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Updating import statements to align with new cgat naming convention. #1

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Updating import statements to align with new cgat naming convention. #1

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19 changes: 10 additions & 9 deletions pipeline_salmonquant.py
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Original file line number Diff line number Diff line change
Expand Up @@ -168,24 +168,25 @@
# load modules
from ruffus import *
from ruffus.combinatorics import *
import CGATCore.Experiment as E
import cgatcore.experiment as E

import sys
import os
import re
import glob
import pandas as pd
import sqlite3
import CGAT.Sra as Sra
import cgat.Sra as Sra

from CGATCore import Pipeline as P
import CGAT.GTF as GTF
import CGATCore.IOTools as IOTools
from cgatcore import pipeline as P
import cgat.GTF as GTF
import cgatcore.iotools as IOTools

import CGATPipelines.PipelineGeneset as PipelineGeneset
import CGATPipelines.PipelineRnaseq as PipelineRnaseq
import CGATPipelines.PipelineTracks as PipelineTracks
from CGATPipelines.Report import run_report
import cgatpipelines.tasks.geneset as PipelineGeneset
import cgatpipelines.tasks.rnaseq as PipelineRnaseq
import cgatpipelines.tasks.tracks as PipelineTracks
from cgatpipelines.report import run_report
import cgatpipelines.tasks.expression as Expression
import CGAT.Expression as Expression

###################################################
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