ENCODE-DCC/atac-seq-pipeline: v1.9.0

Conda users should update pipeline's environment. However, reinstalling is always recommended since we added GNU utils to the installer. # To update env $ bash scripts/update_conda_env.sh # To re-install env $ bash scripts/uninstall_conda_env.sh $ bash scripts/install_conda_env.sh New factor-based resource parameters New parameters are factor-based and those factors are multiplied to task's input file sizes to determine required resources (mem/disk) to run a task (on a cloud instance or as an HCP job). e.g. for each replicate, sum of all R1/R2 FASTQs size will be used to determine resource for task align and BAM size will be used for task filter. e.g. if you have total 20 GB (R1 + R2) of PE FASTQs and default atac.align_mem_factor is 0.15 and base memory is fixed at 4-6 GB for most tasks (5 GB for task align). So instance's memory for task align will be 20 * 0.15 + 5 = 8 GB Also, optimized memory/disk requirements for each task, all tasks should use less memory/disk than previous versions. Use SSD for all tasks on Google Cloud. This will cost x4 than HDD but it's still negligible (cost for SSD 100 GB is $0.5 per hour). Change of default for resource parameters atac.align_cpu: 2 -> 6 atac.filter_cpu: 2 -> 4 atac.call_peak_cpu: 1 -> 2 (peak-caller MACS2 is single-threaded. No more than 2 is required) Added resource parameters atac.spr_disk_factor atac.preseq_disk_factor Change of resource parameters. atac.align_mem_mb -> atac.align_mem_factor atac.align_disks -> atac.align_disk_factor atac.filter_mem_mb -> atac.filter_mem_factor atac.filter_disks -> atac.filter_disk_factor atac.bam2ta_mem_mb -> atac.bam2ta_mem_factor atac.bam2ta_disks -> atac.bam2ta_disk_factor atac.xcor_mem_mb -> atac.xcor_mem_factor atac.xcor_disks -> atac.xcor_disk_factor atac.spr_mem_mb -> atac.spr_mem_factor atac.jsd_mem_mb -> atac.jsd_mem_factor atac.jsd_disks -> atac.jsd_disk_factor atac.call_peak_mem_mb -> atac.call_peak_mem_factor atac.call_peak_disks -> atac.call_peak_disk_factor atac.macs2_signal_track_mem_mb -> atac.macs2_signal_track_mem_factor atac.macs2_signal_track_disks -> atac.macs2_signal_track_disk_factor atac.preseq_mem_mb -> atac.preseq_mem_factor Misc. Better multi-threading samtools view/index/sort. Added GNU utils to Conda environment