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clean up imports from snakefiles
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@pdimens
pdimens committed Sep 4, 2024
1 parent 169f56a commit d15c9ae
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Showing 19 changed files with 0 additions and 26 deletions.
1 change: 0 additions & 1 deletion harpy/snakefiles/align_bwa.smk
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Expand Up @@ -2,7 +2,6 @@ containerized: "docker://pdimens/harpy:latest"

import os
import re
import sys
import logging

onstart:
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2 changes: 0 additions & 2 deletions harpy/snakefiles/align_ema.smk
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Expand Up @@ -2,9 +2,7 @@ containerized: "docker://pdimens/harpy:latest"

import os
import re
import shutil
import logging
from pathlib import Path

onstart:
logger.logger.addHandler(logging.FileHandler(config["snakemake_log"]))
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1 change: 0 additions & 1 deletion harpy/snakefiles/align_strobealign.smk
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Expand Up @@ -2,7 +2,6 @@ containerized: "docker://pdimens/harpy:latest"

import os
import re
import sys
import logging

onstart:
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1 change: 0 additions & 1 deletion harpy/snakefiles/deconvolve.smk
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Expand Up @@ -2,7 +2,6 @@ containerized: "docker://pdimens/harpy:latest"

import os
import re
import sys
import logging

onstart:
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2 changes: 0 additions & 2 deletions harpy/snakefiles/demultiplex_gen1.smk
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containerized: "docker://pdimens/harpy:latest"

import os
import re
import sys
import logging

onstart:
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3 changes: 0 additions & 3 deletions harpy/snakefiles/impute.smk
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containerized: "docker://pdimens/harpy:latest"

import os
import re
import sys
import subprocess
import pandas as pd
import logging
from snakemake.utils import Paramspace
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1 change: 0 additions & 1 deletion harpy/snakefiles/phase.smk
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containerized: "docker://pdimens/harpy:latest"

import os
import sys
import subprocess
import logging
from pathlib import Path
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1 change: 0 additions & 1 deletion harpy/snakefiles/preflight_bam.smk
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Expand Up @@ -2,7 +2,6 @@ containerized: "docker://pdimens/harpy:latest"

import os
import re
import sys
import logging
from pathlib import Path

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2 changes: 0 additions & 2 deletions harpy/snakefiles/preflight_fastq.smk
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Expand Up @@ -2,9 +2,7 @@ containerized: "docker://pdimens/harpy:latest"

import os
import re
import sys
import logging
from pathlib import Path

onstart:
logger.logger.addHandler(logging.FileHandler(config["snakemake_log"]))
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1 change: 0 additions & 1 deletion harpy/snakefiles/qc.smk
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Expand Up @@ -2,7 +2,6 @@ containerized: "docker://pdimens/harpy:latest"

import os
import re
import sys
import logging

onstart:
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2 changes: 0 additions & 2 deletions harpy/snakefiles/simulate_linkedreads.smk
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containerized: "docker://pdimens/harpy:latest"

import os
import sys
import gzip
import shutil
import logging
from pathlib import Path

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1 change: 0 additions & 1 deletion harpy/snakefiles/simulate_snpindel.smk
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containerized: "docker://pdimens/harpy:latest"

import os
import sys
import random
import logging

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1 change: 0 additions & 1 deletion harpy/snakefiles/simulate_variants.smk
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containerized: "docker://pdimens/harpy:latest"

import os
import sys
import random
import logging

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1 change: 0 additions & 1 deletion harpy/snakefiles/sv_leviathan.smk
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Expand Up @@ -2,7 +2,6 @@ containerized: "docker://pdimens/harpy:latest"

import os
import re
import sys
import logging
from pathlib import Path

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1 change: 0 additions & 1 deletion harpy/snakefiles/sv_leviathan_pop.smk
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Expand Up @@ -2,7 +2,6 @@ containerized: "docker://pdimens/harpy:latest"

import os
import re
import sys
import logging

onstart:
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1 change: 0 additions & 1 deletion harpy/snakefiles/sv_naibr.smk
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Expand Up @@ -2,7 +2,6 @@ containerized: "docker://pdimens/harpy:latest"

import os
import re
import sys
import logging
from pathlib import Path

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1 change: 0 additions & 1 deletion harpy/snakefiles/sv_naibr_phase.smk
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Expand Up @@ -2,7 +2,6 @@ containerized: "docker://pdimens/harpy:latest"

import os
import re
import sys
import logging
from pathlib import Path

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2 changes: 0 additions & 2 deletions harpy/snakefiles/sv_naibr_pop.smk
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Expand Up @@ -2,8 +2,6 @@ containerized: "docker://pdimens/harpy:latest"

import os
import re
import sys
import multiprocessing
import logging
from pathlib import Path

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1 change: 0 additions & 1 deletion harpy/snakefiles/sv_naibr_pop_phase.smk
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Expand Up @@ -2,7 +2,6 @@ containerized: "docker://pdimens/harpy:latest"

import os
import re
import sys
import logging
from pathlib import Path

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