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Commit 1ff81596 authored by Valentina Galata's avatar Valentina Galata
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updated step metaT

parent 1a3372a3
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1 merge request!76Merge "cleanup" branch with "master" branch
......@@ -84,10 +84,10 @@ if 'mmseq' in STEPS:
"mmseq_comparison_for_ont.done"
]
# if 'metaT' in STEPS:
# include:
# "workflows/metat.smk"
# TARGETS += ["metaT_mapping_for_ONT.done"]
if 'metaT' in STEPS:
include:
"workflow/steps/metat.smk"
TARGETS += ["metaT_mapping_for_ONT.done"]
# if 'mapping' in STEPS:
# include:
......
......@@ -2,13 +2,13 @@
# specify which rules to run
include:
'../rules/METAT_RULES'
'../rules/metat.smk'
# Rule all for mappinng metaT reads to all assemblies
rule METAT:
input:
expand(os.path.join(RESULTS_DIR, "preprocessing/metaT/{metaT_sample}.fastp.{report_type}"), metaT_sample="FastSelectHalf1_MT_Rashi_S12", report_type=["html", "json"]),
# expand(os.path.join(RESULTS_DIR, "mapping/metaT/lr/{metaT_sample}-x-{barcode}.bam"), metaT_sample="FastSelectHalf1_MT_Rashi_S12", barcode=BARCODES),
# expand(os.path.join(RESULTS_DIR, "mapping/metaT/lr/{metaT_sample}-x-{barcode}.bam"), metaT_sample="FastSelectHalf1_MT_Rashi_S12", barcode=BARCODES),
expand(os.path.join(RESULTS_DIR, "mapping/metaT/sr/{metaT_sample}_reads-x-{sr_sample}-{assembler}_contigs.bam"), metaT_sample="FastSelectHalf1_MT_Rashi_S12", sr_sample="ONT3_MG_xx_Rashi_S11", assembler="megahit"),
expand(os.path.join(RESULTS_DIR, "mapping/metaT/sr/{metaT_sample}_reads-x-lr_{barcode}_sr_{sr_sample}-{assembler}_contigs.bam"), metaT_sample="FastSelectHalf1_MT_Rashi_S12", sr_sample="ONT3_MG_xx_Rashi_S11", barcode=BARCODES, assembler="metaspades_hybrid"),
expand(os.path.join(RESULTS_DIR, "mapping/metaT/lr/{metaT_sample}_reads-x-{barcode}-{assembler}_contigs.bam"), metaT_sample="FastSelectHalf1_MT_Rashi_S12", barcode=BARCODES, assembler=ASSEMBLERS),
......
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