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Syntax corrections 1-4 #75

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1 change: 0 additions & 1 deletion input/sampledata.txt
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Original file line number Diff line number Diff line change
@@ -1,5 +1,4 @@
SampleName SampleID AssemblyGroup FastqFile
HN008_subsampled HN008 samplegroup1 HN008/HN008_subsampled
HN009_subsampled HN009 samplegroup2 HN009_subsampled
HN016_subsampled HN016 samplegroup1 HN016_subsampled
HN036_subsampled HN036 samplegroup1 HN036_subsampled
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4 changes: 2 additions & 2 deletions rules/02-trim.smk
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Expand Up @@ -71,8 +71,8 @@ rule trimmomatic:
"02-trim",\
"{sample}_2.unpaired.fastq.gz")
log:
err = os.path.join(OUTPUTDIR, "logs",\
"01-setup", "02-trim",\
err = os.path.join(OUTPUTDIR, "logs",\
"01-setup", "02-trim",\
"PE_{sample}_err.log"),
out = os.path.join(OUTPUTDIR, "logs",\
"01-setup", "02-trim",\
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4 changes: 2 additions & 2 deletions rules/11-SWAM.smk
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Expand Up @@ -41,9 +41,9 @@ rule merge_all:
'''
echo "" > {output}
for assemblyfile in {params.assemblyfiles}; do
currvar=$(echo $assemblyfile | rev | cut -f1 -d\/ | rev)
currvar=$(echo $assemblyfile | rev | cut -f1 -d\\/ | rev)
sed 's/>.*/&_'"$currvar"'/' $assemblyfile >> {output}
done
#cat {params.assemblyfiles} > {output}
'''


2 changes: 1 addition & 1 deletion rules/12-MAD.smk
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Expand Up @@ -116,7 +116,7 @@ rule replace_mad_ids:
"rename","MAD.{filter_workflow}.fasta")
run:
sequences=[curr for curr in SeqIO.parse(input.mad,"fasta")]
concordance=pd.read_csv(input.concordance,sep="\s+")
concordance=pd.read_csv(input.concordance,sep="\\s+")
concord_dict=dict(zip(concordance["MAD_id"],concordance["Concordance_Short_ID"]))
for i,curr in enumerate(sequences):
curr.id = concord_dict[curr.id]
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