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Commit 97fbac76 authored by ddepanis's avatar ddepanis
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Edit Snakefile

parent 26b9a827
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...@@ -146,7 +146,7 @@ elif set(['sample', 'hifi_reads', 'meryl_kmer_size','trimSMRTbell', 'fastQC']).i ...@@ -146,7 +146,7 @@ elif set(['sample', 'hifi_reads', 'meryl_kmer_size','trimSMRTbell', 'fastQC']).i
if samples['fastQC'].str.contains('True').any(): if samples['fastQC'].str.contains('True').any():
ruleAllQCFiles=[expand(os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/QC/multiqc/{sample}.multiqcReport.html"), sample=key) for key, [value1, value2] in testDictQC.items()] ruleAllQCFiles=[expand(os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/QC/multiqc/{sample}.multiqcReport.html"), sample=key) for key, [value1, value2] in testDictQC.items()]
ruleAll=[expand(os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/merylDb/complete_hifi.{sample}.{kmer}.meryl"), sample=key, kmer=value1) for key, [value1, value2] in dictSamples.items()] ruleAll=[expand(os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/merylDb/complete_hifi.{sample}.{kmer}.meryl"), sample=key, kmer=value1) for key, [value1, value2] in dictSamples.items()]
elif set(['ID', 'ASM_LEVEL', 'busco_lineage', 'PRI_asm', 'ALT_asm', 'merylDB', 'merylDB_kmer', 'genomeSize', 'HiC_R1', 'HiC_R2']).issubset(samples.columns): elif set(['ID', 'ASM_LEVEL', 'busco_lineage', 'PRI_asm', 'ALT_asm', 'merylDB', 'merylDB_kmer', 'genomeSize', 'HiC_R1', 'HiC_R2', 'Long_Reads']).issubset(samples.columns):
whichRule = "rules/evaluate.smk" whichRule = "rules/evaluate.smk"
samples['genomeSize']=samples['genomeSize'].apply(genomeSize_auto_or_not) samples['genomeSize']=samples['genomeSize'].apply(genomeSize_auto_or_not)
...@@ -323,8 +323,14 @@ if "Results" not in config: ...@@ -323,8 +323,14 @@ if "Results" not in config:
include: whichRule include: whichRule
sample_ids = list(samples.index)
final_target_outputs = ruleAllQCFiles, ruleAll final_target_outputs = (
ruleAllQCFiles,
ruleAll,
expand(os.path.join(config['Results'], "1_evaluation/{asmID}/KEY_RESULTS/{asmID}_asm1_summary_statistics.inspector"), asmID=sample_ids),
expand(os.path.join(config['Results'], "1_evaluation/{asmID}/KEY_RESULTS/{asmID}_asm2_summary_statistics.inspector"), asmID=sample_ids)
)
rule all: rule all:
input: input:
......
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