Commit 94b406e7 authored by Erwan DELAGE's avatar Erwan DELAGE

Split manifest : on force l'outil à considérer les sample-id comme des string,...

Split manifest : on force l'outil à considérer les sample-id comme des string, maj de la rule quality filter si cutadapt a été utilisé
parent f44a03dc
......@@ -408,7 +408,7 @@ def getInput(tool, given_file=""):
return getOutput("cutadapt", "cutadapt.qza") if "cutadapt" in config else getOutput("import", "import.qza")
if tool == "quality_filter":
return getOutput("join_pairs", "joined_sequences.qza") if config["global"]["library-type"] == "paired-end" else getOutput("cutadapt", "cutadapt.qza") if "cutadapt" in config else getOutput("import")
return getOutput("join_pairs", "joined_sequences.qza") if config["global"]["library-type"] == "paired-end" else getOutput("cutadapt", "cutadapt.qza") if "cutadapt" in config else getOutput("import", "import.qza")
if tool == "merge_qualityfilter_stats":
return getOutput("quality_filter", "stats/stats.csv")
......@@ -641,7 +641,7 @@ if "denoiser" in config["global"]:
if wildcards.sample_id == 'All':
df.to_csv(output[0], index=False)
else:
minDf = df[df["sample-id"] == wildcards.sample_id]
minDf = df[df["sample-id"].astype(str) == wildcards.sample_id]
minDf.to_csv(output[0], index=False)
# Import Fastq files into a QIIME2 artifact
......
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