|
3 | 3 | "content": [ |
4 | 4 | 264, |
5 | 5 | { |
6 | | - |
| 6 | + "BAMTOOLS_FILTER": { |
| 7 | + "samtools": "1.15.1", |
| 8 | + "bamtools": "2.5.2" |
| 9 | + }, |
| 10 | + "BAM_REMOVE_ORPHANS": { |
| 11 | + "samtools": "1.15.1" |
| 12 | + }, |
| 13 | + "BEDTOOLS_GENOMECOV": { |
| 14 | + "bedtools": "2.31.1", |
| 15 | + "sort": 9.5 |
| 16 | + }, |
| 17 | + "DEEPTOOLS_COMPUTEMATRIX_REFERENCE_POINT": { |
| 18 | + "deeptools": "3.5.5" |
| 19 | + }, |
| 20 | + "DEEPTOOLS_COMPUTEMATRIX_SCALE_REGIONS": { |
| 21 | + "deeptools": "3.5.5" |
| 22 | + }, |
| 23 | + "DEEPTOOLS_PLOTHEATMAP": { |
| 24 | + "deeptools": "3.5.5" |
| 25 | + }, |
| 26 | + "DEEPTOOLS_PLOTPROFILE": { |
| 27 | + "deeptools": "3.5.5" |
| 28 | + }, |
| 29 | + "DESEQ2_QC": { |
| 30 | + "r-base": "4.0.3", |
| 31 | + "bioconductor-deseq2": "1.28.0" |
| 32 | + }, |
| 33 | + "FASTQC": { |
| 34 | + "fastqc": "0.12.1" |
| 35 | + }, |
| 36 | + "FRIP_SCORE": { |
| 37 | + "bedtools": "2.30.0", |
| 38 | + "samtools": "1.15.1" |
| 39 | + }, |
| 40 | + "HOMER_ANNOTATEPEAKS": { |
| 41 | + "homer": 4.11 |
| 42 | + }, |
| 43 | + "IGV": { |
| 44 | + "python": "3.8.3" |
| 45 | + }, |
| 46 | + "MACS3_CALLPEAK": { |
| 47 | + "macs3": "3.0.1" |
| 48 | + }, |
| 49 | + "MACS3_CONSENSUS": { |
| 50 | + "python": "3.10.0", |
| 51 | + "r-base": "4.1.1" |
| 52 | + }, |
| 53 | + "MERGED_LIBRARY_ATAQV_ATAQV": { |
| 54 | + "ataqv": "1.3.1" |
| 55 | + }, |
| 56 | + "MERGED_LIBRARY_ATAQV_MKARV": { |
| 57 | + "ataqv": "1.3.1" |
| 58 | + }, |
| 59 | + "MERGED_LIBRARY_DEEPTOOLS_PLOTFINGERPRINT": { |
| 60 | + "deeptools": "3.5.5" |
| 61 | + }, |
| 62 | + "MERGED_LIBRARY_PICARD_COLLECTMULTIPLEMETRICS": { |
| 63 | + "picard": "3.0.0" |
| 64 | + }, |
| 65 | + "MULTIQC_CUSTOM_PEAKS": { |
| 66 | + "sed": 4.7 |
| 67 | + }, |
| 68 | + "PICARD_MARKDUPLICATES": { |
| 69 | + "picard": "3.1.1" |
| 70 | + }, |
| 71 | + "PICARD_MERGESAMFILES_LIBRARY": { |
| 72 | + "picard": "3.4.0" |
| 73 | + }, |
| 74 | + "PICARD_MERGESAMFILES_REPLICATE": { |
| 75 | + "picard": "3.4.0" |
| 76 | + }, |
| 77 | + "PLOT_HOMER_ANNOTATEPEAKS": { |
| 78 | + "r-base": "4.0.3" |
| 79 | + }, |
| 80 | + "PLOT_MACS3_QC": { |
| 81 | + "r-base": "4.0.3" |
| 82 | + }, |
| 83 | + "SAMPLESHEET_CHECK": { |
| 84 | + "python": "3.8.3" |
| 85 | + }, |
| 86 | + "SAMTOOLS_FLAGSTAT": { |
| 87 | + "samtools": "1.19.2" |
| 88 | + }, |
| 89 | + "SAMTOOLS_IDXSTATS": { |
| 90 | + "samtools": "1.19.2" |
| 91 | + }, |
| 92 | + "SAMTOOLS_INDEX": { |
| 93 | + "samtools": "1.19.2" |
| 94 | + }, |
| 95 | + "SAMTOOLS_SORT": { |
| 96 | + "samtools": "1.19.2" |
| 97 | + }, |
| 98 | + "SAMTOOLS_STATS": { |
| 99 | + "samtools": "1.19.2" |
| 100 | + }, |
| 101 | + "STAR_ALIGN": { |
| 102 | + "star": "2.6.1d" |
| 103 | + }, |
| 104 | + "SUBREAD_FEATURECOUNTS": { |
| 105 | + "subread": "2.0.1" |
| 106 | + }, |
| 107 | + "TRIMGALORE": { |
| 108 | + "trimgalore": "0.6.10" |
| 109 | + }, |
| 110 | + "UCSC_BEDGRAPHTOBIGWIG": { |
| 111 | + "ucsc": 445 |
| 112 | + }, |
| 113 | + "Workflow": { |
| 114 | + "nf-core/atacseq": "v2.2.0dev" |
| 115 | + } |
7 | 116 | }, |
8 | 117 | [ |
9 | 118 | "fastqc", |
|
376 | 485 | "multiqc/broad_peak/multiqc_plots/svg/mqc_samtools_alignment_plot_1_pc.svg", |
377 | 486 | "multiqc/broad_peak/multiqc_report.html", |
378 | 487 | "pipeline_info", |
379 | | - "pipeline_info/nf_core_chipseq_software_mqc_versions.yml", |
| 488 | + "pipeline_info/nf_core_atacseq_software_mqc_versions.yml", |
380 | 489 | "pipeline_info/samplesheet.valid.csv", |
381 | 490 | "star", |
382 | 491 | "star/library", |
|
1024 | 1133 | ], |
1025 | 1134 | "meta": { |
1026 | 1135 | "nf-test": "0.9.3", |
1027 | | - "nextflow": "25.04.7" |
| 1136 | + "nextflow": "26.04.1" |
1028 | 1137 | }, |
1029 | | - "timestamp": "2026-03-23T12:10:00.120333021" |
| 1138 | + "timestamp": "2026-05-20T13:22:07.297454404" |
1030 | 1139 | }, |
1031 | 1140 | "star with stub": { |
1032 | 1141 | "content": [ |
|
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