqual(len(g.lanes.keys()), len(g2.lanes.keys()))
+        self.failUnlessEqual(len(g.lanes.items()), len(g2.lanes.items()))
+
+        # test lane specific parameters from gerald config file
+        for i in range(1,9):
+            g_lane = g.lanes[i]
+            g2_lane = g2.lanes[i]
+            self.failUnlessEqual(g_lane.analysis, g2_lane.analysis)
+            self.failUnlessEqual(g_lane.eland_genome, g2_lane.eland_genome)
+            self.failUnlessEqual(g_lane.read_length, g2_lane.read_length)
+            self.failUnlessEqual(g_lane.use_bases, g2_lane.use_bases)
+
+        # test (some) summary elements
+        self.failUnlessEqual(len(g.summary), 1)
+        for i in range(1,9):
+            g_summary = g.summary[0][i]
+            g2_summary = g2.summary[0][i]
+            self.failUnlessEqual(g_summary.cluster, g2_summary.cluster)
+            self.failUnlessEqual(g_summary.lane, g2_summary.lane)
+
+            g_eland = g.eland_results
+            g2_eland = g2.eland_results
+            for lane in g_eland.results[0].keys():
+                g_results = g_eland.results[0][lane]
+                g2_results = g2_eland.results[0][lane]
+                self.failUnlessEqual(g_results.reads,
+                                     g2_results.reads)
+                if isinstance(g_results, eland.ElandLane):
+                  self.failUnlessEqual(len(g_results.mapped_reads),
+                                       len(g2_results.mapped_reads))
+                  for k in g_results.mapped_reads.keys():
+                      self.failUnlessEqual(g_results.mapped_reads[k],
+                                           g2_results.mapped_reads[k])
+
+                  self.failUnlessEqual(len(g_results.match_codes),
+                                       len(g2_results.match_codes))
+                  for k in g_results.match_codes.keys():
+                      self.failUnlessEqual(g_results.match_codes[k],
+                                           g2_results.match_codes[k])
+
+
+    def test_eland(self):
+        return
+        hg_map = {'Lambda.fa': 'Lambda.fa'}
+        for i in range(1,22):
+          short_name = 'chr%d.fa' % (i,)
+          long_name = 'hg18/chr%d.fa' % (i,)
+          hg_map[short_name] = long_name
+
+        genome_maps = { 1:hg_map, 2:hg_map, 3:hg_map, 4:hg_map,
+                        5:hg_map, 6:hg_map, 7:hg_map, 8:hg_map }
+        eland_container = gerald.eland(self.gerald_dir, genome_maps=genome_maps)
+
+        # I added sequence lanes to the last 2 lanes of this test case
+        for i in range(1,7):
+            lane = eland_container.results[0][i]
+            self.failUnlessEqual(lane.reads, 6)
+            self.failUnlessEqual(lane.sample_name, "s")
+            self.failUnlessEqual(lane.lane_id, i)
+            self.failUnlessEqual(len(lane.mapped_reads), 17)
+            self.failUnlessEqual(lane.mapped_reads['hg18/chr5.fa'], 4)
+            self.failUnlessEqual(lane.match_codes['U0'], 3)
+            self.failUnlessEqual(lane.match_codes['R0'], 2)
+            self.failUnlessEqual(lane.match_codes['U1'], 1)
+            self.failUnlessEqual(lane.match_codes['R1'], 9)
+            self.failUnlessEqual(lane.match_codes['U2'], 0)
+            self.failUnlessEqual(lane.match_codes['R2'], 12)
+            self.failUnlessEqual(lane.match_codes['NM'], 1)
+            self.failUnlessEqual(lane.match_codes['QC'], 0)
+
+        # test scarf
+        lane = eland_container.results[0][7]
+        self.failUnlessEqual(lane.reads, 5)
+        self.failUnlessEqual(lane.sample_name, 's')
+        self.failUnlessEqual(lane.lane_id, 7)
+        self.failUnlessEqual(lane.sequence_type, eland.SequenceLane.SCARF_TYPE)
+
+        # test fastq
+        lane = eland_container.results[0][8]
+        self.failUnlessEqual(lane.reads, 3)
+        self.failUnlessEqual(lane.sample_name, 's')
+        self.failUnlessEqual(lane.lane_id, 8)
+        self.failUnlessEqual(lane.sequence_type, eland.SequenceLane.FASTQ_TYPE)
+
+        xml = eland_container.get_elements()
+        # just make sure that element tree can serialize the tree
+        xml_str = ElementTree.tostring(xml)
+        e2 = gerald.ELAND(xml=xml)
+
+        for i in range(1,9):
+            l1 = eland_container.results[0][i]
+            l2 = e2.results[0][i]
+            self.failUnlessEqual(l1.reads, l2.reads)
+            self.failUnlessEqual(l1.sample_name, l2.sample_name)
+            self.failUnlessEqual(l1.lane_id, l2.lane_id)
+            if isinstance(l1, eland.ElandLane):
+              self.failUnlessEqual(len(l1.mapped_reads), len(l2.mapped_reads))
+              self.failUnlessEqual(len(l1.mapped_reads), 17)
+              for k in l1.mapped_reads.keys():
+                  self.failUnlessEqual(l1.mapped_reads[k],
+                                       l2.mapped_reads[k])
+
+              self.failUnlessEqual(len(l1.match_codes), 9)
+              self.failUnlessEqual(len(l1.match_codes), len(l2.match_codes))
+              for k in l1.match_codes.keys():
+                  self.failUnlessEqual(l1.match_codes[k],
+                                       l2.match_codes[k])
+            elif isinstance(l1, eland.SequenceLane):
+                self.failUnlessEqual(l1.sequence_type, l2.sequence_type)
+
+    def test_runfolder(self):
+        return
+        runs = runfolder.get_runs(self.runfolder_dir)
+
+        # do we get the flowcell id from the filename?
+        self.failUnlessEqual(len(runs), 1)
+        name = 'run_4286GAAXX_%s.xml' % ( date.today().strftime('%Y-%m-%d'),)
+        self.failUnlessEqual(runs[0].name, name)
+
+        # do we get the flowcell id from the FlowcellId.xml file
+        make_flowcell_id(self.runfolder_dir, '207BTAAXY')
+        runs = runfolder.get_runs(self.runfolder_dir)
+        self.failUnlessEqual(len(runs), 1)
+        name = 'run_207BTAAXY_%s.xml' % ( date.today().strftime('%Y-%m-%d'),)
+        self.failUnlessEqual(runs[0].name, name)
+
+        r1 = runs[0]
+        xml = r1.get_elements()
+        xml_str = ElementTree.tostring(xml)
+
+        r2 = runfolder.PipelineRun(xml=xml)
+        self.failUnlessEqual(r1.name, r2.name)
+        self.failIfEqual(r2.image_analysis, None)
+        self.failIfEqual(r2.bustard, None)
+        self.failIfEqual(r2.gerald, None)
+
+
+def suite():
+    return unittest.makeSuite(RunfolderTests,'test')
+
+if __name__ == "__main__":
+    #unittest.main(defaultTest="suite")
+    class Test(object): pass
+    t = Test()
+    make_runfolder(t)
+    print ('path ' + t.runfolder_dir)
+
diff --git a/htsworkflow/pipelines/test/testdata/aligned_config_1_12.xml b/htsworkflow/pipelines/test/testdata/aligned_config_1_12.xml
new file mode 100644 (file)
index 0000000..2b7f3af
--- /dev/null
@@ -0,0 +1,234 @@
+<?xml version="1.0"?>
+<RunParameters>
+  <Barcodes>
+  </Barcodes>
+  <Defaults>
+    <ANALYSIS>none</ANALYSIS>
+    <CHROM_NAME_SOURCE>fileName</CHROM_NAME_SOURCE>
+    <CHROM_NAME_VALIDATION>on</CHROM_NAME_VALIDATION>
+    <CMDPREFIX></CMDPREFIX>
+    <DATASET_POST_RUN_COMMAND></DATASET_POST_RUN_COMMAND>
+    <ELAND_EXTENDED_MULTI_READS>off</ELAND_EXTENDED_MULTI_READS>
+    <ELAND_FASTQ_FILES_PER_PROCESS>3</ELAND_FASTQ_FILES_PER_PROCESS>
+    <ELAND_GENOME></ELAND_GENOME>
+    <ELAND_GENOME_MASK>*.fa</ELAND_GENOME_MASK>
+    <ELAND_MAX_MATCHES></ELAND_MAX_MATCHES>
+    <ELAND_PARAMS></ELAND_PARAMS>
+    <ELAND_REPEAT></ELAND_REPEAT>
+    <ELAND_RNA_GENE_MD_GROUP_LABEL></ELAND_RNA_GENE_MD_GROUP_LABEL>
+    <ELAND_RNA_GENOME_ANNOTATION></ELAND_RNA_GENOME_ANNOTATION>
+    <ELAND_RNA_GENOME_CONTAM></ELAND_RNA_GENOME_CONTAM>
+    <ELAND_RNA_GENOME_CONTAM_MASK>*.fa</ELAND_RNA_GENOME_CONTAM_MASK>
+    <ELAND_RNA_MULTI_READS>off</ELAND_RNA_MULTI_READS>
+    <ELAND_SEED_LENGTH1>32</ELAND_SEED_LENGTH1>
+    <ELAND_SEED_LENGTH2></ELAND_SEED_LENGTH2>
+    <EMAIL_DOMAIN>domain.com</EMAIL_DOMAIN>
+    <EMAIL_LIST>${logName}</EMAIL_LIST>
+    <EMAIL_SERVER>localhost:25</EMAIL_SERVER>
+    <EXPT_DIR>/mmjggl/nicodemus/data01/sequencer/110815_SN787_0101_AD07K6ACXX/Unaligned_1MM</EXPT_DIR>
+    <FLAT_TXT_GZ_SUFFIX>Flat.txt.gz</FLAT_TXT_GZ_SUFFIX>
+    <FLOWCELL>D07K6ACXX</FLOWCELL>
+    <GENE_MD_GZ_SUFFIX>_gene.md.gz</GENE_MD_GZ_SUFFIX>
+    <INCREASED_SENSITIVITY></INCREASED_SENSITIVITY>
+    <KAGU_PAIR_PARAMS>--muf 0</KAGU_PAIR_PARAMS>
+    <KAGU_PARAMS>--mmaq 4</KAGU_PARAMS>
+    <NUM_LEADING_DIRS_TO_STRIP>2</NUM_LEADING_DIRS_TO_STRIP>
+    <OA_SUFFIX>.oa</OA_SUFFIX>
+    <ORIGINAL_READS>1</ORIGINAL_READS>
+    <ORIGINAL_READ_LENGTH1>50</ORIGINAL_READ_LENGTH1>
+    <ORPHAN_ALIGNER_PARAMS>2</ORPHAN_ALIGNER_PARAMS>
+    <OUT_DIR>/mmjggl/nicodemus/data01/sequencer/110815_SN787_0101_AD07K6ACXX/Aligned_1MM</OUT_DIR>
+    <PAS_PARAMS></PAS_PARAMS>
+    <RAMM_REPORT_TYPE></RAMM_REPORT_TYPE>
+    <READS>1</READS>
+    <READ_LENGTH1>49</READ_LENGTH1>
+    <RNAQC_COUNT_CLUSTERS_CMD>$(WC) -l</RNAQC_COUNT_CLUSTERS_CMD>
+    <RNAQC_COUNT_CLUSTERS_NAME>totalClusters</RNAQC_COUNT_CLUSTERS_NAME>
+    <RNAQC_COUNT_GENOME_CMD>($(GREP) -cvE '^((NM|QC|RM|[0-9]+:[0-9]+:[0-9]+)$$|splice_sites)' || exit 0)</RNAQC_COUNT_GENOME_CMD>
+    <RNAQC_COUNT_GENOME_NAME>genomeUsable</RNAQC_COUNT_GENOME_NAME>
+    <RNAQC_COUNT_NM_CMD>($(FGREP) -wc NM || exit 0)</RNAQC_COUNT_NM_CMD>
+    <RNAQC_COUNT_NM_NAME>noMatch</RNAQC_COUNT_NM_NAME>
+    <RNAQC_COUNT_PF_CMD>$(WC) -l</RNAQC_COUNT_PF_CMD>
+    <RNAQC_COUNT_PF_NAME>PFClusters</RNAQC_COUNT_PF_NAME>
+    <RNAQC_COUNT_QC_CMD>($(FGREP) -wc QC || exit 0)</RNAQC_COUNT_QC_CMD>
+    <RNAQC_COUNT_QC_NAME>QC</RNAQC_COUNT_QC_NAME>
+    <RNAQC_COUNT_RM_CMD>($(FGREP) -wc RM || exit 0)</RNAQC_COUNT_RM_CMD>
+    <RNAQC_COUNT_RM_NAME>repeatMasked</RNAQC_COUNT_RM_NAME>
+    <RNAQC_COUNT_SPLICE_CMD>($(FGREP) -c splice_sites || exit 0)</RNAQC_COUNT_SPLICE_CMD>
+    <RNAQC_COUNT_SPLICE_NAME>spliceUsable</RNAQC_COUNT_SPLICE_NAME>
+    <RNAQC_COUNT_USABLE_CMD>$(CUT) -f13 |($(EGREP) [0-9] || exit 0)|$(WC) -l</RNAQC_COUNT_USABLE_CMD>
+    <RNAQC_COUNT_USABLE_NAME>usable</RNAQC_COUNT_USABLE_NAME>
+    <RNAQC_FIND_CONTAMS_CMD>($(GREP) -vE '^(NM|QC|RM|[0-9]+:[0-9]+:[0-9]+)$$' || exit 0)</RNAQC_FIND_CONTAMS_CMD>
+    <SAMTOOLS_GENOME></SAMTOOLS_GENOME>
+    <SEQGENEMD2REFFLAT_PARAMS></SEQGENEMD2REFFLAT_PARAMS>
+    <SINGLESEED></SINGLESEED>
+    <SPLCSTS_PARAMS>-v $(CASAVA_LOG_LEVEL)</SPLCSTS_PARAMS>
+    <SQUASH_GENOME_PARAMS></SQUASH_GENOME_PARAMS>
+    <UNGAPPED></UNGAPPED>
+    <USE_BASES>y*n</USE_BASES>
+    <USE_BASES1>yyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyn</USE_BASES1>
+    <WEB_DIR_ROOT>http://host.domain.com/yourshare/</WEB_DIR_ROOT>
+    <WITH_ORPHAN_ALIGNER>true</WITH_ORPHAN_ALIGNER>
+  </Defaults>
+  <Lanes>
+    <Lane index="1">
+      <Barcodes></Barcodes>
+      <Defaults>
+        <ANALYSIS>eland_extended</ANALYSIS>
+        <CHROM_NAME_SOURCE>fileName</CHROM_NAME_SOURCE>
+        <ELAND_GENOME>/mmjggl/nicodemus/data01/genomes/elegans190/chromosomes/</ELAND_GENOME>
+        <ELAND_GENOME_MASK>*.fa</ELAND_GENOME_MASK>
+        <ELAND_SEED_LENGTH1>32</ELAND_SEED_LENGTH1>
+        <READS>1</READS>
+        <READ_LENGTH1>49</READ_LENGTH1>
+        <Tiles>1101 1102 1103 1104 1105 1106 1107 1108 1201 1202 1203 1204 1205 1206 1207 1208 1301 1302 1303 1304 1305 1306 1307 1308 2101 2102 2103 2104 2105 2106 2107 2108 2201 2202 2203 2204 2205 2206 2207 2208 2301 2302 2303 2304 2305 2306 2307 2308</Tiles>
+        <USE_BASES>Y*n</USE_BASES>
+        <USE_BASES1>yyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyn</USE_BASES1>
+      </Defaults>
+      <Projects></Projects>
+      <References></References>
+      <Samples></Samples>
+    </Lane>
+    <Lane index="2">
+      <Barcodes></Barcodes>
+      <Defaults>
+        <ANALYSIS>eland_extended</ANALYSIS>
+        <CHROM_NAME_SOURCE>fileName</CHROM_NAME_SOURCE>
+        <ELAND_GENOME>/mmjggl/nicodemus/data01/genomes/elegans190/chromosomes/</ELAND_GENOME>
+        <ELAND_GENOME_MASK>*.fa</ELAND_GENOME_MASK>
+        <ELAND_SEED_LENGTH1>32</ELAND_SEED_LENGTH1>
+        <READS>1</READS>
+        <READ_LENGTH1>49</READ_LENGTH1>
+        <Tiles>1101 1102 1103 1104 1105 1106 1107 1108 1201 1202 1203 1204 1205 1206 1207 1208 1301 1302 1303 1304 1305 1306 1307 1308 2101 2102 2103 2104 2105 2106 2107 2108 2201 2202 2203 2204 2205 2206 2207 2208 2301 2302 2303 2304 2305 2306 2307 2308</Tiles>
+        <USE_BASES>Y*n</USE_BASES>
+        <USE_BASES1>yyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyn</USE_BASES1>
+      </Defaults>
+      <Projects></Projects>
+      <References></References>
+      <Samples></Samples>
+    </Lane>
+    <Lane index="4">
+      <Barcodes></Barcodes>
+      <Defaults>
+        <ANALYSIS>eland_extended</ANALYSIS>
+        <CHROM_NAME_SOURCE>fileName</CHROM_NAME_SOURCE>
+        <ELAND_GENOME>/mmjggl/nicodemus/data01/genomes/hg18/chromosomes/</ELAND_GENOME>
+        <ELAND_GENOME_MASK>*.fa</ELAND_GENOME_MASK>
+        <ELAND_SEED_LENGTH1>32</ELAND_SEED_LENGTH1>
+        <READS>1</READS>
+        <READ_LENGTH1>49</READ_LENGTH1>
+        <Tiles>1101 1102 1103 1104 1105 1106 1107 1108 1201 1202 1203 1204 1205 1206 1207 1208 1301 1302 1303 1304 1305 1306 1307 1308 2101 2102 2103 2104 2105 2106 2107 2108 2201 2202 2203 2204 2205 2206 2207 2208 2301 2302 2303 2304 2305 2306 2307 2308</Tiles>
+        <USE_BASES>Y*n</USE_BASES>
+        <USE_BASES1>yyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyn</USE_BASES1>
+      </Defaults>
+      <Projects></Projects>
+      <References></References>
+      <Samples></Samples>
+    </Lane>
+    <Lane index="5">
+      <Barcodes></Barcodes>
+      <Defaults>
+        <ANALYSIS>eland_extended</ANALYSIS>
+        <CHROM_NAME_SOURCE>fileName</CHROM_NAME_SOURCE>
+        <ELAND_GENOME>/mmjggl/nicodemus/data01/genomes/hg18/chromosomes/</ELAND_GENOME>
+        <ELAND_GENOME_MASK>*.fa</ELAND_GENOME_MASK>
+        <ELAND_SEED_LENGTH1>32</ELAND_SEED_LENGTH1>
+        <READS>1</READS>
+        <READ_LENGTH1>49</READ_LENGTH1>
+        <Tiles>1101 1102 1103 1104 1105 1106 1107 1108 1201 1202 1203 1204 1205 1206 1207 1208 1301 1302 1303 1304 1305 1306 1307 1308 2101 2102 2103 2104 2105 2106 2107 2108 2201 2202 2203 2204 2205 2206 2207 2208 2301 2302 2303 2304 2305 2306 2307 2308</Tiles>
+        <USE_BASES>Y*n</USE_BASES>
+        <USE_BASES1>yyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyn</USE_BASES1>
+      </Defaults>
+      <Projects></Projects>
+      <References></References>
+      <Samples></Samples>
+    </Lane>
+    <Lane index="6">
+      <Barcodes></Barcodes>
+      <Defaults>
+        <ANALYSIS>eland_extended</ANALYSIS>
+        <CHROM_NAME_SOURCE>fileName</CHROM_NAME_SOURCE>
+        <ELAND_GENOME>/mmjggl/nicodemus/data01/genomes/hg18/chromosomes/</ELAND_GENOME>
+        <ELAND_GENOME_MASK>*.fa</ELAND_GENOME_MASK>
+        <ELAND_SEED_LENGTH1>32</ELAND_SEED_LENGTH1>
+        <READS>1</READS>
+        <READ_LENGTH1>49</READ_LENGTH1>
+        <Tiles>1101 1102 1103 1104 1105 1106 1107 1108 1201 1202 1203 1204 1205 1206 1207 1208 1301 1302 1303 1304 1305 1306 1307 1308 2101 2102 2103 2104 2105 2106 2107 2108 2201 2202 2203 2204 2205 2206 2207 2208 2301 2302 2303 2304 2305 2306 2307 2308</Tiles>
+        <USE_BASES>Y*n</USE_BASES>
+        <USE_BASES1>yyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyn</USE_BASES1>
+      </Defaults>
+      <Projects></Projects>
+      <References></References>
+      <Samples></Samples>
+    </Lane>
+    <Lane index="7">
+      <Barcodes></Barcodes>
+      <Defaults>
+        <ANALYSIS>none</ANALYSIS>
+        <Tiles>1101 1102 1103 1104 1105 1106 1107 1108 1201 1202 1203 1204 1205 1206 1207 1208 1301 1302 1303 1304 1305 1306 1307 1308 2101 2102 2103 2104 2105 2106 2107 2108 2201 2202 2203 2204 2205 2206 2207 2208 2301 2302 2303 2304 2305 2306 2307 2308</Tiles>
+      </Defaults>
+      <Projects></Projects>
+      <References></References>
+      <Samples></Samples>
+    </Lane>
+    <Lane index="8">
+      <Barcodes></Barcodes>
+      <Defaults>
+        <ANALYSIS>none</ANALYSIS>
+        <Tiles>1101 1102 1103 1104 1105 1106 1107 1108 1201 1202 1203 1204 1205 1206 1207 1208 1301 1302 1303 1304 1305 1306 1307 1308 2101 2102 2103 2104 2105 2106 2107 2108 2201 2202 2203 2204 2205 2206 2207 2208 2301 2302 2303 2304 2305 2306 2307 2308</Tiles>
+      </Defaults>
+      <Projects></Projects>
+      <References></References>
+      <Samples></Samples>
+    </Lane>
+    <Lane index="3">
+      <Barcodes></Barcodes>
+      <Defaults>
+        <Tiles>1101 1102 1103 1104 1105 1106 1107 1108 1201 1202 1203 1204 1205 1206 1207 1208 1301 1302 1303 1304 1305 1306 1307 1308 2101 2102 2103 2104 2105 2106 2107 2108 2201 2202 2203 2204 2205 2206 2207 2208 2301 2302 2303 2304 2305 2306 2307 2308</Tiles>
+      </Defaults>
+      <Projects></Projects>
+      <References></References>
+      <Samples></Samples>
+    </Lane>
+  </Lanes>
+  <Projects>
+    <Project name="12383">
+      <ANALYSIS>eland_extended</ANALYSIS>
+      <CHROM_NAME_SOURCE>fileName</CHROM_NAME_SOURCE>
+      <ELAND_GENOME>/mmjggl/nicodemus/data01/genomes/hg18/chromosomes/</ELAND_GENOME>
+      <ELAND_GENOME_MASK>*.fa</ELAND_GENOME_MASK>
+      <ELAND_SEED_LENGTH1>32</ELAND_SEED_LENGTH1>
+      <READS>1</READS>
+      <READ_LENGTH1>49</READ_LENGTH1>
+      <USE_BASES>Y*n</USE_BASES>
+      <USE_BASES1>yyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyn</USE_BASES1>
+    </Project>
+    <Project name="Undetermined_indices">
+      <ANALYSIS>none</ANALYSIS>
+    </Project>
+  </Projects>
+  <References>
+    <Reference name="mm9">
+      <ANALYSIS>eland_extended</ANALYSIS>
+      <CHROM_NAME_SOURCE>fileName</CHROM_NAME_SOURCE>
+      <ELAND_GENOME>/mmjggl/nicodemus/data01/genomes/mm9/chromosomes/</ELAND_GENOME>
+      <ELAND_GENOME_MASK>*.fa</ELAND_GENOME_MASK>
+      <ELAND_SEED_LENGTH1>32</ELAND_SEED_LENGTH1>
+      <READS>1</READS>
+      <READ_LENGTH1>49</READ_LENGTH1>
+      <USE_BASES>Y*n</USE_BASES>
+      <USE_BASES1>yyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyn</USE_BASES1>
+    </Reference>
+  </References>
+  <Samples>
+  </Samples>
+  <Software CmdAndArgs="/mmjggl/nicodemus/data01/casava-v1.8.1/bin/configureAlignment.pl config.txt --EXPT_DIR /mmjggl/nicodemus/data01/sequencer/110815_SN787_0101_AD07K6ACXX/Unaligned_1MM/ --OUT_DIR /mmjggl/nicodemus/data01/sequencer/110815_SN787_0101_AD07K6ACXX/Aligned_1MM -make" Name="configureAlignment.pl" Version="CASAVA-1.8.1">
+    <Software CmdAndArgs="/mmjggl/nicodemus/data01/casava-v1.8.1/bin/configureBclToFastq.pl --input-dir Data/Intensities/BaseCalls/ --output-dir Unaligned_1MM --sample-sheet Data/Intensities/BaseCalls/SampleSheet.csv --mismatches 1" Name="configureBclToFastq.pl" Version="CASAVA-1.8.1">
+      <Software Name="RTA" Version="1.12.4.2">
+        <Software Name="RTA" Version="1.12.4.2">
+          <Software Name="HiSeq Control Software" Platform="HiSeq" Version="1.4.8" />
+        </Software>
+      </Software>
+    </Software>
+  </Software>
+</RunParameters>
diff --git a/htsworkflow/pipelines/test/testdata/demultiplex_1.12.4.2.xml b/htsworkflow/pipelines/test/testdata/demultiplex_1.12.4.2.xml
new file mode 100644 (file)
index 0000000..e7ee38d
--- /dev/null
@@ -0,0 +1,71 @@
+<DemultiplexConfig>
+  <Software Version="CASAVA-1.8.1" CmdAndArgs="/mmjggl/nicodemus/data01/casava-v1.8.1/bin/configureBclToFastq.pl --input-dir Data/Intensities/BaseCalls/ --output-dir Unaligned --sample-sheet Data/Intensities/BaseCalls/SampleSheet.csv" Name="configureBclToFastq.pl">
+    <Software Version="1.12.4.2" Name="RTA">
+      <Software Version="1.12.4.2" Name="RTA">
+        <Software Version="1.4.8" Platform="HiSeq" Name="HiSeq Control Software" />
+      </Software>
+    </Software>
+  </Software>
+  <FlowcellInfo ID="D07K6ACXX" Operator="Lorian" Recipe="SR_indexing" Desc="">
+    <Lane Number="1">
+      <Sample ProjectId="12281" Control="N" Index="ACAGTG" SampleId="12281" Desc="Index #5 AWCon cell#3_N2" Ref="elegans190" />
+      <Sample ProjectId="12279" Control="N" Index="CGATGT" SampleId="12279" Desc="Index #2 AWCon cell#1_N2" Ref="elegans190" />
+      <Sample ProjectId="12280" Control="N" Index="TGACCA" SampleId="12280" Desc="Index #4 AWCon cell#2_N2" Ref="elegans190" />
+      <Sample ProjectId="Undetermined_indices" Control="N" Index="Undetermined" SampleId="lane1" Desc="Clusters with unmatched barcodes for lane 1" Ref="unknown" />
+    </Lane>
+    <Lane Number="2">
+      <Sample ProjectId="12345" Control="N" Index="ACAGTG" SampleId="12345" Desc="Index #5 3 AWC ablated CX3695" Ref="elegans190" />
+      <Sample ProjectId="12283" Control="N" Index="CAGATC" SampleId="12283" Desc="Index #7 AWCon cell#5_N2" Ref="elegans190" />
+      <Sample ProjectId="12282" Control="N" Index="GCCAAT" SampleId="12282" Desc="Index #6 AWCon cell#4_N2" Ref="elegans190" />
+      <Sample ProjectId="Undetermined_indices" Control="N" Index="Undetermined" SampleId="lane2" Desc="Clusters with unmatched barcodes for lane 2" Ref="unknown" />
+    </Lane>
+    <Lane Number="3">
+      <Sample ProjectId="12331" Control="N" Index="ACAGTG" SampleId="12331" Desc="Index #5 060111 FLDN2b(d8.5) H3K4me3 ChIP" Ref="mm9" />
+      <Sample ProjectId="12383" Control="N" Index="CGATGT" SampleId="12383" Desc="Index #2 jwp ix-65 ni 16h" Ref="hg18" />
+      <Sample ProjectId="12330" Control="N" Index="TGACCA" SampleId="12330" Desc="Index #4 060111 Bcl11bKO DL4 FLDN2a H3K4me3 ChIP" Ref="mm9" />
+      <Sample ProjectId="Undetermined_indices" Control="N" Index="Undetermined" SampleId="lane3" Desc="Clusters with unmatched barcodes for lane 3" Ref="unknown" />
+    </Lane>
+    <Lane Number="4">
+      <Sample ProjectId="12385" Control="N" Index="ACAGTG" SampleId="12385" Desc="Index #5 jwp ix-65 i 16h" Ref="hg18" />
+      <Sample ProjectId="12386" Control="N" Index="GCCAAT" SampleId="12386" Desc="Index #6 jwp ix-71 NI 16h" Ref="hg18" />
+      <Sample ProjectId="12384" Control="N" Index="TGACCA" SampleId="12384" Desc="index #4 jwp ix-65 RD 16h" Ref="hg18" />
+      <Sample ProjectId="Undetermined_indices" Control="N" Index="Undetermined" SampleId="lane4" Desc="Clusters with unmatched barcodes for lane 4" Ref="unknown" />
+    </Lane>
+    <Lane Number="5">
+      <Sample ProjectId="12387" Control="N" Index="CAGATC" SampleId="12387" Desc="Index #7 jwp ix-71 RD 16h" Ref="hg18" />
+      <Sample ProjectId="12388" Control="N" Index="CTTGTA" SampleId="12388" Desc="Index #12 jwp ix-71 i 16h" Ref="hg18" />
+      <Sample ProjectId="Undetermined_indices" Control="N" Index="Undetermined" SampleId="lane5" Desc="Clusters with unmatched barcodes for lane 5" Ref="unknown" />
+    </Lane>
+    <Lane Number="6">
+      <Sample ProjectId="12391" Control="N" Index="ACTTGA" SampleId="12391" Desc="Index #8 jwp ix-63 NI 4h" Ref="hg18" />
+      <Sample ProjectId="12392" Control="N" Index="GATCAG" SampleId="12392" Desc="Index #9 jwp ix-63 DHT 10uM PA 4h" Ref="hg18" />
+      <Sample ProjectId="12393" Control="N" Index="TAGCTT" SampleId="12393" Desc="Index #10 jwp ix-63 DHT 4h" Ref="hg18" />
+      <Sample ProjectId="Undetermined_indices" Control="N" Index="Undetermined" SampleId="lane6" Desc="Clusters with unmatched barcodes for lane 6" Ref="unknown" />
+    </Lane>
+    <Lane Number="7">
+      <Sample ProjectId="12348_Index5" Control="N" Index="ACAGTG" SampleId="12348" Desc="Indices #1-9 Small RNA OSS TJ-GFP and constr.E-H" Ref="dm3" />
+      <Sample ProjectId="12348_Index8" Control="N" Index="ACTTGA" SampleId="12348" Desc="Indices #1-9 Small RNA OSS TJ-GFP and constr.E-H" Ref="dm3" />
+      <Sample ProjectId="12348_Index1" Control="N" Index="ATCACG" SampleId="12348" Desc="Indices #1-9 Small RNA OSS TJ-GFP and constr.E-H" Ref="dm3" />
+      <Sample ProjectId="12348_Index7" Control="N" Index="CAGATC" SampleId="12348" Desc="Indices #1-9 Small RNA OSS TJ-GFP and constr.E-H" Ref="dm3" />
+      <Sample ProjectId="12348_Index2" Control="N" Index="CGATGT" SampleId="12348" Desc="Indices #1-9 Small RNA OSS TJ-GFP and constr.E-H" Ref="dm3" />
+      <Sample ProjectId="12348_Index9" Control="N" Index="GATCAG" SampleId="12348" Desc="Indices #1-9 Small RNA OSS TJ-GFP and constr.E-H" Ref="dm3" />
+      <Sample ProjectId="12348_Index6" Control="N" Index="GCCAAT" SampleId="12348" Desc="Indices #1-9 Small RNA OSS TJ-GFP and constr.E-H" Ref="dm3" />
+      <Sample ProjectId="12348_Index4" Control="N" Index="TGACCA" SampleId="12348" Desc="Indices #1-9 Small RNA OSS TJ-GFP and constr.E-H" Ref="dm3" />
+      <Sample ProjectId="12348_Index3" Control="N" Index="TTAGGC" SampleId="12348" Desc="Indices #1-9 Small RNA OSS TJ-GFP and constr.E-H" Ref="dm3" />
+      <Sample ProjectId="Undetermined_indices" Control="N" Index="Undetermined" SampleId="lane7" Desc="Clusters with unmatched barcodes for lane 7" Ref="unknown" />
+    </Lane>
+    <Lane Number="8">
+      <Sample ProjectId="12382_Index5" Control="N" Index="ACAGTG" SampleId="12382" Desc="Small RNA Index #RPI1-RPI10 Human bladder cancer small RNA" Ref="hg18" />
+      <Sample ProjectId="12382_Index8" Control="N" Index="ACTTGA" SampleId="12382" Desc="Small RNA Index #RPI1-RPI10 Human bladder cancer small RNA" Ref="hg18" />
+      <Sample ProjectId="12382_Index1" Control="N" Index="ATCACG" SampleId="12382" Desc="Small RNA Index #RPI1-RPI10 Human bladder cancer small RNA" Ref="hg18" />
+      <Sample ProjectId="12382_Index7" Control="N" Index="CAGATC" SampleId="12382" Desc="Small RNA Index #RPI1-RPI10 Human bladder cancer small RNA" Ref="hg18" />
+      <Sample ProjectId="12382_Index2" Control="N" Index="CGATGT" SampleId="12382" Desc="Small RNA Index #RPI1-RPI10 Human bladder cancer small RNA" Ref="hg18" />
+      <Sample ProjectId="12382_Index9" Control="N" Index="GATCAG" SampleId="12382" Desc="Small RNA Index #RPI1-RPI10 Human bladder cancer small RNA" Ref="hg18" />
+      <Sample ProjectId="12382_Index6" Control="N" Index="GCCAAT" SampleId="12382" Desc="Small RNA Index #RPI1-RPI10 Human bladder cancer small RNA" Ref="hg18" />
+      <Sample ProjectId="12382_Index10" Control="N" Index="TAGCTT" SampleId="12382" Desc="Small RNA Index #RPI1-RPI10 Human bladder cancer small RNA" Ref="hg18" />
+      <Sample ProjectId="12382_Index4" Control="N" Index="TGACCA" SampleId="12382" Desc="Small RNA Index #RPI1-RPI10 Human bladder cancer small RNA" Ref="hg18" />
+      <Sample ProjectId="12382_Index3" Control="N" Index="TTAGGC" SampleId="12382" Desc="Small RNA Index #RPI1-RPI10 Human bladder cancer small RNA" Ref="hg18" />
+      <Sample ProjectId="Undetermined_indices" Control="N" Index="Undetermined" SampleId="lane8" Desc="Clusters with unmatched barcodes for lane 8" Ref="unknown" />
+    </Lane>
+  </FlowcellInfo>
+</DemultiplexConfig>
diff --git a/htsworkflow/pipelines/test/testdata/demultiplexed_bustard_1.12.4.2.xml b/htsworkflow/pipelines/test/testdata/demultiplexed_bustard_1.12.4.2.xml
new file mode 100644 (file)
index 0000000..ea6a596
--- /dev/null
@@ -0,0 +1,503 @@
+<?xml version="1.0"?>
+<BaseCallAnalysis xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+  <Run Name="BaseCalls">
+    <BaseCallParameters>
+      <ChastityThreshold>0.6</ChastityThreshold>
+      <Matrix Path="">
+        <AutoFlag>2</AutoFlag>
+        <AutoLane>0</AutoLane>
+        <Cycle>1</Cycle>
+        <CycleOffset>0</CycleOffset>
+        <FirstCycle>1</FirstCycle>
+        <LastCycle>50</LastCycle>
+        <Read>1</Read>
+      </Matrix>
+      <Matrix Path="">
+        <AutoFlag>2</AutoFlag>
+        <AutoLane>0</AutoLane>
+        <Cycle>51</Cycle>
+        <CycleOffset>0</CycleOffset>
+        <FirstCycle>51</FirstCycle>
+        <LastCycle>57</LastCycle>
+        <Read>2</Read>
+      </Matrix>
+      <Phasing Path="">
+        <AutoFlag>2</AutoFlag>
+        <AutoLane>0</AutoLane>
+        <Cycle>2</Cycle>
+        <CycleOffset>1</CycleOffset>
+        <FirstCycle>1</FirstCycle>
+        <LastCycle>50</LastCycle>
+        <PhasingRate>0</PhasingRate>
+        <PrephasingRate>0</PrephasingRate>
+        <Read>1</Read>
+      </Phasing>
+      <Phasing Path="">
+        <AutoFlag>2</AutoFlag>
+        <AutoLane>0</AutoLane>
+        <Cycle>52</Cycle>
+        <CycleOffset>1</CycleOffset>
+        <FirstCycle>51</FirstCycle>
+        <LastCycle>57</LastCycle>
+        <PhasingRate>0</PhasingRate>
+        <PrephasingRate>0</PrephasingRate>
+        <Read>2</Read>
+      </Phasing>
+      <PureBases>0</PureBases>
+      <SmtFilter>failed-chastity</SmtFilter>
+      <SmtRelation>le</SmtRelation>
+      <SmtThreshold>1.0</SmtThreshold>
+    </BaseCallParameters>
+    <Cycles First="1" Last="57" Number="57"/>
+    <RunParameters>
+      <AutoCycleFlag>0</AutoCycleFlag>
+      <Barcode>
+        <Cycle Use="true">51</Cycle>
+        <Cycle Use="true">52</Cycle>
+        <Cycle Use="true">53</Cycle>
+        <Cycle Use="true">54</Cycle>
+        <Cycle Use="true">55</Cycle>
+        <Cycle Use="true">56</Cycle>
+        <Cycle Use="true">57</Cycle>
+      </Barcode>
+      <BasecallFlag>0</BasecallFlag>
+      <Deblocked>0</Deblocked>
+      <DebugFlag>0</DebugFlag>
+      <FirstRunOnlyFlag>0</FirstRunOnlyFlag>
+      <ImagingReads Index="1">
+        <FirstCycle>1</FirstCycle>
+        <LastCycle>50</LastCycle>
+      </ImagingReads>
+      <ImagingReads Index="2">
+        <FirstCycle>51</FirstCycle>
+        <LastCycle>57</LastCycle>
+        <RunFolder>110815_SN787_0101_AD07K6ACXX</RunFolder>
+      </ImagingReads>
+      <Instrument>HWI-ST0787</Instrument>
+      <IterativeMatrixFlag>0</IterativeMatrixFlag>
+      <MakeFlag>0</MakeFlag>
+      <MaxCycle>0</MaxCycle>
+      <MinCycle>0</MinCycle>
+      <QTableVersion>New6</QTableVersion>
+      <RunFlowcellId>D07K6ACXX</RunFlowcellId>
+      <RunFolder>110815_SN787_0101_AD07K6ACXX</RunFolder>
+      <RunFolderDate>110815</RunFolderDate>
+      <RunFolderId>0101</RunFolderId>
+      <Reads Index="1">
+        <FirstCycle>1</FirstCycle>
+        <LastCycle>50</LastCycle>
+      </Reads>
+    </RunParameters>
+    <Software Name="RTA" Version="1.12.4.2"/>
+    <TileSelection>
+      <Lane Index="1">
+        <Sample>s</Sample>
+        <Tile>1102</Tile>
+        <Tile>1101</Tile>
+        <Tile>1103</Tile>
+        <Tile>1106</Tile>
+        <Tile>1104</Tile>
+        <Tile>1105</Tile>
+        <Tile>1108</Tile>
+        <Tile>1107</Tile>
+        <Tile>1202</Tile>
+        <Tile>1201</Tile>
+        <Tile>1206</Tile>
+        <Tile>1204</Tile>
+        <Tile>1203</Tile>
+        <Tile>1205</Tile>
+        <Tile>1302</Tile>
+        <Tile>1208</Tile>
+        <Tile>1207</Tile>
+        <Tile>1301</Tile>
+        <Tile>1306</Tile>
+        <Tile>1304</Tile>
+        <Tile>1305</Tile>
+        <Tile>2102</Tile>
+        <Tile>1303</Tile>
+        <Tile>1308</Tile>
+        <Tile>2101</Tile>
+        <Tile>1307</Tile>
+        <Tile>2106</Tile>
+        <Tile>2104</Tile>
+        <Tile>2105</Tile>
+        <Tile>2103</Tile>
+        <Tile>2202</Tile>
+        <Tile>2108</Tile>
+        <Tile>2201</Tile>
+        <Tile>2206</Tile>
+        <Tile>2107</Tile>
+        <Tile>2205</Tile>
+        <Tile>2204</Tile>
+        <Tile>2203</Tile>
+        <Tile>2302</Tile>
+        <Tile>2301</Tile>
+        <Tile>2208</Tile>
+        <Tile>2306</Tile>
+        <Tile>2207</Tile>
+        <Tile>2305</Tile>
+        <Tile>2303</Tile>
+        <Tile>2304</Tile>
+        <Tile>2308</Tile>
+        <Tile>2307</Tile>
+      </Lane>
+      <Lane Index="2">
+        <Sample>s</Sample>
+        <Tile>1101</Tile>
+        <Tile>1102</Tile>
+        <Tile>1105</Tile>
+        <Tile>1106</Tile>
+        <Tile>1104</Tile>
+        <Tile>1103</Tile>
+        <Tile>1201</Tile>
+        <Tile>1202</Tile>
+        <Tile>1108</Tile>
+        <Tile>1206</Tile>
+        <Tile>1107</Tile>
+        <Tile>1205</Tile>
+        <Tile>1302</Tile>
+        <Tile>1204</Tile>
+        <Tile>1301</Tile>
+        <Tile>1203</Tile>
+        <Tile>1208</Tile>
+        <Tile>1306</Tile>
+        <Tile>1305</Tile>
+        <Tile>1207</Tile>
+        <Tile>1304</Tile>
+        <Tile>2101</Tile>
+        <Tile>2102</Tile>
+        <Tile>1308</Tile>
+        <Tile>2105</Tile>
+        <Tile>1303</Tile>
+        <Tile>2201</Tile>
+        <Tile>2106</Tile>
+        <Tile>2104</Tile>
+        <Tile>1307</Tile>
+        <Tile>2205</Tile>
+        <Tile>2202</Tile>
+        <Tile>2108</Tile>
+        <Tile>2206</Tile>
+        <Tile>2103</Tile>
+        <Tile>2301</Tile>
+        <Tile>2204</Tile>
+        <Tile>2208</Tile>
+        <Tile>2107</Tile>
+        <Tile>2302</Tile>
+        <Tile>2305</Tile>
+        <Tile>2304</Tile>
+        <Tile>2203</Tile>
+        <Tile>2306</Tile>
+        <Tile>2308</Tile>
+        <Tile>2207</Tile>
+        <Tile>2303</Tile>
+        <Tile>2307</Tile>
+      </Lane>
+      <Lane Index="3">
+        <Sample>s</Sample>
+        <Tile>1101</Tile>
+        <Tile>1102</Tile>
+        <Tile>1105</Tile>
+        <Tile>1104</Tile>
+        <Tile>1108</Tile>
+        <Tile>1106</Tile>
+        <Tile>1201</Tile>
+        <Tile>1103</Tile>
+        <Tile>1204</Tile>
+        <Tile>1202</Tile>
+        <Tile>1205</Tile>
+        <Tile>1107</Tile>
+        <Tile>1208</Tile>
+        <Tile>1206</Tile>
+        <Tile>1301</Tile>
+        <Tile>1304</Tile>
+        <Tile>1203</Tile>
+        <Tile>1302</Tile>
+        <Tile>1308</Tile>
+        <Tile>1305</Tile>
+        <Tile>1207</Tile>
+        <Tile>2101</Tile>
+        <Tile>2104</Tile>
+        <Tile>1306</Tile>
+        <Tile>1303</Tile>
+        <Tile>2102</Tile>
+        <Tile>2105</Tile>
+        <Tile>2108</Tile>
+        <Tile>1307</Tile>
+        <Tile>2106</Tile>
+        <Tile>2204</Tile>
+        <Tile>2201</Tile>
+        <Tile>2103</Tile>
+        <Tile>2208</Tile>
+        <Tile>2202</Tile>
+        <Tile>2107</Tile>
+        <Tile>2205</Tile>
+        <Tile>2301</Tile>
+        <Tile>2304</Tile>
+        <Tile>2203</Tile>
+        <Tile>2206</Tile>
+        <Tile>2207</Tile>
+        <Tile>2305</Tile>
+        <Tile>2308</Tile>
+        <Tile>2302</Tile>
+        <Tile>2303</Tile>
+        <Tile>2307</Tile>
+        <Tile>2306</Tile>
+      </Lane>
+      <Lane Index="4">
+        <Sample>s</Sample>
+        <Tile>1101</Tile>
+        <Tile>1104</Tile>
+        <Tile>1103</Tile>
+        <Tile>1102</Tile>
+        <Tile>1108</Tile>
+        <Tile>1105</Tile>
+        <Tile>1107</Tile>
+        <Tile>1106</Tile>
+        <Tile>1204</Tile>
+        <Tile>1201</Tile>
+        <Tile>1203</Tile>
+        <Tile>1202</Tile>
+        <Tile>1208</Tile>
+        <Tile>1205</Tile>
+        <Tile>1207</Tile>
+        <Tile>1206</Tile>
+        <Tile>1304</Tile>
+        <Tile>1301</Tile>
+        <Tile>1302</Tile>
+        <Tile>1308</Tile>
+        <Tile>1303</Tile>
+        <Tile>1305</Tile>
+        <Tile>1306</Tile>
+        <Tile>1307</Tile>
+        <Tile>2104</Tile>
+        <Tile>2101</Tile>
+        <Tile>2108</Tile>
+        <Tile>2102</Tile>
+        <Tile>2103</Tile>
+        <Tile>2105</Tile>
+        <Tile>2204</Tile>
+        <Tile>2106</Tile>
+        <Tile>2107</Tile>
+        <Tile>2201</Tile>
+        <Tile>2208</Tile>
+        <Tile>2202</Tile>
+        <Tile>2203</Tile>
+        <Tile>2304</Tile>
+        <Tile>2205</Tile>
+        <Tile>2206</Tile>
+        <Tile>2207</Tile>
+        <Tile>2308</Tile>
+        <Tile>2301</Tile>
+        <Tile>2302</Tile>
+        <Tile>2303</Tile>
+        <Tile>2305</Tile>
+        <Tile>2307</Tile>
+        <Tile>2306</Tile>
+      </Lane>
+      <Lane Index="5">
+        <Sample>s</Sample>
+        <Tile>1104</Tile>
+        <Tile>1108</Tile>
+        <Tile>1101</Tile>
+        <Tile>1204</Tile>
+        <Tile>1102</Tile>
+        <Tile>1103</Tile>
+        <Tile>1106</Tile>
+        <Tile>1105</Tile>
+        <Tile>1107</Tile>
+        <Tile>1208</Tile>
+        <Tile>1201</Tile>
+        <Tile>1202</Tile>
+        <Tile>1203</Tile>
+        <Tile>1304</Tile>
+        <Tile>1205</Tile>
+        <Tile>1206</Tile>
+        <Tile>1301</Tile>
+        <Tile>1308</Tile>
+        <Tile>1207</Tile>
+        <Tile>1302</Tile>
+        <Tile>2104</Tile>
+        <Tile>1303</Tile>
+        <Tile>1305</Tile>
+        <Tile>1306</Tile>
+        <Tile>2101</Tile>
+        <Tile>2102</Tile>
+        <Tile>1307</Tile>
+        <Tile>2108</Tile>
+        <Tile>2204</Tile>
+        <Tile>2103</Tile>
+        <Tile>2105</Tile>
+        <Tile>2107</Tile>
+        <Tile>2106</Tile>
+        <Tile>2201</Tile>
+        <Tile>2208</Tile>
+        <Tile>2203</Tile>
+        <Tile>2202</Tile>
+        <Tile>2304</Tile>
+        <Tile>2206</Tile>
+        <Tile>2205</Tile>
+        <Tile>2207</Tile>
+        <Tile>2302</Tile>
+        <Tile>2301</Tile>
+        <Tile>2303</Tile>
+        <Tile>2308</Tile>
+        <Tile>2305</Tile>
+        <Tile>2307</Tile>
+        <Tile>2306</Tile>
+      </Lane>
+      <Lane Index="6">
+        <Sample>s</Sample>
+        <Tile>1104</Tile>
+        <Tile>1101</Tile>
+        <Tile>1103</Tile>
+        <Tile>1102</Tile>
+        <Tile>1108</Tile>
+        <Tile>1107</Tile>
+        <Tile>1105</Tile>
+        <Tile>1106</Tile>
+        <Tile>1204</Tile>
+        <Tile>1203</Tile>
+        <Tile>1201</Tile>
+        <Tile>1202</Tile>
+        <Tile>1208</Tile>
+        <Tile>1207</Tile>
+        <Tile>1205</Tile>
+        <Tile>1206</Tile>
+        <Tile>1304</Tile>
+        <Tile>1303</Tile>
+        <Tile>1301</Tile>
+        <Tile>1302</Tile>
+        <Tile>1308</Tile>
+        <Tile>1307</Tile>
+        <Tile>1305</Tile>
+        <Tile>2104</Tile>
+        <Tile>1306</Tile>
+        <Tile>2103</Tile>
+        <Tile>2101</Tile>
+        <Tile>2102</Tile>
+        <Tile>2108</Tile>
+        <Tile>2107</Tile>
+        <Tile>2105</Tile>
+        <Tile>2106</Tile>
+        <Tile>2204</Tile>
+        <Tile>2203</Tile>
+        <Tile>2202</Tile>
+        <Tile>2201</Tile>
+        <Tile>2208</Tile>
+        <Tile>2207</Tile>
+        <Tile>2206</Tile>
+        <Tile>2205</Tile>
+        <Tile>2304</Tile>
+        <Tile>2303</Tile>
+        <Tile>2302</Tile>
+        <Tile>2301</Tile>
+        <Tile>2307</Tile>
+        <Tile>2308</Tile>
+        <Tile>2306</Tile>
+        <Tile>2305</Tile>
+      </Lane>
+      <Lane Index="7">
+        <Sample>s</Sample>
+        <Tile>1103</Tile>
+        <Tile>1107</Tile>
+        <Tile>1104</Tile>
+        <Tile>1108</Tile>
+        <Tile>1203</Tile>
+        <Tile>1101</Tile>
+        <Tile>1102</Tile>
+        <Tile>1204</Tile>
+        <Tile>1105</Tile>
+        <Tile>1207</Tile>
+        <Tile>1106</Tile>
+        <Tile>1208</Tile>
+        <Tile>1201</Tile>
+        <Tile>1202</Tile>
+        <Tile>1303</Tile>
+        <Tile>1205</Tile>
+        <Tile>1206</Tile>
+        <Tile>1307</Tile>
+        <Tile>1304</Tile>
+        <Tile>1301</Tile>
+        <Tile>1302</Tile>
+        <Tile>1305</Tile>
+        <Tile>1308</Tile>
+        <Tile>2103</Tile>
+        <Tile>1306</Tile>
+        <Tile>2101</Tile>
+        <Tile>2107</Tile>
+        <Tile>2104</Tile>
+        <Tile>2105</Tile>
+        <Tile>2102</Tile>
+        <Tile>2108</Tile>
+        <Tile>2203</Tile>
+        <Tile>2201</Tile>
+        <Tile>2106</Tile>
+        <Tile>2205</Tile>
+        <Tile>2207</Tile>
+        <Tile>2202</Tile>
+        <Tile>2204</Tile>
+        <Tile>2301</Tile>
+        <Tile>2303</Tile>
+        <Tile>2206</Tile>
+        <Tile>2208</Tile>
+        <Tile>2305</Tile>
+        <Tile>2307</Tile>
+        <Tile>2302</Tile>
+        <Tile>2304</Tile>
+        <Tile>2306</Tile>
+        <Tile>2308</Tile>
+      </Lane>
+      <Lane Index="8">
+        <Sample>s</Sample>
+        <Tile>1101</Tile>
+        <Tile>1103</Tile>
+        <Tile>1102</Tile>
+        <Tile>1105</Tile>
+        <Tile>1107</Tile>
+        <Tile>1104</Tile>
+        <Tile>1106</Tile>
+        <Tile>1201</Tile>
+        <Tile>1108</Tile>
+        <Tile>1203</Tile>
+        <Tile>1202</Tile>
+        <Tile>1205</Tile>
+        <Tile>1207</Tile>
+        <Tile>1204</Tile>
+        <Tile>1206</Tile>
+        <Tile>1301</Tile>
+        <Tile>1208</Tile>
+        <Tile>1303</Tile>
+        <Tile>1302</Tile>
+        <Tile>1305</Tile>
+        <Tile>1307</Tile>
+        <Tile>1304</Tile>
+        <Tile>1306</Tile>
+        <Tile>2101</Tile>
+        <Tile>1308</Tile>
+        <Tile>2103</Tile>
+        <Tile>2105</Tile>
+        <Tile>2102</Tile>
+        <Tile>2107</Tile>
+        <Tile>2106</Tile>
+        <Tile>2104</Tile>
+        <Tile>2201</Tile>
+        <Tile>2205</Tile>
+        <Tile>2202</Tile>
+        <Tile>2203</Tile>
+        <Tile>2108</Tile>
+        <Tile>2206</Tile>
+        <Tile>2301</Tile>
+        <Tile>2207</Tile>
+        <Tile>2204</Tile>
+        <Tile>2305</Tile>
+        <Tile>2302</Tile>
+        <Tile>2303</Tile>
+        <Tile>2208</Tile>
+        <Tile>2306</Tile>
+        <Tile>2307</Tile>
+        <Tile>2304</Tile>
+        <Tile>2308</Tile>
+      </Lane>
+    </TileSelection>
+  </Run>
+</BaseCallAnalysis>
diff --git a/htsworkflow/pipelines/test/testdata/demultiplexed_summary_1.12.4.2.xml b/htsworkflow/pipelines/test/testdata/demultiplexed_summary_1.12.4.2.xml
new file mode 100644 (file)
index 0000000..ebc9f4a
--- /dev/null
@@ -0,0 +1,3669 @@
+<?xml version="1.0"?>
+<BustardSummary>
+  <ChipResultsSummary>
+    <clusterCountPF>454185731</clusterCountPF>
+    <clusterCountRaw>781064977</clusterCountRaw>
+    <yield>25888586667</yield>
+  </ChipResultsSummary>
+  <ChipSummary>
+    <ChipID>unknown</ChipID>
+    <Machine>HWI-ST0787</Machine>
+    <RunFolder>110815_SN787_0101_AD07K6ACXX</RunFolder>
+  </ChipSummary>
+  <Date>2011-08-18 20:18:19</Date>
+  <ExpandedLaneSummary>
+    <Read>
+      <Lane>
+        <clusterCountRaw>
+          <mean>3707807.14</mean>
+          <stdev>573671.11</stdev>
+          <sumsq>393825007132852.00</sumsq>
+        </clusterCountRaw>
+        <laneNumber>1</laneNumber>
+        <percentClustersPF>
+          <mean>47.64</mean>
+          <stdev>19.64</stdev>
+          <sumsq>73957.00</sumsq>
+        </percentClustersPF>
+        <phasingApplied>0.3810</phasingApplied>
+        <prephasingApplied>0.0844</prephasingApplied>
+        <signalAverage1to3>
+          <mean>677.00</mean>
+          <stdev>148.48</stdev>
+          <sumsq>13428576.43</sumsq>
+        </signalAverage1to3>
+        <signalAverage2to4>
+          <mean>908.15</mean>
+          <stdev>81.51</stdev>
+          <sumsq>23271897.61</sumsq>
+        </signalAverage2to4>
+        <signalLoss10to20>
+          <mean>-0.30</mean>
+          <stdev>0.38</stdev>
+          <sumsq>6.33</sumsq>
+        </signalLoss10to20>
+        <signalLoss2to10>
+          <mean>-34.61</mean>
+          <stdev>26.97</stdev>
+          <sumsq>53175.44</sumsq>
+        </signalLoss2to10>
+      </Lane>
+      <Lane>
+        <clusterCountRaw>
+          <mean>3329777.81</mean>
+          <stdev>1102200.81</stdev>
+          <sumsq>318644092316267.00</sumsq>
+        </clusterCountRaw>
+        <laneNumber>2</laneNumber>
+        <percentClustersPF>
+          <mean>24.71</mean>
+          <stdev>17.39</stdev>
+          <sumsq>23436.66</sumsq>
+        </percentClustersPF>
+        <phasingApplied>0.3694</phasingApplied>
+        <prephasingApplied>0.2507</prephasingApplied>
+        <signalAverage1to3>
+          <mean>820.85</mean>
+          <stdev>175.96</stdev>
+          <sumsq>18292849.43</sumsq>
+        </signalAverage1to3>
+        <signalAverage2to4>
+          <mean>864.16</mean>
+          <stdev>95.34</stdev>
+          <sumsq>19643349.08</sumsq>
+        </signalAverage2to4>
+        <signalLoss10to20>
+          <mean>-5.69</mean>
+          <stdev>12.59</stdev>
+          <sumsq>4807.74</sumsq>
+        </signalLoss10to20>
+        <signalLoss2to10>
+          <mean>-34.31</mean>
+          <stdev>22.59</stdev>
+          <sumsq>43354.50</sumsq>
+        </signalLoss2to10>
+      </Lane>
+      <Lane>
+        <clusterCountRaw>
+          <mean>6268934.50</mean>
+          <stdev>241767.87</stdev>
+          <sumsq>314805480030044.00</sumsq>
+        </clusterCountRaw>
+        <laneNumber>3</laneNumber>
+        <percentClustersPF>
+          <mean>36.04</mean>
+          <stdev>12.81</stdev>
+          <sumsq>11541.60</sumsq>
+        </percentClustersPF>
+        <phasingApplied>0.2469</phasingApplied>
+        <prephasingApplied>0.2002</prephasingApplied>
+        <signalAverage1to3>
+          <mean>1094.84</mean>
+          <stdev>135.96</stdev>
+          <sumsq>9718779.89</sumsq>
+        </signalAverage1to3>
+        <signalAverage2to4>
+          <mean>1114.24</mean>
+          <stdev>57.49</stdev>
+          <sumsq>9955389.55</sumsq>
+        </signalAverage2to4>
+        <signalLoss10to20>
+          <mean>-4.20</mean>
+          <stdev>13.18</stdev>
+          <sumsq>1357.57</sumsq>
+        </signalLoss10to20>
+        <signalLoss2to10>
+          <mean>-53.53</mean>
+          <stdev>38.21</stdev>
+          <sumsq>33143.61</sumsq>
+        </signalLoss2to10>
+      </Lane>
+      <Lane>
+        <clusterCountRaw>
+          <mean>6055508.12</mean>
+          <stdev>166741.39</stdev>
+          <sumsq>293548048051419.00</sumsq>
+        </clusterCountRaw>
+        <laneNumber>4</laneNumber>
+        <percentClustersPF>
+          <mean>32.69</mean>
+          <stdev>7.60</stdev>
+          <sumsq>8952.16</sumsq>
+        </percentClustersPF>
+        <phasingApplied>0.2104</phasingApplied>
+        <prephasingApplied>0.1803</prephasingApplied>
+        <signalAverage1to3>
+          <mean>1106.96</mean>
+          <stdev>62.20</stdev>
+          <sumsq>9829917.93</sumsq>
+        </signalAverage1to3>
+        <signalAverage2to4>
+          <mean>1036.31</mean>
+          <stdev>128.16</stdev>
+          <sumsq>8706439.16</sumsq>
+        </signalAverage2to4>
+        <signalLoss10to20>
+          <mean>-9.55</mean>
+          <stdev>18.68</stdev>
+          <sumsq>3171.25</sumsq>
+        </signalLoss10to20>
+        <signalLoss2to10>
+          <mean>-44.30</mean>
+          <stdev>34.27</stdev>
+          <sumsq>23924.49</sumsq>
+        </signalLoss2to10>
+      </Lane>
+      <Lane>
+        <clusterCountRaw>
+          <mean>5643648.67</mean>
+          <stdev>137235.86</stdev>
+          <sumsq>95589978179428.00</sumsq>
+        </clusterCountRaw>
+        <laneNumber>5</laneNumber>
+        <percentClustersPF>
+          <mean>14.96</mean>
+          <stdev>10.60</stdev>
+          <sumsq>895.87</sumsq>
+        </percentClustersPF>
+        <phasingApplied>0.0000</phasingApplied>
+        <prephasingApplied>0.0000</prephasingApplied>
+        <signalAverage1to3>
+          <mean>-593.62</mean>
+          <stdev>74.55</stdev>
+          <sumsq>1068254.69</sumsq>
+        </signalAverage1to3>
+        <signalAverage2to4>
+          <mean>-623.07</mean>
+          <stdev>71.93</stdev>
+          <sumsq>1174981.61</sumsq>
+        </signalAverage2to4>
+        <signalLoss10to20>
+          <mean>100.00</mean>
+          <stdev>0.00</stdev>
+          <sumsq>30000.00</sumsq>
+        </signalLoss10to20>
+        <signalLoss2to10>
+          <mean>100.00</mean>
+          <stdev>0.00</stdev>
+          <sumsq>30000.00</sumsq>
+        </signalLoss2to10>
+      </Lane>
+      <Lane>
+        <clusterCountRaw>
+          <mean>5707954.48</mean>
+          <stdev>553352.88</stdev>
+          <sumsq>953415170485172.00</sumsq>
+        </clusterCountRaw>
+        <laneNumber>6</laneNumber>
+        <percentClustersPF>
+          <mean>42.22</mean>
+          <stdev>22.39</stdev>
+          <sumsq>65737.40</sumsq>
+        </percentClustersPF>
+        <phasingApplied>0.2670</phasingApplied>
+        <prephasingApplied>0.2116</prephasingApplied>
+        <signalAverage1to3>
+          <mean>976.36</mean>
+          <stdev>216.47</stdev>
+          <sumsq>28956965.77</sumsq>
+        </signalAverage1to3>
+        <signalAverage2to4>
+          <mean>1054.88</mean>
+          <stdev>90.27</stdev>
+          <sumsq>32498684.57</sumsq>
+        </signalAverage2to4>
+        <signalLoss10to20>
+          <mean>0.20</mean>
+          <stdev>0.11</stdev>
+          <sumsq>1.47</sumsq>
+        </signalLoss10to20>
+        <signalLoss2to10>
+          <mean>-79.61</mean>
+          <stdev>16.62</stdev>
+          <sumsq>191509.02</sumsq>
+        </signalLoss2to10>
+      </Lane>
+      <Lane>
+        <clusterCountRaw>
+          <mean>1867305.95</mean>
+          <stdev>444617.44</stdev>
+          <sumsq>158236511701682.00</sumsq>
+        </clusterCountRaw>
+        <laneNumber>7</laneNumber>
+        <percentClustersPF>
+          <mean>94.84</mean>
+          <stdev>11.12</stdev>
+          <sumsq>391931.07</sumsq>
+        </percentClustersPF>
+        <phasingApplied>0.1329</phasingApplied>
+        <prephasingApplied>0.2410</prephasingApplied>
+        <signalAverage1to3>
+          <mean>1399.64</mean>
+          <stdev>129.00</stdev>
+          <sumsq>84935084.50</sumsq>
+        </signalAverage1to3>
+        <signalAverage2to4>
+          <mean>1377.83</mean>
+          <stdev>128.32</stdev>
+          <sumsq>82324018.13</sumsq>
+        </signalAverage2to4>
+        <signalLoss10to20>
+          <mean>0.28</mean>
+          <stdev>0.09</stdev>
+          <sumsq>3.65</sumsq>
+        </signalLoss10to20>
+        <signalLoss2to10>
+          <mean>-4.22</mean>
+          <stdev>14.27</stdev>
+          <sumsq>9317.43</sumsq>
+        </signalLoss2to10>
+      </Lane>
+      <Lane>
+        <clusterCountRaw>
+          <mean>4777517.31</mean>
+          <stdev>599178.35</stdev>
+          <sumsq>1112457930812391.00</sumsq>
+        </clusterCountRaw>
+        <laneNumber>8</laneNumber>
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+        <Tile>
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+        <Tile>
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+        </Tile>
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+        </Tile>
+        <Tile>
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+          <clusterCountRaw>4091803</clusterCountRaw>
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+          <percentClustersPF>91.53</percentClustersPF>
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+        </Tile>
+        <Tile>
+          <clusterCountPF>3938377</clusterCountPF>
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+        </Tile>
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+          <signal20AsPctOf1>88.08</signal20AsPctOf1>
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+        </Tile>
+        <Tile>
+          <clusterCountPF>4282045</clusterCountPF>
+          <clusterCountRaw>4835601</clusterCountRaw>
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+        </Tile>
+        <Tile>
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+        </Tile>
+        <Tile>
+          <clusterCountPF>4602295</clusterCountPF>
+          <clusterCountRaw>5337911</clusterCountRaw>
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+          <signal20AsPctOf1>86.97</signal20AsPctOf1>
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+        </Tile>
+        <Tile>
+          <clusterCountPF>4600782</clusterCountPF>
+          <clusterCountRaw>5501477</clusterCountRaw>
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+          <signal20AsPctOf1>86.53</signal20AsPctOf1>
+          <tileNumber>1307</tileNumber>
+        </Tile>
+        <Tile>
+          <clusterCountPF>4145380</clusterCountPF>
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+          <tileNumber>1308</tileNumber>
+        </Tile>
+        <Tile>
+          <clusterCountPF>3654318</clusterCountPF>
+          <clusterCountRaw>3969110</clusterCountRaw>
+          <oneSig>1467.08</oneSig>
+          <percentClustersPF>92.07</percentClustersPF>
+          <signal20AsPctOf1>90.01</signal20AsPctOf1>
+          <tileNumber>2101</tileNumber>
+        </Tile>
+        <Tile>
+          <clusterCountPF>3839864</clusterCountPF>
+          <clusterCountRaw>4184268</clusterCountRaw>
+          <oneSig>1439.99</oneSig>
+          <percentClustersPF>91.77</percentClustersPF>
+          <signal20AsPctOf1>90.66</signal20AsPctOf1>
+          <tileNumber>2102</tileNumber>
+        </Tile>
+        <Tile>
+          <clusterCountPF>3969051</clusterCountPF>
+          <clusterCountRaw>4413583</clusterCountRaw>
+          <oneSig>1422.63</oneSig>
+          <percentClustersPF>89.93</percentClustersPF>
+          <signal20AsPctOf1>90.66</signal20AsPctOf1>
+          <tileNumber>2103</tileNumber>
+        </Tile>
+        <Tile>
+          <clusterCountPF>4219627</clusterCountPF>
+          <clusterCountRaw>4681613</clusterCountRaw>
+          <oneSig>1403.97</oneSig>
+          <percentClustersPF>90.13</percentClustersPF>
+          <signal20AsPctOf1>90.49</signal20AsPctOf1>
+          <tileNumber>2104</tileNumber>
+        </Tile>
+        <Tile>
+          <clusterCountPF>4414065</clusterCountPF>
+          <clusterCountRaw>4956383</clusterCountRaw>
+          <oneSig>1386.15</oneSig>
+          <percentClustersPF>89.06</percentClustersPF>
+          <signal20AsPctOf1>89.95</signal20AsPctOf1>
+          <tileNumber>2105</tileNumber>
+        </Tile>
+        <Tile>
+          <clusterCountPF>4579204</clusterCountPF>
+          <clusterCountRaw>5232590</clusterCountRaw>
+          <oneSig>1365.53</oneSig>
+          <percentClustersPF>87.51</percentClustersPF>
+          <signal20AsPctOf1>89.26</signal20AsPctOf1>
+          <tileNumber>2106</tileNumber>
+        </Tile>
+        <Tile>
+          <clusterCountPF>4682961</clusterCountPF>
+          <clusterCountRaw>5469205</clusterCountRaw>
+          <oneSig>1333.32</oneSig>
+          <percentClustersPF>85.62</percentClustersPF>
+          <signal20AsPctOf1>89.03</signal20AsPctOf1>
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+        </Tile>
+        <Tile>
+          <clusterCountPF>3928926</clusterCountPF>
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+        </Tile>
+        <Tile>
+          <clusterCountPF>3556282</clusterCountPF>
+          <clusterCountRaw>3852699</clusterCountRaw>
+          <oneSig>1457.50</oneSig>
+          <percentClustersPF>92.31</percentClustersPF>
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+        </Tile>
+        <Tile>
+          <clusterCountPF>3741136</clusterCountPF>
+          <clusterCountRaw>4072130</clusterCountRaw>
+          <oneSig>1441.42</oneSig>
+          <percentClustersPF>91.87</percentClustersPF>
+          <signal20AsPctOf1>89.42</signal20AsPctOf1>
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+        </Tile>
+        <Tile>
+          <clusterCountPF>3842742</clusterCountPF>
+          <clusterCountRaw>4212391</clusterCountRaw>
+          <oneSig>1415.97</oneSig>
+          <percentClustersPF>91.22</percentClustersPF>
+          <signal20AsPctOf1>89.95</signal20AsPctOf1>
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+        </Tile>
+        <Tile>
+          <clusterCountPF>4140127</clusterCountPF>
+          <clusterCountRaw>4577001</clusterCountRaw>
+          <oneSig>1387.43</oneSig>
+          <percentClustersPF>90.46</percentClustersPF>
+          <signal20AsPctOf1>89.88</signal20AsPctOf1>
+          <tileNumber>2204</tileNumber>
+        </Tile>
+        <Tile>
+          <clusterCountPF>4372303</clusterCountPF>
+          <clusterCountRaw>4862284</clusterCountRaw>
+          <oneSig>1384.77</oneSig>
+          <percentClustersPF>89.92</percentClustersPF>
+          <signal20AsPctOf1>88.76</signal20AsPctOf1>
+          <tileNumber>2205</tileNumber>
+        </Tile>
+        <Tile>
+          <clusterCountPF>4531801</clusterCountPF>
+          <clusterCountRaw>5119662</clusterCountRaw>
+          <oneSig>1367.26</oneSig>
+          <percentClustersPF>88.52</percentClustersPF>
+          <signal20AsPctOf1>88.81</signal20AsPctOf1>
+          <tileNumber>2206</tileNumber>
+        </Tile>
+        <Tile>
+          <clusterCountPF>4148375</clusterCountPF>
+          <clusterCountRaw>5301292</clusterCountRaw>
+          <oneSig>1326.28</oneSig>
+          <percentClustersPF>78.25</percentClustersPF>
+          <signal20AsPctOf1>89.46</signal20AsPctOf1>
+          <tileNumber>2207</tileNumber>
+        </Tile>
+        <Tile>
+          <clusterCountPF>3747919</clusterCountPF>
+          <clusterCountRaw>5523881</clusterCountRaw>
+          <oneSig>1328.04</oneSig>
+          <percentClustersPF>67.85</percentClustersPF>
+          <signal20AsPctOf1>85.54</signal20AsPctOf1>
+          <tileNumber>2208</tileNumber>
+        </Tile>
+        <Tile>
+          <clusterCountPF>3685991</clusterCountPF>
+          <clusterCountRaw>4034260</clusterCountRaw>
+          <oneSig>1437.04</oneSig>
+          <percentClustersPF>91.37</percentClustersPF>
+          <signal20AsPctOf1>88.87</signal20AsPctOf1>
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+        </Tile>
+        <Tile>
+          <clusterCountPF>3894450</clusterCountPF>
+          <clusterCountRaw>4285846</clusterCountRaw>
+          <oneSig>1425.73</oneSig>
+          <percentClustersPF>90.87</percentClustersPF>
+          <signal20AsPctOf1>89.86</signal20AsPctOf1>
+          <tileNumber>2302</tileNumber>
+        </Tile>
+        <Tile>
+          <clusterCountPF>3941822</clusterCountPF>
+          <clusterCountRaw>4382141</clusterCountRaw>
+          <oneSig>1397.98</oneSig>
+          <percentClustersPF>89.95</percentClustersPF>
+          <signal20AsPctOf1>90.41</signal20AsPctOf1>
+          <tileNumber>2303</tileNumber>
+        </Tile>
+        <Tile>
+          <clusterCountPF>4299760</clusterCountPF>
+          <clusterCountRaw>4825173</clusterCountRaw>
+          <oneSig>1380.92</oneSig>
+          <percentClustersPF>89.11</percentClustersPF>
+          <signal20AsPctOf1>89.99</signal20AsPctOf1>
+          <tileNumber>2304</tileNumber>
+        </Tile>
+        <Tile>
+          <clusterCountPF>4523197</clusterCountPF>
+          <clusterCountRaw>5101827</clusterCountRaw>
+          <oneSig>1374.81</oneSig>
+          <percentClustersPF>88.66</percentClustersPF>
+          <signal20AsPctOf1>89.72</signal20AsPctOf1>
+          <tileNumber>2305</tileNumber>
+        </Tile>
+        <Tile>
+          <clusterCountPF>4658536</clusterCountPF>
+          <clusterCountRaw>5357124</clusterCountRaw>
+          <oneSig>1362.66</oneSig>
+          <percentClustersPF>86.96</percentClustersPF>
+          <signal20AsPctOf1>88.93</signal20AsPctOf1>
+          <tileNumber>2306</tileNumber>
+        </Tile>
+        <Tile>
+          <clusterCountPF>4706753</clusterCountPF>
+          <clusterCountRaw>5569616</clusterCountRaw>
+          <oneSig>1336.27</oneSig>
+          <percentClustersPF>84.51</percentClustersPF>
+          <signal20AsPctOf1>89.15</signal20AsPctOf1>
+          <tileNumber>2307</tileNumber>
+        </Tile>
+        <Tile>
+          <clusterCountPF>2196707</clusterCountPF>
+          <clusterCountRaw>3787138</clusterCountRaw>
+          <oneSig>1265.29</oneSig>
+          <percentClustersPF>58.00</percentClustersPF>
+          <signal20AsPctOf1>89.55</signal20AsPctOf1>
+          <tileNumber>2308</tileNumber>
+        </Tile>
+        <readNumber>1</readNumber>
+      </Read>
+      
+      <laneNumber>8</laneNumber>
+    </Lane>
+  </TileResultsByLane>
+</BustardSummary>
diff --git a/htsworkflow/pipelines/test/testdata/rta_basecalls_config_1.12.4.2.xml b/htsworkflow/pipelines/test/testdata/rta_basecalls_config_1.12.4.2.xml
new file mode 100755 (executable)
index 0000000..9da5d01
--- /dev/null
@@ -0,0 +1,511 @@
+<?xml version="1.0" encoding="utf-8"?>\r
+<BaseCallAnalysis xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:xsd="http://www.w3.org/2001/XMLSchema">\r
+  <Run Name="BaseCalls">\r
+    <BaseCallParameters>\r
+      <ChastityThreshold>0.6</ChastityThreshold>\r
+      <Matrix Path="">\r
+        <AutoFlag>2</AutoFlag>\r
+        <AutoLane>0</AutoLane>\r
+        <Cycle>1</Cycle>\r
+        <CycleOffset>0</CycleOffset>\r
+        <FirstCycle>1</FirstCycle>\r
+        <LastCycle>50</LastCycle>\r
+        <Read>1</Read>\r
+      </Matrix>\r
+      <Matrix Path="">\r
+        <AutoFlag>2</AutoFlag>\r
+        <AutoLane>0</AutoLane>\r
+        <Cycle>51</Cycle>\r
+        <CycleOffset>0</CycleOffset>\r
+        <FirstCycle>51</FirstCycle>\r
+        <LastCycle>57</LastCycle>\r
+        <Read>2</Read>\r
+      </Matrix>\r
+      <Phasing Path="">\r
+        <AutoFlag>2</AutoFlag>\r
+        <AutoLane>0</AutoLane>\r
+        <Cycle>2</Cycle>\r
+        <CycleOffset>1</CycleOffset>\r
+        <FirstCycle>1</FirstCycle>\r
+        <LastCycle>50</LastCycle>\r
+        <Read>1</Read>\r
+        <PhasingRate>0</PhasingRate>\r
+        <PrephasingRate>0</PrephasingRate>\r
+      </Phasing>\r
+      <Phasing Path="">\r
+        <AutoFlag>2</AutoFlag>\r
+        <AutoLane>0</AutoLane>\r
+        <Cycle>52</Cycle>\r
+        <CycleOffset>1</CycleOffset>\r
+        <FirstCycle>51</FirstCycle>\r
+        <LastCycle>57</LastCycle>\r
+        <Read>2</Read>\r
+        <PhasingRate>0</PhasingRate>\r
+        <PrephasingRate>0</PrephasingRate>\r
+      </Phasing>\r
+      <PureBases>0</PureBases>\r
+      <SmtFilter>failed-chastity</SmtFilter>\r
+      <SmtRelation>le</SmtRelation>\r
+      <SmtThreshold>1.0</SmtThreshold>\r
+    </BaseCallParameters>\r
+    <Cycles First="1" Last="57" Number="57" />\r
+    <Input />\r
+    <RunParameters>\r
+      <AutoCycleFlag>0</AutoCycleFlag>\r
+      <BasecallFlag>0</BasecallFlag>\r
+      <Deblocked>0</Deblocked>\r
+      <DebugFlag>0</DebugFlag>\r
+      <FirstRunOnlyFlag>0</FirstRunOnlyFlag>\r
+      <ImagingReads Index="1">\r
+        <FirstCycle>1</FirstCycle>\r
+        <LastCycle>50</LastCycle>\r
+      </ImagingReads>\r
+      <ImagingReads Index="2">\r
+        <FirstCycle>51</FirstCycle>\r
+        <LastCycle>57</LastCycle>\r
+        <RunFolder>110815_SN787_0101_AD07K6ACXX</RunFolder>\r
+      </ImagingReads>\r
+      <Instrument>HWI-ST0787</Instrument>\r
+      <IterativeMatrixFlag>0</IterativeMatrixFlag>\r
+      <MakeFlag>0</MakeFlag>\r
+      <MaxCycle>0</MaxCycle>\r
+      <MinCycle>0</MinCycle>\r
+      <Reads Index="1">\r
+        <FirstCycle>1</FirstCycle>\r
+        <LastCycle>50</LastCycle>\r
+      </Reads>\r
+      <Reads Index="2">\r
+        <FirstCycle>51</FirstCycle>\r
+        <LastCycle>57</LastCycle>\r
+        <RunFolder>110815_SN787_0101_AD07K6ACXX</RunFolder>\r
+      </Reads>\r
+      <RunFolder>110815_SN787_0101_AD07K6ACXX</RunFolder>\r
+      <RunFolderDate>110815</RunFolderDate>\r
+      <RunFolderId>0101</RunFolderId>\r
+      <RunFlowcellId>D07K6ACXX</RunFlowcellId>\r
+      <Barcode>\r
+        <Cycle Use="true">51</Cycle>\r
+        <Cycle Use="true">52</Cycle>\r
+        <Cycle Use="true">53</Cycle>\r
+        <Cycle Use="true">54</Cycle>\r
+        <Cycle Use="true">55</Cycle>\r
+        <Cycle Use="true">56</Cycle>\r
+        <Cycle Use="true">57</Cycle>\r
+      </Barcode>\r
+      <QTableVersion>New6</QTableVersion>\r
+    </RunParameters>\r
+    <Software Name="RTA" Version="1.12.4.2" />\r
+    <TileSelection>\r
+      <Lane Index="1">\r
+        <Sample>s</Sample>\r
+        <Tile>1102</Tile>\r
+        <Tile>1101</Tile>\r
+        <Tile>1103</Tile>\r
+        <Tile>1106</Tile>\r
+        <Tile>1104</Tile>\r
+        <Tile>1105</Tile>\r
+        <Tile>1108</Tile>\r
+        <Tile>1107</Tile>\r
+        <Tile>1202</Tile>\r
+        <Tile>1201</Tile>\r
+        <Tile>1206</Tile>\r
+        <Tile>1204</Tile>\r
+        <Tile>1203</Tile>\r
+        <Tile>1205</Tile>\r
+        <Tile>1302</Tile>\r
+        <Tile>1208</Tile>\r
+        <Tile>1207</Tile>\r
+        <Tile>1301</Tile>\r
+        <Tile>1306</Tile>\r
+        <Tile>1304</Tile>\r
+        <Tile>1305</Tile>\r
+        <Tile>2102</Tile>\r
+        <Tile>1303</Tile>\r
+        <Tile>1308</Tile>\r
+        <Tile>2101</Tile>\r
+        <Tile>1307</Tile>\r
+        <Tile>2106</Tile>\r
+        <Tile>2104</Tile>\r
+        <Tile>2105</Tile>\r
+        <Tile>2103</Tile>\r
+        <Tile>2202</Tile>\r
+        <Tile>2108</Tile>\r
+        <Tile>2201</Tile>\r
+        <Tile>2206</Tile>\r
+        <Tile>2107</Tile>\r
+        <Tile>2205</Tile>\r
+        <Tile>2204</Tile>\r
+        <Tile>2203</Tile>\r
+        <Tile>2302</Tile>\r
+        <Tile>2301</Tile>\r
+        <Tile>2208</Tile>\r
+        <Tile>2306</Tile>\r
+        <Tile>2207</Tile>\r
+        <Tile>2305</Tile>\r
+        <Tile>2303</Tile>\r
+        <Tile>2304</Tile>\r
+        <Tile>2308</Tile>\r
+        <Tile>2307</Tile>\r
+      </Lane>\r
+      <Lane Index="2">\r
+        <Sample>s</Sample>\r
+        <Tile>1101</Tile>\r
+        <Tile>1102</Tile>\r
+        <Tile>1105</Tile>\r
+        <Tile>1106</Tile>\r
+        <Tile>1104</Tile>\r
+        <Tile>1103</Tile>\r
+        <Tile>1201</Tile>\r
+        <Tile>1202</Tile>\r
+        <Tile>1108</Tile>\r
+        <Tile>1206</Tile>\r
+        <Tile>1107</Tile>\r
+        <Tile>1205</Tile>\r
+        <Tile>1302</Tile>\r
+        <Tile>1204</Tile>\r
+        <Tile>1301</Tile>\r
+        <Tile>1203</Tile>\r
+        <Tile>1208</Tile>\r
+        <Tile>1306</Tile>\r
+        <Tile>1305</Tile>\r
+        <Tile>1207</Tile>\r
+        <Tile>1304</Tile>\r
+        <Tile>2101</Tile>\r
+        <Tile>2102</Tile>\r
+        <Tile>1308</Tile>\r
+        <Tile>2105</Tile>\r
+        <Tile>1303</Tile>\r
+        <Tile>2201</Tile>\r
+        <Tile>2106</Tile>\r
+        <Tile>2104</Tile>\r
+        <Tile>1307</Tile>\r
+        <Tile>2205</Tile>\r
+        <Tile>2202</Tile>\r
+        <Tile>2108</Tile>\r
+        <Tile>2206</Tile>\r
+        <Tile>2103</Tile>\r
+        <Tile>2301</Tile>\r
+        <Tile>2204</Tile>\r
+        <Tile>2208</Tile>\r
+        <Tile>2107</Tile>\r
+        <Tile>2302</Tile>\r
+        <Tile>2305</Tile>\r
+        <Tile>2304</Tile>\r
+        <Tile>2203</Tile>\r
+        <Tile>2306</Tile>\r
+        <Tile>2308</Tile>\r
+        <Tile>2207</Tile>\r
+        <Tile>2303</Tile>\r
+        <Tile>2307</Tile>\r
+      </Lane>\r
+      <Lane Index="3">\r
+        <Sample>s</Sample>\r
+        <Tile>1101</Tile>\r
+        <Tile>1102</Tile>\r
+        <Tile>1105</Tile>\r
+        <Tile>1104</Tile>\r
+        <Tile>1108</Tile>\r
+        <Tile>1106</Tile>\r
+        <Tile>1201</Tile>\r
+        <Tile>1103</Tile>\r
+        <Tile>1204</Tile>\r
+        <Tile>1202</Tile>\r
+        <Tile>1205</Tile>\r
+        <Tile>1107</Tile>\r
+        <Tile>1208</Tile>\r
+        <Tile>1206</Tile>\r
+        <Tile>1301</Tile>\r
+        <Tile>1304</Tile>\r
+        <Tile>1203</Tile>\r
+        <Tile>1302</Tile>\r
+        <Tile>1308</Tile>\r
+        <Tile>1305</Tile>\r
+        <Tile>1207</Tile>\r
+        <Tile>2101</Tile>\r
+        <Tile>2104</Tile>\r
+        <Tile>1306</Tile>\r
+        <Tile>1303</Tile>\r
+        <Tile>2102</Tile>\r
+        <Tile>2105</Tile>\r
+        <Tile>2108</Tile>\r
+        <Tile>1307</Tile>\r
+        <Tile>2106</Tile>\r
+        <Tile>2204</Tile>\r
+        <Tile>2201</Tile>\r
+        <Tile>2103</Tile>\r
+        <Tile>2208</Tile>\r
+        <Tile>2202</Tile>\r
+        <Tile>2107</Tile>\r
+        <Tile>2205</Tile>\r
+        <Tile>2301</Tile>\r
+        <Tile>2304</Tile>\r
+        <Tile>2203</Tile>\r
+        <Tile>2206</Tile>\r
+        <Tile>2207</Tile>\r
+        <Tile>2305</Tile>\r
+        <Tile>2308</Tile>\r
+        <Tile>2302</Tile>\r
+        <Tile>2303</Tile>\r
+        <Tile>2307</Tile>\r
+        <Tile>2306</Tile>\r
+      </Lane>\r
+      <Lane Index="4">\r
+        <Sample>s</Sample>\r
+        <Tile>1101</Tile>\r
+        <Tile>1104</Tile>\r
+        <Tile>1103</Tile>\r
+        <Tile>1102</Tile>\r
+        <Tile>1108</Tile>\r
+        <Tile>1105</Tile>\r
+        <Tile>1107</Tile>\r
+        <Tile>1106</Tile>\r
+        <Tile>1204</Tile>\r
+        <Tile>1201</Tile>\r
+        <Tile>1203</Tile>\r
+        <Tile>1202</Tile>\r
+        <Tile>1208</Tile>\r
+        <Tile>1205</Tile>\r
+        <Tile>1207</Tile>\r
+        <Tile>1206</Tile>\r
+        <Tile>1304</Tile>\r
+        <Tile>1301</Tile>\r
+        <Tile>1302</Tile>\r
+        <Tile>1308</Tile>\r
+        <Tile>1303</Tile>\r
+        <Tile>1305</Tile>\r
+        <Tile>1306</Tile>\r
+        <Tile>1307</Tile>\r
+        <Tile>2104</Tile>\r
+        <Tile>2101</Tile>\r
+        <Tile>2108</Tile>\r
+        <Tile>2102</Tile>\r
+        <Tile>2103</Tile>\r
+        <Tile>2105</Tile>\r
+        <Tile>2204</Tile>\r
+        <Tile>2106</Tile>\r
+        <Tile>2107</Tile>\r
+        <Tile>2201</Tile>\r
+        <Tile>2208</Tile>\r
+        <Tile>2202</Tile>\r
+        <Tile>2203</Tile>\r
+        <Tile>2304</Tile>\r
+        <Tile>2205</Tile>\r
+        <Tile>2206</Tile>\r
+        <Tile>2207</Tile>\r
+        <Tile>2308</Tile>\r
+        <Tile>2301</Tile>\r
+        <Tile>2302</Tile>\r
+        <Tile>2303</Tile>\r
+        <Tile>2305</Tile>\r
+        <Tile>2307</Tile>\r
+        <Tile>2306</Tile>\r
+      </Lane>\r
+      <Lane Index="5">\r
+        <Sample>s</Sample>\r
+        <Tile>1104</Tile>\r
+        <Tile>1108</Tile>\r
+        <Tile>1101</Tile>\r
+        <Tile>1204</Tile>\r
+        <Tile>1102</Tile>\r
+        <Tile>1103</Tile>\r
+        <Tile>1106</Tile>\r
+        <Tile>1105</Tile>\r
+        <Tile>1107</Tile>\r
+        <Tile>1208</Tile>\r
+        <Tile>1201</Tile>\r
+        <Tile>1202</Tile>\r
+        <Tile>1203</Tile>\r
+        <Tile>1304</Tile>\r
+        <Tile>1205</Tile>\r
+        <Tile>1206</Tile>\r
+        <Tile>1301</Tile>\r
+        <Tile>1308</Tile>\r
+        <Tile>1207</Tile>\r
+        <Tile>1302</Tile>\r
+        <Tile>2104</Tile>\r
+        <Tile>1303</Tile>\r
+        <Tile>1305</Tile>\r
+        <Tile>1306</Tile>\r
+        <Tile>2101</Tile>\r
+        <Tile>2102</Tile>\r
+        <Tile>1307</Tile>\r
+        <Tile>2108</Tile>\r
+        <Tile>2204</Tile>\r
+        <Tile>2103</Tile>\r
+        <Tile>2105</Tile>\r
+        <Tile>2107</Tile>\r
+        <Tile>2106</Tile>\r
+        <Tile>2201</Tile>\r
+        <Tile>2208</Tile>\r
+        <Tile>2203</Tile>\r
+        <Tile>2202</Tile>\r
+        <Tile>2304</Tile>\r
+        <Tile>2206</Tile>\r
+        <Tile>2205</Tile>\r
+        <Tile>2207</Tile>\r
+        <Tile>2302</Tile>\r
+        <Tile>2301</Tile>\r
+        <Tile>2303</Tile>\r
+        <Tile>2308</Tile>\r
+        <Tile>2305</Tile>\r
+        <Tile>2307</Tile>\r
+        <Tile>2306</Tile>\r
+      </Lane>\r
+      <Lane Index="6">\r
+        <Sample>s</Sample>\r
+        <Tile>1104</Tile>\r
+        <Tile>1101</Tile>\r
+        <Tile>1103</Tile>\r
+        <Tile>1102</Tile>\r
+        <Tile>1108</Tile>\r
+        <Tile>1107</Tile>\r
+        <Tile>1105</Tile>\r
+        <Tile>1106</Tile>\r
+        <Tile>1204</Tile>\r
+        <Tile>1203</Tile>\r
+        <Tile>1201</Tile>\r
+        <Tile>1202</Tile>\r
+        <Tile>1208</Tile>\r
+        <Tile>1207</Tile>\r
+        <Tile>1205</Tile>\r
+        <Tile>1206</Tile>\r
+        <Tile>1304</Tile>\r
+        <Tile>1303</Tile>\r
+        <Tile>1301</Tile>\r
+        <Tile>1302</Tile>\r
+        <Tile>1308</Tile>\r
+        <Tile>1307</Tile>\r
+        <Tile>1305</Tile>\r
+        <Tile>2104</Tile>\r
+        <Tile>1306</Tile>\r
+        <Tile>2103</Tile>\r
+        <Tile>2101</Tile>\r
+        <Tile>2102</Tile>\r
+        <Tile>2108</Tile>\r
+        <Tile>2107</Tile>\r
+        <Tile>2105</Tile>\r
+        <Tile>2106</Tile>\r
+        <Tile>2204</Tile>\r
+        <Tile>2203</Tile>\r
+        <Tile>2202</Tile>\r
+        <Tile>2201</Tile>\r
+        <Tile>2208</Tile>\r
+        <Tile>2207</Tile>\r
+        <Tile>2206</Tile>\r
+        <Tile>2205</Tile>\r
+        <Tile>2304</Tile>\r
+        <Tile>2303</Tile>\r
+        <Tile>2302</Tile>\r
+        <Tile>2301</Tile>\r
+        <Tile>2307</Tile>\r
+        <Tile>2308</Tile>\r
+        <Tile>2306</Tile>\r
+        <Tile>2305</Tile>\r
+      </Lane>\r
+      <Lane Index="7">\r
+        <Sample>s</Sample>\r
+        <Tile>1103</Tile>\r
+        <Tile>1107</Tile>\r
+        <Tile>1104</Tile>\r
+        <Tile>1108</Tile>\r
+        <Tile>1203</Tile>\r
+        <Tile>1101</Tile>\r
+        <Tile>1102</Tile>\r
+        <Tile>1204</Tile>\r
+        <Tile>1105</Tile>\r
+        <Tile>1207</Tile>\r
+        <Tile>1106</Tile>\r
+        <Tile>1208</Tile>\r
+        <Tile>1201</Tile>\r
+        <Tile>1202</Tile>\r
+        <Tile>1303</Tile>\r
+        <Tile>1205</Tile>\r
+        <Tile>1206</Tile>\r
+        <Tile>1307</Tile>\r
+        <Tile>1304</Tile>\r
+        <Tile>1301</Tile>\r
+        <Tile>1302</Tile>\r
+        <Tile>1305</Tile>\r
+        <Tile>1308</Tile>\r
+        <Tile>2103</Tile>\r
+        <Tile>1306</Tile>\r
+        <Tile>2101</Tile>\r
+        <Tile>2107</Tile>\r
+        <Tile>2104</Tile>\r
+        <Tile>2105</Tile>\r
+        <Tile>2102</Tile>\r
+        <Tile>2108</Tile>\r
+        <Tile>2203</Tile>\r
+        <Tile>2201</Tile>\r
+        <Tile>2106</Tile>\r
+        <Tile>2205</Tile>\r
+        <Tile>2207</Tile>\r
+        <Tile>2202</Tile>\r
+        <Tile>2204</Tile>\r
+        <Tile>2301</Tile>\r
+        <Tile>2303</Tile>\r
+        <Tile>2206</Tile>\r
+        <Tile>2208</Tile>\r
+        <Tile>2305</Tile>\r
+        <Tile>2307</Tile>\r
+        <Tile>2302</Tile>\r
+        <Tile>2304</Tile>\r
+        <Tile>2306</Tile>\r
+        <Tile>2308</Tile>\r
+      </Lane>\r
+      <Lane Index="8">\r
+        <Sample>s</Sample>\r
+        <Tile>1101</Tile>\r
+        <Tile>1103</Tile>\r
+        <Tile>1102</Tile>\r
+        <Tile>1105</Tile>\r
+        <Tile>1107</Tile>\r
+        <Tile>1104</Tile>\r
+        <Tile>1106</Tile>\r
+        <Tile>1201</Tile>\r
+        <Tile>1108</Tile>\r
+        <Tile>1203</Tile>\r
+        <Tile>1202</Tile>\r
+        <Tile>1205</Tile>\r
+        <Tile>1207</Tile>\r
+        <Tile>1204</Tile>\r
+        <Tile>1206</Tile>\r
+        <Tile>1301</Tile>\r
+        <Tile>1208</Tile>\r
+        <Tile>1303</Tile>\r
+        <Tile>1302</Tile>\r
+        <Tile>1305</Tile>\r
+        <Tile>1307</Tile>\r
+        <Tile>1304</Tile>\r
+        <Tile>1306</Tile>\r
+        <Tile>2101</Tile>\r
+        <Tile>1308</Tile>\r
+        <Tile>2103</Tile>\r
+        <Tile>2105</Tile>\r
+        <Tile>2102</Tile>\r
+        <Tile>2107</Tile>\r
+        <Tile>2106</Tile>\r
+        <Tile>2104</Tile>\r
+        <Tile>2201</Tile>\r
+        <Tile>2205</Tile>\r
+        <Tile>2202</Tile>\r
+        <Tile>2203</Tile>\r
+        <Tile>2108</Tile>\r
+        <Tile>2206</Tile>\r
+        <Tile>2301</Tile>\r
+        <Tile>2207</Tile>\r
+        <Tile>2204</Tile>\r
+        <Tile>2305</Tile>\r
+        <Tile>2302</Tile>\r
+        <Tile>2303</Tile>\r
+        <Tile>2208</Tile>\r
+        <Tile>2306</Tile>\r
+        <Tile>2307</Tile>\r
+        <Tile>2304</Tile>\r
+        <Tile>2308</Tile>\r
+      </Lane>\r
+    </TileSelection>\r
+    <Time />\r
+    <User />\r
+  </Run>\r
+</BaseCallAnalysis>
\ No newline at end of file
diff --git a/htsworkflow/pipelines/test/testdata/rta_intensities_config_1.12.4.2.xml b/htsworkflow/pipelines/test/testdata/rta_intensities_config_1.12.4.2.xml
new file mode 100755 (executable)
index 0000000..6d43157
--- /dev/null
@@ -0,0 +1,472 @@
+<?xml version="1.0" encoding="utf-8"?>\r
+<ImageAnalysis xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:xsd="http://www.w3.org/2001/XMLSchema">\r
+  <Run Name="Intensities">\r
+    <Cycles First="1" Last="57" Number="57" />\r
+    <ImageParameters>\r
+      <AutoOffsetFlag>0</AutoOffsetFlag>\r
+      <AutoSizeFlag>0</AutoSizeFlag>\r
+      <Fwhm>0</Fwhm>\r
+      <RemappingDistance>0</RemappingDistance>\r
+      <Threshold>0</Threshold>\r
+    </ImageParameters>\r
+    <RunParameters>\r
+      <AutoCycleFlag>0</AutoCycleFlag>\r
+      <BasecallFlag>0</BasecallFlag>\r
+      <Deblocked>0</Deblocked>\r
+      <DebugFlag>0</DebugFlag>\r
+      <FirstRunOnlyFlag>0</FirstRunOnlyFlag>\r
+      <ImagingReads Index="1">\r
+        <FirstCycle>1</FirstCycle>\r
+        <LastCycle>50</LastCycle>\r
+        <RunFolder>110815_SN787_0101_AD07K6ACXX</RunFolder>\r
+      </ImagingReads>\r
+      <ImagingReads Index="2">\r
+        <FirstCycle>51</FirstCycle>\r
+        <LastCycle>57</LastCycle>\r
+        <RunFolder>110815_SN787_0101_AD07K6ACXX</RunFolder>\r
+      </ImagingReads>\r
+      <Instrument>HWI-ST0787</Instrument>\r
+      <IterativeMatrixFlag>0</IterativeMatrixFlag>\r
+      <MakeFlag>0</MakeFlag>\r
+      <MaxCycle>0</MaxCycle>\r
+      <MinCycle>0</MinCycle>\r
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+        <FirstCycle>1</FirstCycle>\r
+        <LastCycle>50</LastCycle>\r
+        <RunFolder>110815_SN787_0101_AD07K6ACXX</RunFolder>\r
+      </Reads>\r
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+        <FirstCycle>51</FirstCycle>\r
+        <LastCycle>57</LastCycle>\r
+        <RunFolder>110815_SN787_0101_AD07K6ACXX</RunFolder>\r
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+      <RunFolder>110815_SN787_0101_AD07K6ACXX</RunFolder>\r
+      <RunFolderDate>110815</RunFolderDate>\r
+      <RunFolderId>0101</RunFolderId>\r
+      <RunFlowcellId>D07K6ACXX</RunFlowcellId>\r
+      <Barcode>\r
+        <Cycle Use="true">51</Cycle>\r
+        <Cycle Use="true">52</Cycle>\r
+        <Cycle Use="true">53</Cycle>\r
+        <Cycle Use="true">54</Cycle>\r
+        <Cycle Use="true">55</Cycle>\r
+        <Cycle Use="true">56</Cycle>\r
+        <Cycle Use="true">57</Cycle>\r
+      </Barcode>\r
+      <QTableVersion>New6</QTableVersion>\r
+    </RunParameters>\r
+    <Software Name="RTA" Version="1.12.4.2" />\r
+    <TileSelection>\r
+      <Lane Index="1">\r
+        <Sample>s</Sample>\r
+        <Tile>1101</Tile>\r
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+      </Lane>\r
+      <Lane Index="2">\r
+        <Sample>s</Sample>\r
+        <Tile>1101</Tile>\r
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+      </Lane>\r
+      <Lane Index="3">\r
+        <Sample>s</Sample>\r
+        <Tile>1101</Tile>\r
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+        <Tile>2308</Tile>\r
+        <Tile>2307</Tile>\r
+      </Lane>\r
+      <Lane Index="4">\r
+        <Sample>s</Sample>\r
+        <Tile>1101</Tile>\r
+        <Tile>1105</Tile>\r
+        <Tile>1201</Tile>\r
+        <Tile>1102</Tile>\r
+        <Tile>1106</Tile>\r
+        <Tile>1205</Tile>\r
+        <Tile>1104</Tile>\r
+        <Tile>1202</Tile>\r
+        <Tile>1103</Tile>\r
+        <Tile>1301</Tile>\r
+        <Tile>1206</Tile>\r
+        <Tile>1108</Tile>\r
+        <Tile>1107</Tile>\r
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+        <Tile>1203</Tile>\r
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+        <Tile>1307</Tile>\r
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+        <Tile>2202</Tile>\r
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+        <Tile>2108</Tile>\r
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+        <Tile>2107</Tile>\r
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+        <Tile>2204</Tile>\r
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+        <Tile>2208</Tile>\r
+        <Tile>2207</Tile>\r
+        <Tile>2303</Tile>\r
+        <Tile>2304</Tile>\r
+        <Tile>2308</Tile>\r
+        <Tile>2307</Tile>\r
+      </Lane>\r
+      <Lane Index="5">\r
+        <Sample>s</Sample>\r
+        <Tile>1102</Tile>\r
+        <Tile>1101</Tile>\r
+        <Tile>1106</Tile>\r
+        <Tile>1105</Tile>\r
+        <Tile>1202</Tile>\r
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+        <Tile>2304</Tile>\r
+        <Tile>2308</Tile>\r
+      </Lane>\r
+      <Lane Index="6">\r
+        <Sample>s</Sample>\r
+        <Tile>1101</Tile>\r
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+        <Tile>1103</Tile>\r
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+        <Tile>2308</Tile>\r
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+      <Lane Index="7">\r
+        <Sample>s</Sample>\r
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+        <Tile>2304</Tile>\r
+        <Tile>2308</Tile>\r
+      </Lane>\r
+      <Lane Index="8">\r
+        <Sample>s</Sample>\r
+        <Tile>1101</Tile>\r
+        <Tile>1102</Tile>\r
+        <Tile>1105</Tile>\r
+        <Tile>1106</Tile>\r
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+        <Tile>1208</Tile>\r
+        <Tile>1304</Tile>\r
+        <Tile>1308</Tile>\r
+        <Tile>2104</Tile>\r
+        <Tile>2108</Tile>\r
+        <Tile>2204</Tile>\r
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+        <Tile>2304</Tile>\r
+        <Tile>2308</Tile>\r
+      </Lane>\r
+    </TileSelection>\r
+    <Time />\r
+    <User />\r
+  </Run>\r
+</ImageAnalysis>
\ No newline at end of file
diff --git a/htsworkflow/pipelines/test/testdata/sample_summary_1_12.htm b/htsworkflow/pipelines/test/testdata/sample_summary_1_12.htm
new file mode 100644 (file)
index 0000000..468f72d
--- /dev/null
@@ -0,0 +1,434 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<html xmlns:casava="http://www.illumina.com/casava/alignment">
+<link rel="stylesheet" href="../../css/Reports.css" type="text/css">
+<body>
+<p>Sample Summary Information For Experiment (12564_index6)</p>
+<p>Project Summary</p>
+<table border="1" cellpadding="5">
+<tr>
+<td>Project Name</td>
+<td>12564_index6</td>
+</tr>
+<tr>
+<td>Machine</td>
+<td>HWI-ST0787</td>
+</tr>
+<tr>
+<td>Run Folder</td>
+<td>111221_SN787_0107_AD0CV5ACXX</td>
+</tr>
+<tr>
+<td>Flow Cell ID</td>
+<td>D0CV5ACXX</td>
+</tr>
+<tr>
+<td>Platform</td>
+<td></td>
+</tr>
+<tr>
+<td>Control Software</td>
+<td>HiSeq Control Software 1.4.8</td>
+</tr>
+<tr>
+<td>Primary Analysis</td>
+<td>RTA 1.12.4.2</td>
+</tr>
+<tr>
+<td>Secondary Analysis</td>
+<td>CASAVA-1.8.1</td>
+</tr>
+</table>
+<p>Project Results Summary</p>
+<table border="1" cellpadding="5">
+<tr>
+<th>Clusters (Raw)</th>
+<th>Clusters(PF)</th>
+<th>Yield (MBases)</th>
+</tr>
+<tr>
+<td>658,174</td>
+<td>475,618</td>
+<td>23</td>
+</tr>
+</table>
+<p>Barcode-Lane summary</p>
+<div ID="ScrollableTableHeaderDiv"><table width="100%">
+<col>
+<col width="8%">
+<col width="10%">
+<col width="4%">
+<col width="20%">
+<col width="6%">
+<col width="6%">
+<col width="4%">
+<col width="30%">
+<tr>
+<th>Barcode-Lane</th>
+<th>Sample</th>
+<th>Barcode</th>
+<th>Lane</th>
+<th>Species</th>
+<th>Analysis Type</th>
+<th>Length</th>
+<th>Num Tiles</th>
+<th>Genome Directory</th>
+</tr>
+</table></div>
+<div ID="ScrollableTableBodyDiv"><table width="100%">
+<col>
+<col width="8%">
+<col width="10%">
+<col width="4%">
+<col width="20%">
+<col width="6%">
+<col width="6%">
+<col width="4%">
+<col width="30%">
+<tr>
+<td>12564_GCCAAT_L5</td>
+<td>12564</td>
+<td>GCCAAT</td>
+<td>5</td>
+<td>Homo_sapiens</td>
+<td>eland extended</td>
+<td>49 </td>
+<td>48</td>
+<td>/mmjggl/nicodemus/data01/genomes/hg18/chromosomes//*.fa</td>
+</tr>
+</table></div>
+<p>Sample Results Summary : Read 1</p>
+<div ID="ScrollableTableHeaderDiv"><table width="100%">
+<col>
+<col width="7%">
+<col width="8%">
+<col width="8%">
+<col width="12%">
+<col width="12%">
+<col width="8%">
+<col width="7%">
+<col width="9%">
+<col width="8%">
+<col width="6%">
+<col width="6%">
+<tr><th colspan="12">Sample Info</th></tr>
+<tr>
+<th>Sample</th>
+<th>Sample Yield (Mbases)</th>
+<th>Clusters (raw)</th>
+<th>Clusters (PF)</th>
+<th>1st Cycle Int (PF)</th>
+<th>% intensity after 20 cycles (PF)</th>
+<th>% PF Clusters</th>
+<th>% Align (PF)</th>
+<th>Alignment Score (PF)</th>
+<th>% Mismatch Rate (PF)</th>
+<th>% &gt;=Q30 bases (PF)</th>
+<th>Mean Quality SCore (PF)</th>
+</tr>
+</table></div>
+<div ID="ScrollableTableBodyDiv"><table width="100%">
+<col>
+<col width="7%">
+<col width="8%">
+<col width="8%">
+<col width="12%">
+<col width="12%">
+<col width="8%">
+<col width="7%">
+<col width="9%">
+<col width="8%">
+<col width="6%">
+<col width="6%">
+<tr>
+<td>12564</td>
+<td>23</td>
+<td>658,174</td>
+<td>475,618</td>
+<td>1100</td>
+<td>89.39</td>
+<td>72.26</td>
+<td>76.89</td>
+<td>128.73</td>
+<td>0.40</td>
+<td>88.79</td>
+<td>35.13</td>
+</tr>
+</table></div>
+<p>Sample Results Summary : Read 2</p>
+<div ID="ScrollableTableHeaderDiv"><table width="100%">
+<col>
+<col width="7%">
+<col width="8%">
+<col width="8%">
+<col width="12%">
+<col width="12%">
+<col width="8%">
+<col width="7%">
+<col width="9%">
+<col width="8%">
+<col width="6%">
+<col width="6%">
+<tr><th colspan="12">Sample Info</th></tr>
+<tr>
+<th>Sample</th>
+<th>Sample Yield (Mbases)</th>
+<th>Clusters (raw)</th>
+<th>Clusters (PF)</th>
+<th>1st Cycle Int (PF)</th>
+<th>% intensity after 20 cycles (PF)</th>
+<th>% PF Clusters</th>
+<th>% Align (PF)</th>
+<th>Alignment Score (PF)</th>
+<th>% Mismatch Rate (PF)</th>
+<th>% &gt;=Q30 bases (PF)</th>
+<th>Mean Quality SCore (PF)</th>
+</tr>
+</table></div>
+<div ID="ScrollableTableBodyDiv"><table width="100%">
+<col>
+<col width="7%">
+<col width="8%">
+<col width="8%">
+<col width="12%">
+<col width="12%">
+<col width="8%">
+<col width="7%">
+<col width="9%">
+<col width="8%">
+<col width="6%">
+<col width="6%">
+<tr>
+<td>12564</td>
+<td>0</td>
+<td>0</td>
+<td>0</td>
+<td>0</td>
+<td>0</td>
+<td></td>
+<td></td>
+<td></td>
+<td></td>
+<td></td>
+<td></td>
+</tr>
+</table></div>
+<p>Expanded Sample Summary : Read 1</p>
+<div ID="ScrollableTableHeaderDiv"><table width="100%">
+<col>
+<col width="7%">
+<col width="8%">
+<col width="8%">
+<col width="8%">
+<col width="6%">
+<col width="10%">
+<col width="10%">
+<col width="9%">
+<col width="5%">
+<col width="8%">
+<col width="6%">
+<col width="6%">
+<tr>
+<th colspan="2">Sample Info</th>
+<th colspan="2">Phasing Info</th>
+<th colspan="1">Raw data</th>
+<th colspan="8">Filtered data</th>
+</tr>
+<tr>
+<th>Sample</th>
+<th>Clusters (raw)</th>
+<th>% Phasing</th>
+<th>% Prephasing</th>
+<th>% Mismatch Rate (raw)</th>
+<th>% PF Clusters</th>
+<th>Cycle 2-4 Av Int (PF)</th>
+<th>Cycle 2-10 Av % Loss (PF)</th>
+<th>Cycle 10-20 Av % Loss (PF)</th>
+<th>% Align (PF)</th>
+<th>% Mismatch Rate (PF)</th>
+<th>% &gt;=Q30 bases (PF)</th>
+<th>Mean Quality SCore (PF)</th>
+</tr>
+</table></div>
+<div ID="ScrollableTableBodyDiv"><table width="100%">
+<col>
+<col width="7%">
+<col width="8%">
+<col width="8%">
+<col width="8%">
+<col width="6%">
+<col width="10%">
+<col width="10%">
+<col width="9%">
+<col width="5%">
+<col width="8%">
+<col width="6%">
+<col width="6%">
+<tr>
+<td>12564</td>
+<td>658,174</td>
+<td>0.19</td>
+<td>0.31</td>
+<td>0.77</td>
+<td>72.26</td>
+<td>1083.00</td>
+<td>-84.76</td>
+<td>0.48</td>
+<td>76.89</td>
+<td>0.40</td>
+<td>88.79</td>
+<td>35.13</td>
+</tr>
+</table></div>
+<p>Expanded Sample Summary : Read 2</p>
+<div ID="ScrollableTableHeaderDiv"><table width="100%">
+<col>
+<col width="7%">
+<col width="8%">
+<col width="8%">
+<col width="8%">
+<col width="6%">
+<col width="10%">
+<col width="10%">
+<col width="9%">
+<col width="5%">
+<col width="8%">
+<col width="6%">
+<col width="6%">
+<tr>
+<th colspan="2">Sample Info</th>
+<th colspan="2">Phasing Info</th>
+<th colspan="1">Raw data</th>
+<th colspan="8">Filtered data</th>
+</tr>
+<tr>
+<th>Sample</th>
+<th>Clusters (raw)</th>
+<th>% Phasing</th>
+<th>% Prephasing</th>
+<th>% Mismatch Rate (raw)</th>
+<th>% PF Clusters</th>
+<th>Cycle 2-4 Av Int (PF)</th>
+<th>Cycle 2-10 Av % Loss (PF)</th>
+<th>Cycle 10-20 Av % Loss (PF)</th>
+<th>% Align (PF)</th>
+<th>% Mismatch Rate (PF)</th>
+<th>% &gt;=Q30 bases (PF)</th>
+<th>Mean Quality SCore (PF)</th>
+</tr>
+</table></div>
+<div ID="ScrollableTableBodyDiv"><table width="100%">
+<col>
+<col width="7%">
+<col width="8%">
+<col width="8%">
+<col width="8%">
+<col width="6%">
+<col width="10%">
+<col width="10%">
+<col width="9%">
+<col width="5%">
+<col width="8%">
+<col width="6%">
+<col width="6%">
+<tr>
+<td>12564</td>
+<td>0</td>
+<td>0</td>
+<td>0</td>
+<td></td>
+<td></td>
+<td>0</td>
+<td>0</td>
+<td>0</td>
+<td></td>
+<td></td>
+<td></td>
+<td></td>
+</tr>
+</table></div>
+<p>IVC Plots</p>
+<a href="/mmjggl/nicodemus/data01/sequencer/111221_SN787_0107_AD0CV5ACXX/Unaligned/Basecall_Stats_D0CV5ACXX/IVC.htm">
+click here
+</a><p>All Intensity Plots</p>
+<a href="/mmjggl/nicodemus/data01/sequencer/111221_SN787_0107_AD0CV5ACXX/Unaligned/Basecall_Stats_D0CV5ACXX/All.htm">
+click here
+</a><p>Mismatch Graphs</p>
+<a href="FullMismatch.htm">
+click here
+</a><p>Mismatch Curves</p>
+<a href="FullPerfect.htm">
+click here
+</a><p>Additional Paired Statistics</p>
+<div ID="ScrollableTableHeaderDiv"><table width="100%">
+<col>
+<col width="7%">
+<col width="7%">
+<col width="7%">
+<col width="7%">
+<col width="6%">
+<col width="6%">
+<col width="6%">
+<col width="6%">
+<col width="6%">
+<col width="6%">
+<col width="6%">
+<col width="6%">
+<col width="9%">
+<tr>
+<th colspan="1">Sample Info</th>
+<th colspan="5">Relative Orientation Statistics</th>
+<th colspan="5">Insert Size Statistics (for relative orientation R+)</th>
+<th colspan="3">Insert Statistics (% of individually uniquely alignable pairs)</th>
+</tr>
+<tr>
+<th>Sample</th>
+<th>F-:<br>&gt;R2 R1&gt;</th>
+<th>F+:<br>&gt;R1 R2&gt;</th>
+<th>R-:<br>&lt;R2 R1&gt;</th>
+<th>R+:<br>&gt;R1 R2&lt;</th>
+<th>Total</th>
+<th>Median</th>
+<th>Below-median SD</th>
+<th>Above-median SD</th>
+<th>Low thresh.</th>
+<th>High thresh.</th>
+<th>Too small</th>
+<th>Too large</th>
+<th>Orientation and size OK</th>
+</tr>
+</table></div>
+<div ID="ScrollableTableBodyDiv"><table width="100%">
+<col>
+<col width="7%">
+<col width="7%">
+<col width="7%">
+<col width="7%">
+<col width="6%">
+<col width="6%">
+<col width="6%">
+<col width="6%">
+<col width="6%">
+<col width="6%">
+<col width="6%">
+<col width="6%">
+<col width="9%">
+<tr>
+<td>12564</td>
+<td></td>
+<td></td>
+<td></td>
+<td></td>
+<td>0</td>
+<td></td>
+<td></td>
+<td></td>
+<td></td>
+<td></td>
+<td></td>
+<td></td>
+<td></td>
+</tr>
+</table></div>
+<p>CASAVA-1.8.1</p>
+</body>
+</html>