diff --git a/tests/input_files/samples.tsv b/tests/input_files/samples.tsv index cc0ec82c5caa7d5b7fa0618e80260bc6f2676b92..d7ff5bba2366cb611105b667a45815b0d9dd3902 100644 --- a/tests/input_files/samples.tsv +++ b/tests/input_files/samples.tsv @@ -1,3 +1,3 @@ -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 diff --git a/tests/test_integration_workflow/expected_output.md5 b/tests/test_integration_workflow/expected_output.md5 index c017ef0deadeaa12bed607aa1ad25075b6a40732..5abe366507bcb7618106454ce18de9422140805c 100644 --- a/tests/test_integration_workflow/expected_output.md5 +++ b/tests/test_integration_workflow/expected_output.md5 @@ -19,7 +19,7 @@ ea36f062eedc7f54ceffea2b635a25a8 results/star_indexes/homo_sapiens/75/STAR_inde 500dd49da40b16799aba62aa5cf239ba results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.remove_adapters_mate1.fastq e90e31db1ce51d930645eb74ff70d21b results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.remove_adapters_mate2.fastq 500dd49da40b16799aba62aa5cf239ba results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.remove_polya_mate1.fastq -e90e31db1ce51d930645eb74ff70d21b results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.remove_polya_mate2.fastq +1c0796d7e0bdab0e99780b2e11d80c19 results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.remove_polya_mate2.fastq d41d8cd98f00b204e9800998ecf8427e results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/map_genome/synthetic_10_reads_paired_synthetic_10_reads_paired_SJ.out.tab 6c5d2ffd046e24384a7557aa9be0fdfd results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/mate1_fastqc/synthetic.mate_1_fastqc/fastqc_data.txt c0df759ceab72ea4b1a560f991fe6497 results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/mate1_fastqc/synthetic.mate_1_fastqc/fastqc.fo @@ -45,8 +45,8 @@ b28aac49f537b8cba364b6422458ad28 results/paired_end/synthetic_10_reads_paired_s 69b70e3f561b749bf10b186dd2480a8a results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/mate2_fastqc/synthetic.mate_2_fastqc/Images/per_sequence_quality.png b28aac49f537b8cba364b6422458ad28 results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/mate2_fastqc/synthetic.mate_2_fastqc/Images/per_tile_quality.png 5b950b5dfe3c7407e9aac153db330a38 results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/mate2_fastqc/synthetic.mate_2_fastqc/Images/sequence_length_distribution.png -5e07e870d516a91647808bd84068d829 results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/quant_kallisto/abundance.tsv -6180a904511292b0f173794ae98af991 results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/quant_kallisto/pseudoalignments.bam +2e77276535976efccb244627231624bf results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/quant_kallisto/abundance.tsv +d013650f813b815a790c9e6a51c7559b results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/quant_kallisto/pseudoalignments.bam d41d8cd98f00b204e9800998ecf8427e results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/quant_kallisto/synthetic_10_reads_paired_synthetic_10_reads_paired.kallisto.pseudo.sam c77480e0235761f2d7f80dbceb2e2806 results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/salmon_quant/lib_format_counts.json 989d6ee63b728fced9ec0249735ab83d results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/salmon_quant/aux_info/ambig_info.tsv @@ -78,10 +78,10 @@ e72f5d798c99272f8c0166dc77247db1 results/single_end/synthetic_10_reads_mate_1_s 92bcd0592d22a6a58d0360fc76103e56 results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/salmon_quant/aux_info/observed_bias 92bcd0592d22a6a58d0360fc76103e56 results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/salmon_quant/aux_info/observed_bias_3p d41d8cd98f00b204e9800998ecf8427e results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/salmon_quant/aux_info/unmapped_names.txt -0139e75ddbfe6eb081c2c2d9b9108ab4 results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/STAR_coverage/synthetic_10_reads_paired_synthetic_10_reads_paired_Signal.UniqueMultiple.str1.out.bg -c266d31e0a2ad84975cb9de335891e64 results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/STAR_coverage/synthetic_10_reads_paired_synthetic_10_reads_paired_Signal.UniqueMultiple.str2.out.bg -0139e75ddbfe6eb081c2c2d9b9108ab4 results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/STAR_coverage/synthetic_10_reads_paired_synthetic_10_reads_paired_Signal.Unique.str1.out.bg -c266d31e0a2ad84975cb9de335891e64 results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/STAR_coverage/synthetic_10_reads_paired_synthetic_10_reads_paired_Signal.Unique.str2.out.bg +16652c037090f3eed1123618a2e75107 results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/STAR_coverage/synthetic_10_reads_paired_synthetic_10_reads_paired_Signal.UniqueMultiple.str1.out.bg +90ae442ebf35015eab2dd4e804c2bafb results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/STAR_coverage/synthetic_10_reads_paired_synthetic_10_reads_paired_Signal.UniqueMultiple.str2.out.bg +16652c037090f3eed1123618a2e75107 results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/STAR_coverage/synthetic_10_reads_paired_synthetic_10_reads_paired_Signal.Unique.str1.out.bg +90ae442ebf35015eab2dd4e804c2bafb results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/STAR_coverage/synthetic_10_reads_paired_synthetic_10_reads_paired_Signal.Unique.str2.out.bg ea91b4f85622561158bff2f7c9c312b3 results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/STAR_coverage/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Signal.UniqueMultiple.str1.out.bg bcccf679a8c083d01527514c9f5680a0 results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/STAR_coverage/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Signal.UniqueMultiple.str2.out.bg ea91b4f85622561158bff2f7c9c312b3 results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/STAR_coverage/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Signal.Unique.str1.out.bg @@ -89,9 +89,9 @@ bcccf679a8c083d01527514c9f5680a0 results/single_end/synthetic_10_reads_mate_1_s 3ce47cb1d62482c5d62337751d7e8552 results/transcriptome/homo_sapiens/transcriptome.fa 6b44c507f0a1c9f7369db0bb1deef0fd results/alfa_indexes/homo_sapiens/75/ALFA/sorted_genes.stranded.ALFA_index 2caebc23faf78fdbbbdbb118d28bd6b5 results/alfa_indexes/homo_sapiens/75/ALFA/sorted_genes.unstranded.ALFA_index -c1254a0bae19ac3ffc39f73099ffcf2b results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/synthetic_10_reads_paired_synthetic_10_reads_paired.ALFA_feature_counts.tsv -c266d31e0a2ad84975cb9de335891e64 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