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Fix s3 output #73

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merged 4 commits into from
May 9, 2022
Merged

Fix s3 output #73

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d5a7a82
define data directory as variable
ellisrichardj May 6, 2022
3516ee4
Use nextflow workflow property for commitID
ellisrichardj May 6, 2022
d8ab09a
Merge pull request #74 from APHA-CSU/FixCommitIDcapture
ellisrichardj May 9, 2022
b6dd69d
Update combineCsv.py
ellisrichardj May 9, 2022
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10 changes: 7 additions & 3 deletions bTB-WGS_process.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -78,8 +78,12 @@ FirstFile = file( params.reads ).first()
params.DataDir = TopDir.last()
params.today = new Date().format('ddMMMYY')

seqplate = "${params.DataDir}"

publishDir = "$params.outdir/Results_${params.DataDir}_${params.today}/"

commitId = "${workflow.commitId}"

/* remove duplicates from raw data
This process removes potential duplicate data (sequencing and optical replcaites from the raw data set */
process Deduplicate {
Expand Down Expand Up @@ -334,14 +338,14 @@ process CombineOutput {
publishDir "$params.outdir/Results_${params.DataDir}_${params.today}", mode: 'copy', pattern: '*.csv'

input:
file('Assigned.csv') from Assigned
file('Qbovis.csv') from Qbovis
file('assigned_csv') from Assigned
file('qbovis_csv') from Qbovis

output:
file('*.csv') into FinalOut

"""
combineCsv.py Assigned.csv Qbovis.csv ${params.DataDir}
combineCsv.py assigned_csv qbovis_csv $seqplate $commitId
"""
}

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7 changes: 4 additions & 3 deletions bin/combineCsv.py
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Expand Up @@ -10,13 +10,13 @@
import os
from datetime import datetime, date

def combine(assigned_csv, bovis_csv, seq_run, read_threshold, abundance_threshold):
def combine(assigned_csv, bovis_csv, seq_run, commitId, read_threshold, abundance_threshold):

date_out = date.today().strftime('%d%b%y')
user = getpass.getuser()
scriptpath = os.path.dirname(os.path.abspath(__file__))
repo = git.Repo(scriptpath, search_parent_directories=True)
commit = repo.head.object.__str__()
#commit = repo.head.object.__str__()
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remove the commented line?


#Read Assigned Clade csv and replace blank cells with 'NA'
assigned_df = pd.read_csv(assigned_csv)
Expand Down Expand Up @@ -51,14 +51,15 @@ def combine(assigned_csv, bovis_csv, seq_run, read_threshold, abundance_threshol

#Append log info
with open("{}_FinalOut_{}.csv".format(seq_run, date_out), "a") as outFile:
outFile.write("# Operator: " +user +"\n" +"# BovTB-nf commit: " +commit)
outFile.write("# Operator: " +user +"\n" +"# BovTB-nf commit: " +commitId)
outFile.close

if __name__ == '__main__':
parser = argparse.ArgumentParser()
parser.add_argument('assigned_csv', help='path to AssignedWGSClade.csv')
parser.add_argument('bovis_csv', help='path to Bovis.csv')
parser.add_argument('seq_run', help='Unique sequencer run number')
parser.add_argument('commitId', help='Nextflow capture of git commit')
parser.add_argument('--read_threshold', type=int, default=500, help='threshold for number of M.bovis reads')
parser.add_argument('--abundance_threshold', type=int, default=1, help='threshold for M.bovis abundance')

Expand Down