for l in sfile:
if i == 0:
command+= l + "`\n\n"
i+=1
return command;
title = getSampleList(snakemake.wildcards.PROJECT+"/runs/"+snakemake.wildcards.run+"/samples.log")
catCommand = getCombinedSamplesList(snakemake.wildcards.PROJECT+"/runs/"+snakemake.wildcards.run+"/cat_samples.log")
################################################################################
# Benchmark Section #
# This section is to generate a pre-formatted text with the benchmark info for #
# All the executed rules. #
################################################################################
combineBenchmark = readBenchmark(snakemake.wildcards.PROJECT+"/runs/"+snakemake.wildcards.run+"/combine_seqs_fw_rev.benchmark")
otuBenchmark = readBenchmark(snakemake.wildcards.PROJECT+"/runs/"+snakemake.wildcards.run+"/otu.benchmark")
pikRepBenchmark = readBenchmark(snakemake.wildcards.PROJECT+"/runs/"+snakemake.wildcards.run+"/pick_reps.benchmark")
assignTaxaBenchmark = readBenchmark(snakemake.wildcards.PROJECT+"/runs/"+snakemake.wildcards.run+"/otu/taxonomy_"+snakemake.config["assignTaxonomy"]["tool"]+"/assign_taxa.benchmark")
otuTableBenchmark = readBenchmark(snakemake.wildcards.PROJECT+"/runs/"+snakemake.wildcards.run+"/otu/taxonomy_"+snakemake.config["assignTaxonomy"]["tool"]+"/otuTable.biom.benchmark")
convertOtuBenchmark = readBenchmark(snakemake.wildcards.PROJECT+"/runs/"+snakemake.wildcards.run+"/otu/taxonomy_"+snakemake.config["assignTaxonomy"]["tool"]+"/otuTable.txt.benchmark")
summTaxaBenchmark = readBenchmark(snakemake.wildcards.PROJECT+"/runs/"+snakemake.wildcards.run+"/otu/taxonomy_"+snakemake.config["assignTaxonomy"]["tool"]+"/summary/summarize_taxa.benchmark")
otuNoSingletonsBenchmark = readBenchmark(snakemake.wildcards.PROJECT+"/runs/"+snakemake.wildcards.run+"/otu/taxonomy_"+snakemake.config["assignTaxonomy"]["tool"]+"/otuTable_nosingletons.bio.benchmark")
filterBenchmark = readBenchmark(snakemake.wildcards.PROJECT+"/runs/"+snakemake.wildcards.run+"/otu/taxonomy_"+snakemake.config["assignTaxonomy"]["tool"]+"/representative_seq_set_noSingletons.benchmark")
deRepBenchmark=""
if snakemake.config["derep"]["dereplicate"] == "T" and snakemake.config["pickOTU"]["m"] != "swarm" and snakemake.config["pickOTU"]["m"] != "usearch":
deRepBenchmark = readBenchmark(snakemake.wildcards.PROJECT+"/runs/"+snakemake.wildcards.run+"/derep/derep.benchmark")
if snakemake.config["alignRep"]["align"] == "T":
#align_seqs.py -m {config[alignRep][m]} -i {input} -o {params.outdir} {config[alignRep][extra_params]}
alignBenchmark = readBenchmark(snakemake.wildcards.PROJECT+"/runs/"+snakemake.wildcards.run+"/otu/taxonomy_"+snakemake.config["assignTaxonomy"]["tool"]+"/aligned/align_rep_seqs.benchmark")
#"filter_alignment.py -i {input} -o {params.outdir} {config[filterAlignment][extra_params]}"
snakemake.wildcards.run + "/" + snakemake.wildcards.sample +
"_data/chimera/chimera.log") as chimlog:
for line in chimlog:
chimera_log += line
chimlog.close()
except FileNotFoundError:
chiemra_log = "No Log for identify_chimeric_seqs.py"
if "The chimeric sequences were removed" in chimera_log:
removeChimeras = True
################################################################################
# Benchmark Section #
# This section is to generate a pre-formatted text with the benchmark info for #
# All the executed rules. #
################################################################################
fqBench = readBenchmark(snakemake.wildcards.PROJECT + "/samples/" +
snakemake.wildcards.sample + "/qc/fq.benchmark")
pearBench = readBenchmark(snakemake.wildcards.PROJECT + "/runs/" +
snakemake.wildcards.run + "/" +
snakemake.wildcards.sample +
"_data/peared/pear.benchmark")
if snakemake.config["demultiplexing"]["demultiplex"] != "F":
barBench = readBenchmark(snakemake.wildcards.PROJECT + "/runs/" +
snakemake.wildcards.run + "/" +
snakemake.wildcards.sample +
"_data/barcodes/barcodes.benchmark")
splitLibsBench = readBenchmark(snakemake.wildcards.PROJECT + "/runs/" +
snakemake.wildcards.run + "/" +
snakemake.wildcards.sample +
"_data/splitLibs/splitLibs.benchmark")
splitLibsRCBench = readBenchmark(snakemake.wildcards.PROJECT + "/runs/" +
snakemake.wildcards.run + "/" +
if i == 0:
command+= l + "`\n\n"
i+=1
return command;
#title = getSampleList(snakemake.wildcards.PROJECT+"/runs/"+snakemake.wildcards.run+"/samples.log")
#catCommand = getCombinedSamplesList(snakemake.wildcards.PROJECT+"/runs/"+snakemake.wildcards.run+"/cat_samples.log")
title = "Amplicon Analysis Report\n===========================\n\n"
################################################################################
# Benchmark Section #
# This section is to generate a pre-formatted text with the benchmark info for #
# All the executed rules. #
################################################################################
#combineBenchmark = readBenchmark(snakemake.wildcards.PROJECT+"/runs/"+snakemake.wildcards.run+"/combine_seqs_fw_rev.benchmark")
dada2Benchmark = readBenchmark(snakemake.wildcards.PROJECT+"/runs/"+snakemake.wildcards.run+"/asv/dada2.benchmark")
asvFilterBenchmark = readBenchmark(snakemake.wildcards.PROJECT+"/runs/"+snakemake.wildcards.run+"/asv/filter.benchmark")
#pikRepBenchmark = readBenchmark(snakemake.wildcards.PROJECT+"/runs/"+snakemake.wildcards.run+"/pick_reps.benchmark")
#assignTaxaBenchmark = readBenchmark(snakemake.wildcards.PROJECT+"/runs/"+snakemake.wildcards.run+"/otu/taxonomy_"+snakemake.config["assignTaxonomy"]["tool"]+"/assign_taxa.benchmark")
otuTableBenchmark = readBenchmark(snakemake.wildcards.PROJECT+"/runs/"+snakemake.wildcards.run+"/asv/taxonomy_dada2/dada2.table.benchmark")
convertOtuBenchmark = readBenchmark(snakemake.wildcards.PROJECT+"/runs/"+snakemake.wildcards.run+"/asv/taxonomy_dada2/dada2.biom.benchmark")
#convertOtuBenchmark = readBenchmark(snakemake.wildcards.PROJECT+"/runs/"+snakemake.wildcards.run+"/otu/taxonomy_"+snakemake.config["assignTaxonomy"]["tool"]+"/otuTable.txt.benchmark")
summTaxaBenchmark = readBenchmark(snakemake.wildcards.PROJECT+"/runs/"+snakemake.wildcards.run+"/otu/taxonomy_"+snakemake.config["assignTaxonomy"]["tool"]+"/summary/summarize_taxa.benchmark")
asvNoSingletonsBenchmark = readBenchmark(snakemake.wildcards.PROJECT+"/runs/"+snakemake.wildcards.run+"/asv/taxonomy_dada2/asvTable_nosingletons.bio.benchmark")
filterASVTableBenchmark = readBenchmark(snakemake.wildcards.PROJECT+"/runs/"+snakemake.wildcards.run+"/asv/taxonomy_dada2/asvTable_nosingletons.txt.benchmark")
filterBenchmark = readBenchmark(snakemake.wildcards.PROJECT+"/runs/"+snakemake.wildcards.run+"/asv/taxonomy_dada2/representative_seq_set_noSingletons.benchmark")
deRepBenchmark=""
#if snakemake.config["derep"]["dereplicate"] == "T" and snakemake.config["pickOTU"]["m"] != "swarm" and snakemake.config["pickOTU"]["m"] != "usearch":
# deRepBenchmark = readBenchmark(snakemake.wildcards.PROJECT+"/runs/"+snakemake.wildcards.run+"/derep/derep.benchmark")
if snakemake.config["alignRep"]["align"] == "T":
