diff --git a/tests/test_integration_workflow/expected_output.files b/tests/test_integration_workflow/expected_output.files index a9026e6abe1da853ccee4e74f395d5a441de8cbf..e0b085901238577b7f1d7aff47b237ddacdb943c 100644 --- a/tests/test_integration_workflow/expected_output.files +++ b/tests/test_integration_workflow/expected_output.files @@ -81,26 +81,26 @@ results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/synthetic_10 results/transcriptome/homo_sapiens/transcriptome.fa results/alfa_indexes/homo_sapiens/75/ALFA/sorted_genes.stranded.ALFA_index results/alfa_indexes/homo_sapiens/75/ALFA/sorted_genes.unstranded.ALFA_index -results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/UniqueMultiple/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.UniqueMultiple.minus.bg -results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/UniqueMultiple/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.UniqueMultiple.plus.bg -results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/Unique/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.Unique.minus.bg -results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/Unique/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.Unique.plus.bg -results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/UniqueMultiple/synthetic_10_reads_paired_synthetic_10_reads_paired.UniqueMultiple.minus.bg -results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/UniqueMultiple/synthetic_10_reads_paired_synthetic_10_reads_paired.UniqueMultiple.plus.bg -results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/Unique/synthetic_10_reads_paired_synthetic_10_reads_paired.Unique.minus.bg -results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/Unique/synthetic_10_reads_paired_synthetic_10_reads_paired.Unique.plus.bg -results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/UniqueMultiple/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.ALFA_feature_counts.tsv -results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/Unique/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.ALFA_feature_counts.tsv -results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/UniqueMultiple/synthetic_10_reads_paired_synthetic_10_reads_paired.ALFA_feature_counts.tsv -results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/Unique/synthetic_10_reads_paired_synthetic_10_reads_paired.ALFA_feature_counts.tsv -results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/bigWig/UniqueMultiple/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_UniqueMultiple_minus.bw -results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/bigWig/UniqueMultiple/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_UniqueMultiple_plus.bw -results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/bigWig/Unique/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Unique_minus.bw -results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/bigWig/Unique/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Unique_plus.bw -results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/bigWig/UniqueMultiple/synthetic_10_reads_paired_synthetic_10_reads_paired_UniqueMultiple_minus.bw -results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/bigWig/UniqueMultiple/synthetic_10_reads_paired_synthetic_10_reads_paired_UniqueMultiple_plus.bw -results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/bigWig/Unique/synthetic_10_reads_paired_synthetic_10_reads_paired_Unique_minus.bw -results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/bigWig/Unique/synthetic_10_reads_paired_synthetic_10_reads_paired_Unique_plus.bw +results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/MultimappersIncluded/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.MultimappersIncluded.minus.bg +results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/MultimappersIncluded/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.MultimappersIncluded.plus.bg +results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/UniqueMappers/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.UniqueMappers.minus.bg +results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/UniqueMappers/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.UniqueMappers.plus.bg +results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/MultimappersIncluded/synthetic_10_reads_paired_synthetic_10_reads_paired.MultimappersIncluded.minus.bg +results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/MultimappersIncluded/synthetic_10_reads_paired_synthetic_10_reads_paired.MultimappersIncluded.plus.bg +results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/UniqueMappers/synthetic_10_reads_paired_synthetic_10_reads_paired.UniqueMappers.minus.bg +results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/UniqueMappers/synthetic_10_reads_paired_synthetic_10_reads_paired.UniqueMappers.plus.bg +results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/MultimappersIncluded/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.ALFA_feature_counts.tsv +results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/UniqueMappers/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.ALFA_feature_counts.tsv +results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/MultimappersIncluded/synthetic_10_reads_paired_synthetic_10_reads_paired.ALFA_feature_counts.tsv +results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/UniqueMappers/synthetic_10_reads_paired_synthetic_10_reads_paired.ALFA_feature_counts.tsv +results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/bigWig/MultimappersIncluded/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_MultimappersIncluded_minus.bw +results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/bigWig/MultimappersIncluded/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_MultimappersIncluded_plus.bw +results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/bigWig/UniqueMappers/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_UniqueMappers_minus.bw +results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/bigWig/UniqueMappers/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_UniqueMappers_plus.bw +results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/bigWig/MultimappersIncluded/synthetic_10_reads_paired_synthetic_10_reads_paired_MultimappersIncluded_minus.bw +results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/bigWig/MultimappersIncluded/synthetic_10_reads_paired_synthetic_10_reads_paired_MultimappersIncluded_plus.bw +results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/bigWig/UniqueMappers/synthetic_10_reads_paired_synthetic_10_reads_paired_UniqueMappers_minus.bw +results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/bigWig/UniqueMappers/synthetic_10_reads_paired_synthetic_10_reads_paired_UniqueMappers_plus.bw results/multiqc_summary/multiqc_data/multiqc_fastqc.txt results/multiqc_summary/multiqc_data/multiqc_cutadapt.txt results/multiqc_summary/multiqc_data/multiqc_cutadapt_1.txt diff --git a/tests/test_integration_workflow/expected_output.md5 b/tests/test_integration_workflow/expected_output.md5 index 266f992944fb3e19dd0b0941d852c0e18f7a99f0..67dbbec0095f478b4288764f3e65cfb3a25313ca 100644 --- a/tests/test_integration_workflow/expected_output.md5 +++ b/tests/test_integration_workflow/expected_output.md5 @@ -63,26 +63,26 @@ d41d8cd98f00b204e9800998ecf8427e results/samples/synthetic_10_reads_mate_1_synt 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 -bcccf679a8c083d01527514c9f5680a0 results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/UniqueMultiple/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.UniqueMultiple.minus.bg -ea91b4f85622561158bff2f7c9c312b3 results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/UniqueMultiple/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.UniqueMultiple.plus.bg -bcccf679a8c083d01527514c9f5680a0 results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/Unique/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.Unique.minus.bg -ea91b4f85622561158bff2f7c9c312b3 results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/Unique/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.Unique.plus.bg -90ae442ebf35015eab2dd4e804c2bafb results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/UniqueMultiple/synthetic_10_reads_paired_synthetic_10_reads_paired.UniqueMultiple.minus.bg -16652c037090f3eed1123618a2e75107 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/UniqueMultiple/synthetic_10_reads_paired_synthetic_10_reads_paired.UniqueMultiple.plus.bg -90ae442ebf35015eab2dd4e804c2bafb results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/Unique/synthetic_10_reads_paired_synthetic_10_reads_paired.Unique.minus.bg -16652c037090f3eed1123618a2e75107 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/Unique/synthetic_10_reads_paired_synthetic_10_reads_paired.Unique.plus.bg -c1254a0bae19ac3ffc39f73099ffcf2b results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/UniqueMultiple/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.ALFA_feature_counts.tsv -c1254a0bae19ac3ffc39f73099ffcf2b results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/Unique/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.ALFA_feature_counts.tsv -53fd53f884352d0493b2ca99cef5d76d results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/UniqueMultiple/synthetic_10_reads_paired_synthetic_10_reads_paired.ALFA_feature_counts.tsv -53fd53f884352d0493b2ca99cef5d76d results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/Unique/synthetic_10_reads_paired_synthetic_10_reads_paired.ALFA_feature_counts.tsv -ed3428feeb7257b0a69ead76a417e339 results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/bigWig/UniqueMultiple/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_UniqueMultiple_minus.bw -2767ca6a648f3e37b7e3b05ce7845460 results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/bigWig/UniqueMultiple/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_UniqueMultiple_plus.bw -ed3428feeb7257b0a69ead76a417e339 results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/bigWig/Unique/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Unique_minus.bw -2767ca6a648f3e37b7e3b05ce7845460 results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/bigWig/Unique/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Unique_plus.bw -69e2bf688165e9fb7c9c49a8763f5632 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/bigWig/UniqueMultiple/synthetic_10_reads_paired_synthetic_10_reads_paired_UniqueMultiple_minus.bw -ec5aab1b79e7880dfa590e5bc7db5232 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/bigWig/UniqueMultiple/synthetic_10_reads_paired_synthetic_10_reads_paired_UniqueMultiple_plus.bw -69e2bf688165e9fb7c9c49a8763f5632 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/bigWig/Unique/synthetic_10_reads_paired_synthetic_10_reads_paired_Unique_minus.bw -ec5aab1b79e7880dfa590e5bc7db5232 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/bigWig/Unique/synthetic_10_reads_paired_synthetic_10_reads_paired_Unique_plus.bw +bcccf679a8c083d01527514c9f5680a0 results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/MultimappersIncluded/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.MultimappersIncluded.minus.bg +ea91b4f85622561158bff2f7c9c312b3 results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/MultimappersIncluded/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.MultimappersIncluded.plus.bg +bcccf679a8c083d01527514c9f5680a0 results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/UniqueMappers/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.UniqueMappers.minus.bg +ea91b4f85622561158bff2f7c9c312b3 results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/UniqueMappers/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.UniqueMappers.plus.bg +90ae442ebf35015eab2dd4e804c2bafb results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/MultimappersIncluded/synthetic_10_reads_paired_synthetic_10_reads_paired.MultimappersIncluded.minus.bg +16652c037090f3eed1123618a2e75107 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/MultimappersIncluded/synthetic_10_reads_paired_synthetic_10_reads_paired.MultimappersIncluded.plus.bg +90ae442ebf35015eab2dd4e804c2bafb results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/UniqueMappers/synthetic_10_reads_paired_synthetic_10_reads_paired.UniqueMappers.minus.bg +16652c037090f3eed1123618a2e75107 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/UniqueMappers/synthetic_10_reads_paired_synthetic_10_reads_paired.UniqueMappers.plus.bg +c1254a0bae19ac3ffc39f73099ffcf2b results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/MultimappersIncluded/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.ALFA_feature_counts.tsv +c1254a0bae19ac3ffc39f73099ffcf2b results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/UniqueMappers/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.ALFA_feature_counts.tsv +53fd53f884352d0493b2ca99cef5d76d results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/MultimappersIncluded/synthetic_10_reads_paired_synthetic_10_reads_paired.ALFA_feature_counts.tsv +53fd53f884352d0493b2ca99cef5d76d results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/UniqueMappers/synthetic_10_reads_paired_synthetic_10_reads_paired.ALFA_feature_counts.tsv +ed3428feeb7257b0a69ead76a417e339 results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/bigWig/MultimappersIncluded/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_MultimappersIncluded_minus.bw +2767ca6a648f3e37b7e3b05ce7845460 results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/bigWig/MultimappersIncluded/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_MultimappersIncluded_plus.bw +ed3428feeb7257b0a69ead76a417e339 results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/bigWig/UniqueMappers/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_UniqueMappers_minus.bw +2767ca6a648f3e37b7e3b05ce7845460 results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/bigWig/UniqueMappers/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_UniqueMappers_plus.bw +69e2bf688165e9fb7c9c49a8763f5632 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/bigWig/MultimappersIncluded/synthetic_10_reads_paired_synthetic_10_reads_paired_MultimappersIncluded_minus.bw +ec5aab1b79e7880dfa590e5bc7db5232 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/bigWig/MultimappersIncluded/synthetic_10_reads_paired_synthetic_10_reads_paired_MultimappersIncluded_plus.bw +69e2bf688165e9fb7c9c49a8763f5632 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/bigWig/UniqueMappers/synthetic_10_reads_paired_synthetic_10_reads_paired_UniqueMappers_minus.bw +ec5aab1b79e7880dfa590e5bc7db5232 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/bigWig/UniqueMappers/synthetic_10_reads_paired_synthetic_10_reads_paired_UniqueMappers_plus.bw ba090b1b4a2473891de97493d3244956 results/multiqc_summary/multiqc_data/multiqc_fastqc.txt d8118d944149eecc691d182448696e7f results/multiqc_summary/multiqc_data/multiqc_cutadapt.txt a127fabda5c3aad9d95414dc4fbc11c3 results/multiqc_summary/multiqc_data/multiqc_cutadapt_1.txt diff --git a/tests/test_integration_workflow_multiple_lanes/expected_output.md5 b/tests/test_integration_workflow_multiple_lanes/expected_output.md5 index 37f1119767ecde51f4b657886539e52ed63494ca..4d6290def3a8543352fa755616cbda7a19823ed6 100644 --- a/tests/test_integration_workflow_multiple_lanes/expected_output.md5 +++ b/tests/test_integration_workflow_multiple_lanes/expected_output.md5 @@ -63,26 +63,26 @@ d41d8cd98f00b204e9800998ecf8427e results/samples/synthetic_10_reads_mate_1_synt 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 -bcccf679a8c083d01527514c9f5680a0 results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/UniqueMultiple/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.UniqueMultiple.minus.bg -ea91b4f85622561158bff2f7c9c312b3 results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/UniqueMultiple/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.UniqueMultiple.plus.bg -bcccf679a8c083d01527514c9f5680a0 results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/Unique/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.Unique.minus.bg -ea91b4f85622561158bff2f7c9c312b3 results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/Unique/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.Unique.plus.bg -90ae442ebf35015eab2dd4e804c2bafb results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/UniqueMultiple/synthetic_10_reads_paired_synthetic_10_reads_paired.UniqueMultiple.minus.bg -16652c037090f3eed1123618a2e75107 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/UniqueMultiple/synthetic_10_reads_paired_synthetic_10_reads_paired.UniqueMultiple.plus.bg -90ae442ebf35015eab2dd4e804c2bafb results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/Unique/synthetic_10_reads_paired_synthetic_10_reads_paired.Unique.minus.bg -16652c037090f3eed1123618a2e75107 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/Unique/synthetic_10_reads_paired_synthetic_10_reads_paired.Unique.plus.bg -c1254a0bae19ac3ffc39f73099ffcf2b results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/UniqueMultiple/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.ALFA_feature_counts.tsv -c1254a0bae19ac3ffc39f73099ffcf2b results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/Unique/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.ALFA_feature_counts.tsv -53fd53f884352d0493b2ca99cef5d76d results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/UniqueMultiple/synthetic_10_reads_paired_synthetic_10_reads_paired.ALFA_feature_counts.tsv -53fd53f884352d0493b2ca99cef5d76d results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/Unique/synthetic_10_reads_paired_synthetic_10_reads_paired.ALFA_feature_counts.tsv -ed3428feeb7257b0a69ead76a417e339 results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/bigWig/UniqueMultiple/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_UniqueMultiple_minus.bw -2767ca6a648f3e37b7e3b05ce7845460 results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/bigWig/UniqueMultiple/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_UniqueMultiple_plus.bw -ed3428feeb7257b0a69ead76a417e339 results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/bigWig/Unique/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Unique_minus.bw -2767ca6a648f3e37b7e3b05ce7845460 results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/bigWig/Unique/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Unique_plus.bw -69e2bf688165e9fb7c9c49a8763f5632 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/bigWig/UniqueMultiple/synthetic_10_reads_paired_synthetic_10_reads_paired_UniqueMultiple_minus.bw -ec5aab1b79e7880dfa590e5bc7db5232 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/bigWig/UniqueMultiple/synthetic_10_reads_paired_synthetic_10_reads_paired_UniqueMultiple_plus.bw -69e2bf688165e9fb7c9c49a8763f5632 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/bigWig/Unique/synthetic_10_reads_paired_synthetic_10_reads_paired_Unique_minus.bw -ec5aab1b79e7880dfa590e5bc7db5232 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/bigWig/Unique/synthetic_10_reads_paired_synthetic_10_reads_paired_Unique_plus.bw +bcccf679a8c083d01527514c9f5680a0 results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/MultimappersIncluded/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.MultimappersIncluded.minus.bg +ea91b4f85622561158bff2f7c9c312b3 results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/MultimappersIncluded/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.MultimappersIncluded.plus.bg +bcccf679a8c083d01527514c9f5680a0 results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/UniqueMappers/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.UniqueMappers.minus.bg +ea91b4f85622561158bff2f7c9c312b3 results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/UniqueMappers/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.UniqueMappers.plus.bg +90ae442ebf35015eab2dd4e804c2bafb results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/MultimappersIncluded/synthetic_10_reads_paired_synthetic_10_reads_paired.MultimappersIncluded.minus.bg +16652c037090f3eed1123618a2e75107 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/MultimappersIncluded/synthetic_10_reads_paired_synthetic_10_reads_paired.MultimappersIncluded.plus.bg +90ae442ebf35015eab2dd4e804c2bafb results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/UniqueMappers/synthetic_10_reads_paired_synthetic_10_reads_paired.UniqueMappers.minus.bg +16652c037090f3eed1123618a2e75107 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/UniqueMappers/synthetic_10_reads_paired_synthetic_10_reads_paired.UniqueMappers.plus.bg +c1254a0bae19ac3ffc39f73099ffcf2b results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/MultimappersIncluded/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.ALFA_feature_counts.tsv +c1254a0bae19ac3ffc39f73099ffcf2b results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/UniqueMappers/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.ALFA_feature_counts.tsv +53fd53f884352d0493b2ca99cef5d76d results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/MultimappersIncluded/synthetic_10_reads_paired_synthetic_10_reads_paired.ALFA_feature_counts.tsv +53fd53f884352d0493b2ca99cef5d76d results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/UniqueMappers/synthetic_10_reads_paired_synthetic_10_reads_paired.ALFA_feature_counts.tsv +ed3428feeb7257b0a69ead76a417e339 results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/bigWig/MultimappersIncluded/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_MultimappersIncluded_minus.bw +2767ca6a648f3e37b7e3b05ce7845460 results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/bigWig/MultimappersIncluded/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_MultimappersIncluded_plus.bw +ed3428feeb7257b0a69ead76a417e339 results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/bigWig/UniqueMappers/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_UniqueMappers_minus.bw +2767ca6a648f3e37b7e3b05ce7845460 results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/bigWig/UniqueMappers/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_UniqueMappers_plus.bw +69e2bf688165e9fb7c9c49a8763f5632 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/bigWig/MultimappersIncluded/synthetic_10_reads_paired_synthetic_10_reads_paired_MultimappersIncluded_minus.bw +ec5aab1b79e7880dfa590e5bc7db5232 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/bigWig/MultimappersIncluded/synthetic_10_reads_paired_synthetic_10_reads_paired_MultimappersIncluded_plus.bw +69e2bf688165e9fb7c9c49a8763f5632 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/bigWig/UniqueMappers/synthetic_10_reads_paired_synthetic_10_reads_paired_UniqueMappers_minus.bw +ec5aab1b79e7880dfa590e5bc7db5232 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/bigWig/UniqueMappers/synthetic_10_reads_paired_synthetic_10_reads_paired_UniqueMappers_plus.bw d8118d944149eecc691d182448696e7f results/multiqc_summary/multiqc_data/multiqc_cutadapt.txt a127fabda5c3aad9d95414dc4fbc11c3 results/multiqc_summary/multiqc_data/multiqc_cutadapt_1.txt 0c6363588cf6ff74d49f27c164185918 results/multiqc_summary/multiqc_data/multiqc_star.txt diff --git a/tests/test_integration_workflow_with_conda/expected_output.files b/tests/test_integration_workflow_with_conda/expected_output.files index a9026e6abe1da853ccee4e74f395d5a441de8cbf..e0b085901238577b7f1d7aff47b237ddacdb943c 100644 --- a/tests/test_integration_workflow_with_conda/expected_output.files +++ b/tests/test_integration_workflow_with_conda/expected_output.files @@ -81,26 +81,26 @@ results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/synthetic_10 results/transcriptome/homo_sapiens/transcriptome.fa results/alfa_indexes/homo_sapiens/75/ALFA/sorted_genes.stranded.ALFA_index results/alfa_indexes/homo_sapiens/75/ALFA/sorted_genes.unstranded.ALFA_index -results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/UniqueMultiple/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.UniqueMultiple.minus.bg -results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/UniqueMultiple/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.UniqueMultiple.plus.bg -results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/Unique/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.Unique.minus.bg -results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/Unique/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.Unique.plus.bg -results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/UniqueMultiple/synthetic_10_reads_paired_synthetic_10_reads_paired.UniqueMultiple.minus.bg -results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/UniqueMultiple/synthetic_10_reads_paired_synthetic_10_reads_paired.UniqueMultiple.plus.bg -results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/Unique/synthetic_10_reads_paired_synthetic_10_reads_paired.Unique.minus.bg -results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/Unique/synthetic_10_reads_paired_synthetic_10_reads_paired.Unique.plus.bg -results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/UniqueMultiple/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.ALFA_feature_counts.tsv -results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/Unique/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.ALFA_feature_counts.tsv -results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/UniqueMultiple/synthetic_10_reads_paired_synthetic_10_reads_paired.ALFA_feature_counts.tsv -results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/Unique/synthetic_10_reads_paired_synthetic_10_reads_paired.ALFA_feature_counts.tsv -results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/bigWig/UniqueMultiple/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_UniqueMultiple_minus.bw -results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/bigWig/UniqueMultiple/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_UniqueMultiple_plus.bw -results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/bigWig/Unique/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Unique_minus.bw -results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/bigWig/Unique/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Unique_plus.bw -results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/bigWig/UniqueMultiple/synthetic_10_reads_paired_synthetic_10_reads_paired_UniqueMultiple_minus.bw -results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/bigWig/UniqueMultiple/synthetic_10_reads_paired_synthetic_10_reads_paired_UniqueMultiple_plus.bw -results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/bigWig/Unique/synthetic_10_reads_paired_synthetic_10_reads_paired_Unique_minus.bw -results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/bigWig/Unique/synthetic_10_reads_paired_synthetic_10_reads_paired_Unique_plus.bw +results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/MultimappersIncluded/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.MultimappersIncluded.minus.bg +results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/MultimappersIncluded/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.MultimappersIncluded.plus.bg +results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/UniqueMappers/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.UniqueMappers.minus.bg +results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/UniqueMappers/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.UniqueMappers.plus.bg +results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/MultimappersIncluded/synthetic_10_reads_paired_synthetic_10_reads_paired.MultimappersIncluded.minus.bg +results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/MultimappersIncluded/synthetic_10_reads_paired_synthetic_10_reads_paired.MultimappersIncluded.plus.bg +results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/UniqueMappers/synthetic_10_reads_paired_synthetic_10_reads_paired.UniqueMappers.minus.bg +results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/UniqueMappers/synthetic_10_reads_paired_synthetic_10_reads_paired.UniqueMappers.plus.bg +results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/MultimappersIncluded/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.ALFA_feature_counts.tsv +results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/UniqueMappers/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.ALFA_feature_counts.tsv +results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/MultimappersIncluded/synthetic_10_reads_paired_synthetic_10_reads_paired.ALFA_feature_counts.tsv +results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/UniqueMappers/synthetic_10_reads_paired_synthetic_10_reads_paired.ALFA_feature_counts.tsv +results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/bigWig/MultimappersIncluded/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_MultimappersIncluded_minus.bw +results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/bigWig/MultimappersIncluded/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_MultimappersIncluded_plus.bw +results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/bigWig/UniqueMappers/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_UniqueMappers_minus.bw +results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/bigWig/UniqueMappers/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_UniqueMappers_plus.bw +results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/bigWig/MultimappersIncluded/synthetic_10_reads_paired_synthetic_10_reads_paired_MultimappersIncluded_minus.bw +results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/bigWig/MultimappersIncluded/synthetic_10_reads_paired_synthetic_10_reads_paired_MultimappersIncluded_plus.bw +results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/bigWig/UniqueMappers/synthetic_10_reads_paired_synthetic_10_reads_paired_UniqueMappers_minus.bw +results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/bigWig/UniqueMappers/synthetic_10_reads_paired_synthetic_10_reads_paired_UniqueMappers_plus.bw results/multiqc_summary/multiqc_data/multiqc_fastqc.txt results/multiqc_summary/multiqc_data/multiqc_cutadapt.txt results/multiqc_summary/multiqc_data/multiqc_cutadapt_1.txt diff --git a/tests/test_integration_workflow_with_conda/expected_output.md5 b/tests/test_integration_workflow_with_conda/expected_output.md5 index 266f992944fb3e19dd0b0941d852c0e18f7a99f0..67dbbec0095f478b4288764f3e65cfb3a25313ca 100644 --- a/tests/test_integration_workflow_with_conda/expected_output.md5 +++ b/tests/test_integration_workflow_with_conda/expected_output.md5 @@ -63,26 +63,26 @@ d41d8cd98f00b204e9800998ecf8427e results/samples/synthetic_10_reads_mate_1_synt 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 -bcccf679a8c083d01527514c9f5680a0 results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/UniqueMultiple/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.UniqueMultiple.minus.bg -ea91b4f85622561158bff2f7c9c312b3 results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/UniqueMultiple/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.UniqueMultiple.plus.bg -bcccf679a8c083d01527514c9f5680a0 results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/Unique/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.Unique.minus.bg -ea91b4f85622561158bff2f7c9c312b3 results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/Unique/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.Unique.plus.bg -90ae442ebf35015eab2dd4e804c2bafb results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/UniqueMultiple/synthetic_10_reads_paired_synthetic_10_reads_paired.UniqueMultiple.minus.bg -16652c037090f3eed1123618a2e75107 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/UniqueMultiple/synthetic_10_reads_paired_synthetic_10_reads_paired.UniqueMultiple.plus.bg -90ae442ebf35015eab2dd4e804c2bafb results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/Unique/synthetic_10_reads_paired_synthetic_10_reads_paired.Unique.minus.bg -16652c037090f3eed1123618a2e75107 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/Unique/synthetic_10_reads_paired_synthetic_10_reads_paired.Unique.plus.bg -c1254a0bae19ac3ffc39f73099ffcf2b results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/UniqueMultiple/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.ALFA_feature_counts.tsv -c1254a0bae19ac3ffc39f73099ffcf2b results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/Unique/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.ALFA_feature_counts.tsv -53fd53f884352d0493b2ca99cef5d76d results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/UniqueMultiple/synthetic_10_reads_paired_synthetic_10_reads_paired.ALFA_feature_counts.tsv -53fd53f884352d0493b2ca99cef5d76d results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/Unique/synthetic_10_reads_paired_synthetic_10_reads_paired.ALFA_feature_counts.tsv -ed3428feeb7257b0a69ead76a417e339 results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/bigWig/UniqueMultiple/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_UniqueMultiple_minus.bw -2767ca6a648f3e37b7e3b05ce7845460 results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/bigWig/UniqueMultiple/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_UniqueMultiple_plus.bw -ed3428feeb7257b0a69ead76a417e339 results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/bigWig/Unique/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Unique_minus.bw -2767ca6a648f3e37b7e3b05ce7845460 results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/bigWig/Unique/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Unique_plus.bw -69e2bf688165e9fb7c9c49a8763f5632 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/bigWig/UniqueMultiple/synthetic_10_reads_paired_synthetic_10_reads_paired_UniqueMultiple_minus.bw -ec5aab1b79e7880dfa590e5bc7db5232 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/bigWig/UniqueMultiple/synthetic_10_reads_paired_synthetic_10_reads_paired_UniqueMultiple_plus.bw -69e2bf688165e9fb7c9c49a8763f5632 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/bigWig/Unique/synthetic_10_reads_paired_synthetic_10_reads_paired_Unique_minus.bw -ec5aab1b79e7880dfa590e5bc7db5232 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/bigWig/Unique/synthetic_10_reads_paired_synthetic_10_reads_paired_Unique_plus.bw +bcccf679a8c083d01527514c9f5680a0 results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/MultimappersIncluded/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.MultimappersIncluded.minus.bg +ea91b4f85622561158bff2f7c9c312b3 results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/MultimappersIncluded/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.MultimappersIncluded.plus.bg +bcccf679a8c083d01527514c9f5680a0 results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/UniqueMappers/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.UniqueMappers.minus.bg +ea91b4f85622561158bff2f7c9c312b3 results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/UniqueMappers/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.UniqueMappers.plus.bg +90ae442ebf35015eab2dd4e804c2bafb results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/MultimappersIncluded/synthetic_10_reads_paired_synthetic_10_reads_paired.MultimappersIncluded.minus.bg +16652c037090f3eed1123618a2e75107 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/MultimappersIncluded/synthetic_10_reads_paired_synthetic_10_reads_paired.MultimappersIncluded.plus.bg +90ae442ebf35015eab2dd4e804c2bafb results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/UniqueMappers/synthetic_10_reads_paired_synthetic_10_reads_paired.UniqueMappers.minus.bg +16652c037090f3eed1123618a2e75107 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/UniqueMappers/synthetic_10_reads_paired_synthetic_10_reads_paired.UniqueMappers.plus.bg +c1254a0bae19ac3ffc39f73099ffcf2b results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/MultimappersIncluded/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.ALFA_feature_counts.tsv +c1254a0bae19ac3ffc39f73099ffcf2b results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/UniqueMappers/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.ALFA_feature_counts.tsv +53fd53f884352d0493b2ca99cef5d76d results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/MultimappersIncluded/synthetic_10_reads_paired_synthetic_10_reads_paired.ALFA_feature_counts.tsv +53fd53f884352d0493b2ca99cef5d76d results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/UniqueMappers/synthetic_10_reads_paired_synthetic_10_reads_paired.ALFA_feature_counts.tsv +ed3428feeb7257b0a69ead76a417e339 results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/bigWig/MultimappersIncluded/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_MultimappersIncluded_minus.bw +2767ca6a648f3e37b7e3b05ce7845460 results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/bigWig/MultimappersIncluded/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_MultimappersIncluded_plus.bw +ed3428feeb7257b0a69ead76a417e339 results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/bigWig/UniqueMappers/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_UniqueMappers_minus.bw +2767ca6a648f3e37b7e3b05ce7845460 results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/bigWig/UniqueMappers/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_UniqueMappers_plus.bw +69e2bf688165e9fb7c9c49a8763f5632 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/bigWig/MultimappersIncluded/synthetic_10_reads_paired_synthetic_10_reads_paired_MultimappersIncluded_minus.bw +ec5aab1b79e7880dfa590e5bc7db5232 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/bigWig/MultimappersIncluded/synthetic_10_reads_paired_synthetic_10_reads_paired_MultimappersIncluded_plus.bw +69e2bf688165e9fb7c9c49a8763f5632 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/bigWig/UniqueMappers/synthetic_10_reads_paired_synthetic_10_reads_paired_UniqueMappers_minus.bw +ec5aab1b79e7880dfa590e5bc7db5232 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/bigWig/UniqueMappers/synthetic_10_reads_paired_synthetic_10_reads_paired_UniqueMappers_plus.bw ba090b1b4a2473891de97493d3244956 results/multiqc_summary/multiqc_data/multiqc_fastqc.txt d8118d944149eecc691d182448696e7f results/multiqc_summary/multiqc_data/multiqc_cutadapt.txt a127fabda5c3aad9d95414dc4fbc11c3 results/multiqc_summary/multiqc_data/multiqc_cutadapt_1.txt