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Polya trimming correction

Merged Polya trimming correction
polya_trimming_correction into master
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Merged BIOPZ-Katsantoni Maria requested to merge polya_trimming_correction into master
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tests/input_files/samples.tsv
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sample seqmode fq1 index_size kmer fq2 fq1_3p fq1_5p fq2_3p fq2_5p organism gtf gtf_filtered genome tr_fasta_filtered sd mean multimappers soft_clip pass_mode libtype kallisto_directionality fq1_polya fq2_polya
synthetic_10_reads_paired_synthetic_10_reads_paired paired_end ../input_files/project1/synthetic.mate_1.fastq.gz 75 31 ../input_files/project1/synthetic.mate_2.fastq.gz AGATCGGAAGAGCACA XXXXXXXXXXXXX AGATCGGAAGAGCGT XXXXXXXXXXXXX homo_sapiens ../input_files/homo_sapiens/annotation.gtf ../input_files/homo_sapiens/annotation.gtf ../input_files/homo_sapiens/genome.fa ../input_files/homo_sapiens/transcriptome.fa 100 250 10 EndToEnd None A --fr AAAAAAAAAAAAAAAAA TTTTTTTTTTTTTTTTT
synthetic_10_reads_mate_1_synthetic_10_reads_mate_1 single_end ../input_files/project2/synthetic.mate_1.fastq.gz 75 31 XXXXXXXXXXXXX AGATCGGAAGAGCACA XXXXXXXXXXXXX XXXXXXXXXXXXX XXXXXXXXXXXXX homo_sapiens ../input_files/homo_sapiens/annotation.gtf ../input_files/homo_sapiens/annotation.gtf ../input_files/homo_sapiens/genome.fa ../input_files/homo_sapiens/transcriptome.fa 100 250 10 EndToEnd None A --fr AAAAAAAAAAAAAAAAA XXXXXXXXXXXXX
sample seqmode fq1 index_size kmer fq1_3p fq1_5p organism gtf gtf_filtered genome tr_fasta_filtered sd mean multimappers soft_clip pass_mode libtype fq1_polya_3p fq1_polya_5p kallisto_directionality fq2 fq2_3p fq2_5p fq2_polya_3p fq2_polya_5p
synthetic_10_reads_paired_synthetic_10_reads_paired paired_end ../input_files/project1/synthetic.mate_1.fastq.gz 75 31 AGATCGGAAGAGCACA XXXXXXXXXXXXX homo_sapiens ../input_files/homo_sapiens/annotation.gtf ../input_files/homo_sapiens/annotation.gtf ../input_files/homo_sapiens/genome.fa ../input_files/homo_sapiens/transcriptome.fa 100 250 10 EndToEnd None A AAAAAAAAAAAAAAAAA XXXXXXXXXXXXXXXXX --fr ../input_files/project1/synthetic.mate_2.fastq.gz AGATCGGAAGAGCGT XXXXXXXXXXXXX XXXXXXXXXXXXXXXXX TTTTTTTTTTTTTTTTT
synthetic_10_reads_mate_1_synthetic_10_reads_mate_1 single_end ../input_files/project2/synthetic.mate_1.fastq.gz 75 31 AGATCGGAAGAGCACA XXXXXXXXXXXXX homo_sapiens ../input_files/homo_sapiens/annotation.gtf ../input_files/homo_sapiens/annotation.gtf ../input_files/homo_sapiens/genome.fa ../input_files/homo_sapiens/transcriptome.fa 100 250 10 EndToEnd None A AAAAAAAAAAAAAAAAA XXXXXXXXXXXXXXXXX --fr XXXXXXXXXXXXX XXXXXXXXXXXXX XXXXXXXXXXXXX XXXXXXXXXXXXX XXXXXXXXXXXXX