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BIOPZ-Katsantoni Maria's avatar
get Snakemake input from LabKey API  
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cbaebdb67aee4784b64aff7fec9fda42  results/kallisto_indexes/homo_sapiens/kallisto.idx
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Use biocontainers images for star, gffread, salmon, kallisto, cutadapt,...  
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204865f645102587c4953fccb256797c  results/salmon_indexes/homo_sapiens/31/salmon.idx/versionInfo.json
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Add rule that combines TPM values from Salmon  
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51b5292e3a874119c0e1aa566e95d70c  results/salmon_indexes/homo_sapiens/31/salmon.idx/duplicate_clusters.tsv
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Use biocontainers images for star, gffread, salmon, kallisto, cutadapt,...  
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4e10114bb8f9096d594776181424a302  results/salmon_indexes/homo_sapiens/31/salmon.idx/info.json
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get Snakemake input from LabKey API  
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dee7cdc194d5d0617552b7a3b5ad8dfb  results/star_indexes/homo_sapiens/75/STAR_index/chrLength.txt
8e2e96e2d6b7f29940ad5de40662b7cb  results/star_indexes/homo_sapiens/75/STAR_index/chrNameLength.txt
d0826904b8afa45352906ad9591f2bfb  results/star_indexes/homo_sapiens/75/STAR_index/chrName.txt
8d3291e6bcdbe9902fbd7c887494173f  results/star_indexes/homo_sapiens/75/STAR_index/chrStart.txt
83ea3c15ab782b5c55bfaefda8e7aad8  results/star_indexes/homo_sapiens/75/STAR_index/exonGeTrInfo.tab
bad9d837f9a988694cc7080ee6d2997a  results/star_indexes/homo_sapiens/75/STAR_index/exonInfo.tab
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Use minified docker images  
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0c0b013fb8cbb8f3cb7a7bf92f3b1544  results/star_indexes/homo_sapiens/75/STAR_index/geneInfo.tab
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get Snakemake input from LabKey API  
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00dda17b3c3983873d1474e9a758d6e6  results/star_indexes/homo_sapiens/75/STAR_index/Genome
c0d91c3af633d9439bfd0160d11efe4d  results/star_indexes/homo_sapiens/75/STAR_index/SA
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Use biocontainers images for star, gffread, salmon, kallisto, cutadapt,...  
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a8dfc49713c053a8a1a2cc2527f15186  results/star_indexes/homo_sapiens/75/STAR_index/SAindex
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get Snakemake input from LabKey API  
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bae93882f9148a6c55816b733c32a3a2  results/star_indexes/homo_sapiens/75/STAR_index/sjdbInfo.txt
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Use minified docker images  
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875030141343fca11f0b5aa1a37e1b66  results/star_indexes/homo_sapiens/75/STAR_index/sjdbList.fromGTF.out.tab
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get Snakemake input from LabKey API  
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ea36f062eedc7f54ceffea2b635a25a8  results/star_indexes/homo_sapiens/75/STAR_index/sjdbList.out.tab
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Use minified docker images  
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65e794aa5096551254af18a678d02264  results/star_indexes/homo_sapiens/75/STAR_index/transcriptInfo.tab
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Add rules for bigWig creation  
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500dd49da40b16799aba62aa5cf239ba  results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.pe.remove_adapters_mate1.fastq
500dd49da40b16799aba62aa5cf239ba  results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.pe.remove_polya_mate1.fastq
e90e31db1ce51d930645eb74ff70d21b  results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.pe.remove_adapters_mate2.fastq
1c0796d7e0bdab0e99780b2e11d80c19  results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.pe.remove_polya_mate2.fastq
9896744dd90ff3eef00c91fa1f721366  results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq1/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1_fastqc/fastqc_data.txt
6946ba80af318b9c1052b264dc674a51  results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq1/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1_fastqc/fastqc.fo
2603f3031242e97411a71571f6ad9e53  results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq1/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1_fastqc/summary.txt
c39fc9108e6f6c0df45acc9391daad9c  results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq2/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2_fastqc/fastqc_data.txt
82c37e4cb9c1e167383d589ccb5c80b4  results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq2/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2_fastqc/fastqc.fo
2029b1ecea0c5fb3c54238813cf02a26  results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq2/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2_fastqc/summary.txt
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Use biocontainers images for star, gffread, salmon, kallisto, cutadapt,...  
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caf24c834f9f8aa31473c3d5826227ac  results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq1/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1_fastqc/Images/adapter_content.png
909c316306050c8f7dfb9ad72dfe0334  results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq1/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1_fastqc/Images/duplication_levels.png
3f7d7acd0b42a4e3642f3cc8f81e7b8d  results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq1/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1_fastqc/Images/per_base_n_content.png
5475f0266800b9febf00979b8dc561e6  results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq1/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1_fastqc/Images/per_base_quality.png
42462f1beeecb7820682284f7d5518cf  results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq1/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1_fastqc/Images/per_base_sequence_content.png
dc6b69c56474f492bbc9824631ac84d3  results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq1/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1_fastqc/Images/per_sequence_gc_content.png
b5a5a126e3f85478abdac1074aaf2fe1  results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq1/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1_fastqc/Images/per_sequence_quality.png
f399fa5792cdfb72fac7ae2226723122  results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq1/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1_fastqc/Images/per_tile_quality.png
e342ab7fae5112b9ebca5a04cc6230a2  results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq1/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1_fastqc/Images/sequence_length_distribution.png
caf24c834f9f8aa31473c3d5826227ac  results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq2/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2_fastqc/Images/adapter_content.png
909c316306050c8f7dfb9ad72dfe0334  results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq2/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2_fastqc/Images/duplication_levels.png
3f7d7acd0b42a4e3642f3cc8f81e7b8d  results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq2/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2_fastqc/Images/per_base_n_content.png
5475f0266800b9febf00979b8dc561e6  results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq2/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2_fastqc/Images/per_base_quality.png
1c5ddee8a651c196e1b0ecdd8b406e71  results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq2/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2_fastqc/Images/per_base_sequence_content.png
eedd2f45539f47e163c2b390ba6fbcfc  results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq2/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2_fastqc/Images/per_sequence_gc_content.png
b5a5a126e3f85478abdac1074aaf2fe1  results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq2/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2_fastqc/Images/per_sequence_quality.png
f399fa5792cdfb72fac7ae2226723122  results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq2/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2_fastqc/Images/per_tile_quality.png
e342ab7fae5112b9ebca5a04cc6230a2  results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq2/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2_fastqc/Images/sequence_length_distribution.png
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Add rules for bigWig creation  
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d41d8cd98f00b204e9800998ecf8427e  results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/quant_kallisto/synthetic_10_reads_paired_synthetic_10_reads_paired.pe.kallisto.pseudo.sam
500dd49da40b16799aba62aa5cf239ba  results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.se.remove_adapters_mate1.fastq
500dd49da40b16799aba62aa5cf239ba  results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.se.remove_polya_mate1.fastq
fdb8c6ddd39b606414b2785d6ec2da8a  results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/fastqc/fq1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.fq1_fastqc/fastqc_data.txt
3cb70940acdcca512207bd8613085538  results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/fastqc/fq1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.fq1_fastqc/fastqc.fo
fc276a1711cc35f7a9d5328bdbbab810  results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/fastqc/fq1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.fq1_fastqc/summary.txt
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Use biocontainers images for star, gffread, salmon, kallisto, cutadapt,...  
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caf24c834f9f8aa31473c3d5826227ac  results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/fastqc/fq1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.fq1_fastqc/Images/adapter_content.png
909c316306050c8f7dfb9ad72dfe0334  results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/fastqc/fq1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.fq1_fastqc/Images/duplication_levels.png
3f7d7acd0b42a4e3642f3cc8f81e7b8d  results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/fastqc/fq1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.fq1_fastqc/Images/per_base_n_content.png
5475f0266800b9febf00979b8dc561e6  results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/fastqc/fq1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.fq1_fastqc/Images/per_base_quality.png
42462f1beeecb7820682284f7d5518cf  results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/fastqc/fq1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.fq1_fastqc/Images/per_base_sequence_content.png
dc6b69c56474f492bbc9824631ac84d3  results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/fastqc/fq1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.fq1_fastqc/Images/per_sequence_gc_content.png
b5a5a126e3f85478abdac1074aaf2fe1  results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/fastqc/fq1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.fq1_fastqc/Images/per_sequence_quality.png
f399fa5792cdfb72fac7ae2226723122  results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/fastqc/fq1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.fq1_fastqc/Images/per_tile_quality.png
e342ab7fae5112b9ebca5a04cc6230a2  results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/fastqc/fq1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.fq1_fastqc/Images/sequence_length_distribution.png
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Add rules for bigWig creation  
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d41d8cd98f00b204e9800998ecf8427e  results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/quant_kallisto/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.se.kallisto.pseudo.sam
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Replace cufflinks image with gffread image  
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3ce47cb1d62482c5d62337751d7e8552  results/transcriptome/homo_sapiens/transcriptome.fa
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included tests for ALFA qc  
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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
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Major refactoring  
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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
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extend ALFA functionality  
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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
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Add rules for bigWig creation  
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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
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Major refactoring  
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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
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Merge kallisto rules: kallisto_merge_genes and kallisto_merge_transcript  
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ba090b1b4a2473891de97493d3244956  results/multiqc_summary/multiqc_data/multiqc_fastqc.txt
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MultiQC plugins for TIN scores and ALFA Fixes #138  
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d8118d944149eecc691d182448696e7f  results/multiqc_summary/multiqc_data/multiqc_cutadapt.txt
a127fabda5c3aad9d95414dc4fbc11c3  results/multiqc_summary/multiqc_data/multiqc_cutadapt_1.txt
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Add rules for bigWig creation  
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0c6363588cf6ff74d49f27c164185918  results/multiqc_summary/multiqc_data/multiqc_star.txt
dd81441ca97912a62292d317af2c107c  results/multiqc_summary/multiqc_data/multiqc_kallisto.txt
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Major refactoring  
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0703b4cb7ec2abfab13ccd5f58c2d536  results/multiqc_summary/multiqc_data/multiqc_general_stats.txt
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Merge kallisto rules: kallisto_merge_genes and kallisto_merge_transcript  
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9f22fcd1b38d9dd692e77cb27f2e52f2  results/summary_kallisto/tx2geneID.tsv
a9514da3fe2c94b9dca71d9e0160be69  results/summary_kallisto/genes_counts.tsv
0d288e71d017a090152384fd915dc2a1  results/summary_kallisto/transcripts_counts.tsv
58a075e4e938d690748b556141912d1c  results/summary_kallisto/transcripts_tpm.tsv
8f29696ede8e5d290513f56d3a0b4bff  results/summary_kallisto/genes_tpm.tsv