rule all: 
	input: '/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/GenerateMosaic/tasks/GenerateMosaic.done','/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/ExportBarcodes/tasks/ExportBarcodes.done'

rule FiducialCorrelationWarp:
	input: 
	output: '/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/FiducialCorrelationWarp/tasks/FiducialCorrelationWarp_{i}.done'
	message: 'Running FiducialCorrelationWarp {wildcards.i}'
	shell: '/home/lbinan/miniconda/envs/merlin_env/bin/python -m merlin -t FiducialCorrelationWarp -e "gs://thp1homemademerfish_1/thp1homemademerfish_1" -s "/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1" -i {wildcards.i} Data'

rule FiducialCorrelationWarpDone:
	input: expand('/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/FiducialCorrelationWarp/tasks/FiducialCorrelationWarp_{g}.done', g=list(range(1276)))
	output: '/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/FiducialCorrelationWarp/tasks/FiducialCorrelationWarp.done'
	message: 'Checking FiducialCorrelationWarp done'
	shell: '/home/lbinan/miniconda/envs/merlin_env/bin/python -m merlin -t FiducialCorrelationWarp -e "gs://thp1homemademerfish_1/thp1homemademerfish_1" -s "/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1" --check-done Data'


rule DeconvolutionPreprocess:
	input: ancient('/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/FiducialCorrelationWarp/tasks/FiducialCorrelationWarp.done')
	output: '/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/DeconvolutionPreprocess/tasks/DeconvolutionPreprocess_{i}.done'
	message: 'Running DeconvolutionPreprocess {wildcards.i}'
	shell: '/home/lbinan/miniconda/envs/merlin_env/bin/python -m merlin -t DeconvolutionPreprocess -e "gs://thp1homemademerfish_1/thp1homemademerfish_1" -s "/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1" -i {wildcards.i} Data'

rule DeconvolutionPreprocessDone:
	input: expand('/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/DeconvolutionPreprocess/tasks/DeconvolutionPreprocess_{g}.done', g=list(range(1276)))
	output: '/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/DeconvolutionPreprocess/tasks/DeconvolutionPreprocess.done'
	message: 'Checking DeconvolutionPreprocess done'
	shell: '/home/lbinan/miniconda/envs/merlin_env/bin/python -m merlin -t DeconvolutionPreprocess -e "gs://thp1homemademerfish_1/thp1homemademerfish_1" -s "/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1" --check-done Data'


rule Optimize1:
	input: ancient('/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/DeconvolutionPreprocess/tasks/DeconvolutionPreprocess.done'),ancient('/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/FiducialCorrelationWarp/tasks/FiducialCorrelationWarp.done')
	output: '/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/Optimize1/tasks/Optimize1_{i}.done'
	message: 'Running Optimize1 {wildcards.i}'
	shell: '/home/lbinan/miniconda/envs/merlin_env/bin/python -m merlin -t Optimize1 -e "gs://thp1homemademerfish_1/thp1homemademerfish_1" -s "/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1" -i {wildcards.i} Data'

rule Optimize1Done:
	input: expand('/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/Optimize1/tasks/Optimize1_{g}.done', g=list(range(50)))
	output: '/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/Optimize1/tasks/Optimize1.done'
	message: 'Checking Optimize1 done'
	shell: '/home/lbinan/miniconda/envs/merlin_env/bin/python -m merlin -t Optimize1 -e "gs://thp1homemademerfish_1/thp1homemademerfish_1" -s "/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1" --check-done Data'


rule Optimize2:
	input: ancient('/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/DeconvolutionPreprocess/tasks/DeconvolutionPreprocess.done'),ancient('/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/FiducialCorrelationWarp/tasks/FiducialCorrelationWarp.done'),ancient('/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/Optimize1/tasks/Optimize1.done')
	output: '/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/Optimize2/tasks/Optimize2_{i}.done'
	message: 'Running Optimize2 {wildcards.i}'
	shell: '/home/lbinan/miniconda/envs/merlin_env/bin/python -m merlin -t Optimize2 -e "gs://thp1homemademerfish_1/thp1homemademerfish_1" -s "/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1" -i {wildcards.i} Data'

rule Optimize2Done:
	input: expand('/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/Optimize2/tasks/Optimize2_{g}.done', g=list(range(50)))
	output: '/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/Optimize2/tasks/Optimize2.done'
	message: 'Checking Optimize2 done'
	shell: '/home/lbinan/miniconda/envs/merlin_env/bin/python -m merlin -t Optimize2 -e "gs://thp1homemademerfish_1/thp1homemademerfish_1" -s "/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1" --check-done Data'


rule Optimize3:
	input: ancient('/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/DeconvolutionPreprocess/tasks/DeconvolutionPreprocess.done'),ancient('/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/FiducialCorrelationWarp/tasks/FiducialCorrelationWarp.done'),ancient('/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/Optimize2/tasks/Optimize2.done')
	output: '/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/Optimize3/tasks/Optimize3_{i}.done'
	message: 'Running Optimize3 {wildcards.i}'
	shell: '/home/lbinan/miniconda/envs/merlin_env/bin/python -m merlin -t Optimize3 -e "gs://thp1homemademerfish_1/thp1homemademerfish_1" -s "/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1" -i {wildcards.i} Data'

rule Optimize3Done:
	input: expand('/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/Optimize3/tasks/Optimize3_{g}.done', g=list(range(50)))
	output: '/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/Optimize3/tasks/Optimize3.done'
	message: 'Checking Optimize3 done'
	shell: '/home/lbinan/miniconda/envs/merlin_env/bin/python -m merlin -t Optimize3 -e "gs://thp1homemademerfish_1/thp1homemademerfish_1" -s "/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1" --check-done Data'


rule Optimize4:
	input: ancient('/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/DeconvolutionPreprocess/tasks/DeconvolutionPreprocess.done'),ancient('/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/FiducialCorrelationWarp/tasks/FiducialCorrelationWarp.done'),ancient('/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/Optimize3/tasks/Optimize3.done')
	output: '/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/Optimize4/tasks/Optimize4_{i}.done'
	message: 'Running Optimize4 {wildcards.i}'
	shell: '/home/lbinan/miniconda/envs/merlin_env/bin/python -m merlin -t Optimize4 -e "gs://thp1homemademerfish_1/thp1homemademerfish_1" -s "/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1" -i {wildcards.i} Data'

rule Optimize4Done:
	input: expand('/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/Optimize4/tasks/Optimize4_{g}.done', g=list(range(50)))
	output: '/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/Optimize4/tasks/Optimize4.done'
	message: 'Checking Optimize4 done'
	shell: '/home/lbinan/miniconda/envs/merlin_env/bin/python -m merlin -t Optimize4 -e "gs://thp1homemademerfish_1/thp1homemademerfish_1" -s "/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1" --check-done Data'


rule Optimize5:
	input: ancient('/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/DeconvolutionPreprocess/tasks/DeconvolutionPreprocess.done'),ancient('/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/FiducialCorrelationWarp/tasks/FiducialCorrelationWarp.done'),ancient('/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/Optimize4/tasks/Optimize4.done')
	output: '/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/Optimize5/tasks/Optimize5_{i}.done'
	message: 'Running Optimize5 {wildcards.i}'
	shell: '/home/lbinan/miniconda/envs/merlin_env/bin/python -m merlin -t Optimize5 -e "gs://thp1homemademerfish_1/thp1homemademerfish_1" -s "/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1" -i {wildcards.i} Data'

rule Optimize5Done:
	input: expand('/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/Optimize5/tasks/Optimize5_{g}.done', g=list(range(50)))
	output: '/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/Optimize5/tasks/Optimize5.done'
	message: 'Checking Optimize5 done'
	shell: '/home/lbinan/miniconda/envs/merlin_env/bin/python -m merlin -t Optimize5 -e "gs://thp1homemademerfish_1/thp1homemademerfish_1" -s "/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1" --check-done Data'


rule Optimize6:
	input: ancient('/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/DeconvolutionPreprocess/tasks/DeconvolutionPreprocess.done'),ancient('/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/FiducialCorrelationWarp/tasks/FiducialCorrelationWarp.done'),ancient('/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/Optimize5/tasks/Optimize5.done')
	output: '/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/Optimize6/tasks/Optimize6_{i}.done'
	message: 'Running Optimize6 {wildcards.i}'
	shell: '/home/lbinan/miniconda/envs/merlin_env/bin/python -m merlin -t Optimize6 -e "gs://thp1homemademerfish_1/thp1homemademerfish_1" -s "/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1" -i {wildcards.i} Data'

rule Optimize6Done:
	input: expand('/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/Optimize6/tasks/Optimize6_{g}.done', g=list(range(50)))
	output: '/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/Optimize6/tasks/Optimize6.done'
	message: 'Checking Optimize6 done'
	shell: '/home/lbinan/miniconda/envs/merlin_env/bin/python -m merlin -t Optimize6 -e "gs://thp1homemademerfish_1/thp1homemademerfish_1" -s "/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1" --check-done Data'


rule Optimize7:
	input: ancient('/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/DeconvolutionPreprocess/tasks/DeconvolutionPreprocess.done'),ancient('/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/FiducialCorrelationWarp/tasks/FiducialCorrelationWarp.done'),ancient('/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/Optimize6/tasks/Optimize6.done')
	output: '/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/Optimize7/tasks/Optimize7_{i}.done'
	message: 'Running Optimize7 {wildcards.i}'
	shell: '/home/lbinan/miniconda/envs/merlin_env/bin/python -m merlin -t Optimize7 -e "gs://thp1homemademerfish_1/thp1homemademerfish_1" -s "/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1" -i {wildcards.i} Data'

rule Optimize7Done:
	input: expand('/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/Optimize7/tasks/Optimize7_{g}.done', g=list(range(50)))
	output: '/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/Optimize7/tasks/Optimize7.done'
	message: 'Checking Optimize7 done'
	shell: '/home/lbinan/miniconda/envs/merlin_env/bin/python -m merlin -t Optimize7 -e "gs://thp1homemademerfish_1/thp1homemademerfish_1" -s "/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1" --check-done Data'


rule Optimize8:
	input: ancient('/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/DeconvolutionPreprocess/tasks/DeconvolutionPreprocess.done'),ancient('/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/FiducialCorrelationWarp/tasks/FiducialCorrelationWarp.done'),ancient('/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/Optimize7/tasks/Optimize7.done')
	output: '/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/Optimize8/tasks/Optimize8_{i}.done'
	message: 'Running Optimize8 {wildcards.i}'
	shell: '/home/lbinan/miniconda/envs/merlin_env/bin/python -m merlin -t Optimize8 -e "gs://thp1homemademerfish_1/thp1homemademerfish_1" -s "/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1" -i {wildcards.i} Data'

rule Optimize8Done:
	input: expand('/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/Optimize8/tasks/Optimize8_{g}.done', g=list(range(50)))
	output: '/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/Optimize8/tasks/Optimize8.done'
	message: 'Checking Optimize8 done'
	shell: '/home/lbinan/miniconda/envs/merlin_env/bin/python -m merlin -t Optimize8 -e "gs://thp1homemademerfish_1/thp1homemademerfish_1" -s "/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1" --check-done Data'


rule Optimize9:
	input: ancient('/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/DeconvolutionPreprocess/tasks/DeconvolutionPreprocess.done'),ancient('/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/FiducialCorrelationWarp/tasks/FiducialCorrelationWarp.done'),ancient('/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/Optimize8/tasks/Optimize8.done')
	output: '/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/Optimize9/tasks/Optimize9_{i}.done'
	message: 'Running Optimize9 {wildcards.i}'
	shell: '/home/lbinan/miniconda/envs/merlin_env/bin/python -m merlin -t Optimize9 -e "gs://thp1homemademerfish_1/thp1homemademerfish_1" -s "/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1" -i {wildcards.i} Data'

rule Optimize9Done:
	input: expand('/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/Optimize9/tasks/Optimize9_{g}.done', g=list(range(50)))
	output: '/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/Optimize9/tasks/Optimize9.done'
	message: 'Checking Optimize9 done'
	shell: '/home/lbinan/miniconda/envs/merlin_env/bin/python -m merlin -t Optimize9 -e "gs://thp1homemademerfish_1/thp1homemademerfish_1" -s "/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1" --check-done Data'


rule Optimize10:
	input: ancient('/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/DeconvolutionPreprocess/tasks/DeconvolutionPreprocess.done'),ancient('/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/FiducialCorrelationWarp/tasks/FiducialCorrelationWarp.done'),ancient('/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/Optimize9/tasks/Optimize9.done')
	output: '/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/Optimize10/tasks/Optimize10_{i}.done'
	message: 'Running Optimize10 {wildcards.i}'
	shell: '/home/lbinan/miniconda/envs/merlin_env/bin/python -m merlin -t Optimize10 -e "gs://thp1homemademerfish_1/thp1homemademerfish_1" -s "/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1" -i {wildcards.i} Data'

rule Optimize10Done:
	input: expand('/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/Optimize10/tasks/Optimize10_{g}.done', g=list(range(50)))
	output: '/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/Optimize10/tasks/Optimize10.done'
	message: 'Checking Optimize10 done'
	shell: '/home/lbinan/miniconda/envs/merlin_env/bin/python -m merlin -t Optimize10 -e "gs://thp1homemademerfish_1/thp1homemademerfish_1" -s "/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1" --check-done Data'


rule Decode:
	input: ancient('/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/DeconvolutionPreprocess/tasks/DeconvolutionPreprocess.done'),ancient('/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/Optimize10/tasks/Optimize10.done'),ancient('/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/SimpleGlobalAlignment/tasks/SimpleGlobalAlignment.done')
	output: '/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/Decode/tasks/Decode_{i}.done'
	message: 'Running Decode {wildcards.i}'
	shell: '/home/lbinan/miniconda/envs/merlin_env/bin/python -m merlin -t Decode -e "gs://thp1homemademerfish_1/thp1homemademerfish_1" -s "/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1" -i {wildcards.i} Data'

rule DecodeDone:
	input: expand('/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/Decode/tasks/Decode_{g}.done', g=list(range(1276)))
	output: '/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/Decode/tasks/Decode.done'
	message: 'Checking Decode done'
	shell: '/home/lbinan/miniconda/envs/merlin_env/bin/python -m merlin -t Decode -e "gs://thp1homemademerfish_1/thp1homemademerfish_1" -s "/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1" --check-done Data'


rule SimpleGlobalAlignment:
	input: 
	output: '/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/SimpleGlobalAlignment/tasks/SimpleGlobalAlignment.done'
	message: 'Running SimpleGlobalAlignment'
	shell: '/home/lbinan/miniconda/envs/merlin_env/bin/python -m merlin -t SimpleGlobalAlignment -e "gs://thp1homemademerfish_1/thp1homemademerfish_1" -s "/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1" Data'


rule GenerateMosaic:
	input: ancient('/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/SimpleGlobalAlignment/tasks/SimpleGlobalAlignment.done'),ancient('/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/FiducialCorrelationWarp/tasks/FiducialCorrelationWarp.done')
	output: '/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/GenerateMosaic/tasks/GenerateMosaic.done'
	message: 'Running GenerateMosaic'
	shell: '/home/lbinan/miniconda/envs/merlin_env/bin/python -m merlin -t GenerateMosaic -e "gs://thp1homemademerfish_1/thp1homemademerfish_1" -s "/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1" Data'


rule ExportBarcodes:
	input: ancient('/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/AdaptiveFilterBarcodes/tasks/AdaptiveFilterBarcodes.done')
	output: '/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/ExportBarcodes/tasks/ExportBarcodes.done'
	message: 'Running ExportBarcodes'
	shell: '/home/lbinan/miniconda/envs/merlin_env/bin/python -m merlin -t ExportBarcodes -e "gs://thp1homemademerfish_1/thp1homemademerfish_1" -s "/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1" Data'


rule GenerateAdaptiveThreshold:
	input: ancient('/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/Optimize10/tasks/Optimize10.done')
	output: '/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/GenerateAdaptiveThreshold/tasks/GenerateAdaptiveThreshold.done'
	message: 'Running GenerateAdaptiveThreshold'
	shell: '/home/lbinan/miniconda/envs/merlin_env/bin/python -m merlin -t GenerateAdaptiveThreshold -e "gs://thp1homemademerfish_1/thp1homemademerfish_1" -s "/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1" Data'


rule AdaptiveFilterBarcodes:
	input: ancient('/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/GenerateAdaptiveThreshold/tasks/GenerateAdaptiveThreshold.done'),ancient('/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/Decode/tasks/Decode.done')
	output: '/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/AdaptiveFilterBarcodes/tasks/AdaptiveFilterBarcodes_{i}.done'
	message: 'Running AdaptiveFilterBarcodes {wildcards.i}'
	shell: '/home/lbinan/miniconda/envs/merlin_env/bin/python -m merlin -t AdaptiveFilterBarcodes -e "gs://thp1homemademerfish_1/thp1homemademerfish_1" -s "/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1" -i {wildcards.i} Data'

rule AdaptiveFilterBarcodesDone:
	input: expand('/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/AdaptiveFilterBarcodes/tasks/AdaptiveFilterBarcodes_{g}.done', g=list(range(1276)))
	output: '/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1/Data/AdaptiveFilterBarcodes/tasks/AdaptiveFilterBarcodes.done'
	message: 'Checking AdaptiveFilterBarcodes done'
	shell: '/home/lbinan/miniconda/envs/merlin_env/bin/python -m merlin -t AdaptiveFilterBarcodes -e "gs://thp1homemademerfish_1/thp1homemademerfish_1" -s "/mnt/disks/pep/thp1homemademerfish_1/thp1homemademerfish_1" --check-done Data'