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charles-cowartcharles-cowart
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Seqcount support (#159)
* Updates based on testing * Tellseq support added to GenPrepFileJob * update ref * Update uri * Update * Updated test data, Reverted metapool url to master
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‎sequence_processing_pipeline/Commands.py

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@@ -14,15 +14,13 @@ def split_similar_size_bins(data_location_path, max_file_list_size_in_gb,
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:param batch_prefix: Path + file-name prefix for output-files.
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:return: The number of output-files created, size of largest bin.
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'''
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# to prevent issues w/filenames like the ones below from being mistaken
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# for R1 or R2 files, use determine_orientation().
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# LS_8_22_2014_R2_SRE_S2_L007_I1_001.fastq.gz
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# LS_8_22_2014_R1_SRE_S3_L007_I1_001.fastq.gz
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# since the names of all fastq files are being scanned for orientation,
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# collect all of them instead of mistakenly pre-filtering some files.
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# fastq_paths = glob.glob(data_location_path + '/*/*_R?_*.fastq.gz')
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fastq_paths = glob.glob(data_location_path + '/*/*.fastq.gz')
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fastq_paths = [x for x in fastq_paths
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if determine_orientation(x) in ['R1', 'R2']]

‎sequence_processing_pipeline/tests/data/SeqCounts.csv

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Sample_ID,raw_reads_r1r2,Lane
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LS_8_22_2014_R1_SRE,140798056,1
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LS_8_22_2014_R2_SRE,128928324,1
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Test_8_22_2014_R1_example,140798056,4
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Test_8_22_2014_R2_example,128928324,4

‎sequence_processing_pipeline/tests/data/seq_counts_logs/seq_count_2679966_1.err

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This is an example .err file produced by seq_counts.sbatch.
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+ seqtk size REMOVED/working_dir/8edbdee2-da52-4278-af40-267185bbcd7e/TRIntegrateJob/integrated/Test_8_22_2014_R2_example_S2_L007_R1_001.fastq.gz

‎sequence_processing_pipeline/tests/data/seq_counts_logs/seq_count_2679966_1.out

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‎sequence_processing_pipeline/tests/data/seq_counts_logs/seq_count_2679966_2.err

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This is an example .err file produced by seq_counts.sbatch.
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‎sequence_processing_pipeline/tests/data/seq_counts_logs/seq_count_2679966_2.out

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‎sequence_processing_pipeline/tests/data/seq_counts_logs/seq_count_2679966_4.err

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This is an example .err file produced by seq_counts.sbatch.
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‎sequence_processing_pipeline/tests/data/seq_counts_logs/seq_count_2679966_4.out

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‎sequence_processing_pipeline/tests/data/seq_counts_logs/seq_count_2679966_5.err

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‎sequence_processing_pipeline/tests/data/seq_counts_logs/seq_count_2679966_5.out

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