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| Original file line number | Diff line number | Diff line change |
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| @@ -1,48 +1,54 @@ | ||
| ## FireCloud | ||
| ### preprocess_hic | ||
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| Snapshot ID 24 | ||
| - More accurate fastq file size calculation for many small files | ||
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| Snapshot ID 25 | ||
| - Fix to allow calculation of very small fastq sizes (that use scientific notation) | ||
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| Snapshot ID 26 | ||
| - Added cooler file as output | ||
| Snapshot ID 39 | ||
| - Fixed hicpro Dockerfile bug resulting in missing Hindiii resfrag files | ||
| - Increased disk size for sum_fastq_size task. TODO: replace with simpler docker image | ||
| - Use zcat -f for fastqs to allow compressed and/or uncompressed files | ||
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| Snapshot ID 29 | ||
| - Added juicebox .hic as output | ||
| Snapshot ID 38 | ||
| - sparseHic task: increased memory from 60GB to 104GB and use a single core | ||
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| Snapshot ID 31 | ||
| - Specify genome_id annotation for juicebox .hic | ||
| Snapshot ID 37 | ||
| - Fixed missing space bug (echo`date`) in cooler task | ||
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| Snapshot ID 32 | ||
| - Added sparseHiC .rds as output | ||
| Snapshot ID 36 | ||
| - Dropped memory and disk size for hicpro_align now that iced memory leak is fixed | ||
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| Snapshot ID 33 | ||
| - Increased disk size for hicpro_contact_matrices | ||
| Snapshot ID 35 | ||
| - Increased disk size for hicpro_align from 20GB to 40GB | ||
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| Snapshot ID 34 | ||
| - Increased memory for hicpro_contact_matrices from 60GB to 208GB | ||
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| Snapshot ID 35 | ||
| - Increased disk size for hicpro_align from 20GB to 40GB | ||
| Snapshot ID 33 | ||
| - Increased disk size for hicpro_contact_matrices | ||
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| Snapshot ID 32 | ||
| - Added sparseHiC .rds as output | ||
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| Snapshot ID 36 | ||
| - Dropped memory and disk size for hicpro_align now that iced memory leak is fixed | ||
| Snapshot ID 31 | ||
| - Specify genome_id annotation for juicebox .hic | ||
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| Snapshot ID 29 | ||
| - Added juicebox .hic as output | ||
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| Snapshot ID 37 | ||
| - Fixed missing space bug (echo`date`) in cooler task | ||
| Snapshot ID 26 | ||
| - Added cooler file as output | ||
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||
| Snapshot ID 38 | ||
| - sparseHic task: increased memory from 60GB to 104GB and use a single core | ||
| Snapshot ID 25 | ||
| - Fix to allow calculation of very small fastq sizes (that use scientific notation) | ||
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| Snapshot ID 24 | ||
| - More accurate fastq file size calculation for many small files | ||
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| ### merge_hic_replicates | ||
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| Snapshot ID 14 | ||
| - sparseHic task: increased memory from 60GB to 104GB and use a single core | ||
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| Snapshot ID 10 | ||
| - Changed cis_long_range_percent num_pairs input from Int to String to match count_pairs output (to allow 2+ billion reads) | ||
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| Snapshot ID 14 | ||
| - sparseHic task: increased memory from 60GB to 104GB and use a single core | ||
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