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Maintenance - Mise à jour mensuelle Lundi 6 Février entre 7h00 et 9h00

  • genotoul-bioinfo
  • ng6ng6
  • Issues
  • #134
Closed
Open
Issue created Oct 14, 2019 by Claire Kuchly@ckuchlyMaintainer

Debug about add index files in sample definition

with the definition with index files for 10X analysis, error in illumina_qc launched.

in src/ng6/ng6workflow.py

def __preprocess_samples__(self):
        samples_ids = []
        pidx = 1
        nidx = 1
        for index, sample in enumerate(self.samples) :
            if sample.name :
                self.samples_names.append(sample.name)
            else :
                sample.name = 'SAMPLE_' + str(nidx)
                nidx += 1

            if sample.sample_id :
                if sample.sample_id in samples_ids :
                    display_error_message( "Sample identifier %s must be uniq ( sample %s ).\n" % sample.sample_id, sample.name )
            # add an automatic id for samples
            else :
                sample.sample_id = 'sample_' + str(pidx)
                pidx += 1
            samples_ids.append(sample.sample_id)

            for rfile in sample.reads1 :
                self.reads1_indexes.append(sample.sample_id)
                self.reads1.append(rfile)

            for rfile in sample.reads2 :
                self.reads2_indexes.append(sample.sample_id)
                self.reads2.append(rfile)
                
            **for rfile in sample.index :
                self.index.append(rfile)**
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