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There was not as much output as I expected
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@MaartenPostuma
MaartenPostuma committed Oct 12, 2021
1 parent 413e8f2 commit 869875a
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Showing 2 changed files with 8 additions and 20 deletions.
14 changes: 4 additions & 10 deletions src/rules/denovo.rules
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Original file line number Diff line number Diff line change
Expand Up @@ -140,18 +140,12 @@ rule methylation_calling_denovo_bismark:
output:
calling=temp(expand("{out}/methylation_calling/{{sample}}_trimmed_filt_merged.1_bismark_bt2_pe.CX_report.txt",out=config["output_dir"])),
coveragecompr=expand("{out}/methylation_calling/{{sample}}_trimmed_filt_merged.1_bismark_bt2_pe.bismark.cov.gz",out=config["output_dir"]),
cHH_CTOB=temp(expand("{out}/methylation_calling/CHH_CTOB_{{sample}}_trimmed_filt_merged.1_bismark_bt2_pe.txt",out=config["output_dir"])),
cHH_OB=temp(expand("{out}/methylation_calling/CHH_OB_{{sample}}_trimmed_filt_merged.1_bismark_bt2_pe.txt",out=config["output_dir"])),
cHG_CTOB=temp(expand("{out}/methylation_calling/CHG_CTOB_{{sample}}_trimmed_filt_merged.1_bismark_bt2_pe.txt",out=config["output_dir"])),
cHG_OB=temp(expand("{out}/methylation_calling/CHG_CTOB_{{sample}}_trimmed_filt_merged.1_bismark_bt2_pe.txt",out=config["output_dir"])),
cG_CTOB=temp(expand("{out}/methylation_calling/CG_CTOB_{{sample}}_trimmed_filt_merged.1_bismark_bt2_pe.txt",out=config["output_dir"])),
cG_OB=temp(expand("{out}/methylation_calling/CG_CTOB_{{sample}}_trimmed_filt_merged.1_bismark_bt2_pe.txt",out=config["output_dir"])),
cHH_CTOT=temp(expand("{out}/methylation_calling/CHH_CTOT_{{sample}}_trimmed_filt_merged.1_bismark_bt2_pe.txt",out=config["output_dir"])),
cHG_OB=temp(expand("{out}/methylation_calling/CHG_OB_{{sample}}_trimmed_filt_merged.1_bismark_bt2_pe.txt",out=config["output_dir"])),
cG_OB=temp(expand("{out}/methylation_calling/CpG_OB_{{sample}}_trimmed_filt_merged.1_bismark_bt2_pe.txt",out=config["output_dir"])),
cHH_OT=temp(expand("{out}/methylation_calling/CHH_OT_{{sample}}_trimmed_filt_merged.1_bismark_bt2_pe.txt",out=config["output_dir"])),
cHG_CTOT=temp(expand("{out}/methylation_calling/CHG_CTOT_{{sample}}_trimmed_filt_merged.1_bismark_bt2_pe.txt",out=config["output_dir"])),
cHG_OT=temp(expand("{out}/methylation_calling/CHG_CTOT_{{sample}}_trimmed_filt_merged.1_bismark_bt2_pe.txt",out=config["output_dir"])),
cG_CTOT=temp(expand("{out}/methylation_calling/CG_CTOT_{{sample}}_trimmed_filt_merged.1_bismark_bt2_pe.txt",out=config["output_dir"])),
cG_OT=temp(expand("{out}/methylation_calling/CG_CTOT_{{sample}}_trimmed_filt_merged.1_bismark_bt2_pe.txt",out=config["output_dir"]))
cHG_OT=temp(expand("{out}/methylation_calling/CHG_OT_{{sample}}_trimmed_filt_merged.1_bismark_bt2_pe.txt",out=config["output_dir"])),
cG_OT=temp(expand("{out}/methylation_calling/CpG_OT_{{sample}}_trimmed_filt_merged.1_bismark_bt2_pe.txt",out=config["output_dir"]))
params:
out=expand("{path}",path=config["output_dir"]),
NNrefDir=expand("{path}/output_denovo/NNNNref/",path=config["output_dir"])
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14 changes: 4 additions & 10 deletions src/rules/reference.rules
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Original file line number Diff line number Diff line change
Expand Up @@ -52,18 +52,12 @@ rule methylation_calling_reference_bismark:
output:
calling=temp(expand("{out}/methylation_calling/{{sample}}_trimmed_filt_merged.1_bismark_bt2_pe.CX_report.txt",out=config["output_dir"])),
coveragecompr=expand("{out}/methylation_calling/{{sample}}_trimmed_filt_merged.1_bismark_bt2_pe.bismark.cov.gz",out=config["output_dir"]),
cHH_CTOB=temp(expand("{out}/methylation_calling/CHH_CTOB_{{sample}}_trimmed_filt_merged.1_bismark_bt2_pe.txt",out=config["output_dir"])),
cHH_OB=temp(expand("{out}/methylation_calling/CHH_OB_{{sample}}_trimmed_filt_merged.1_bismark_bt2_pe.txt",out=config["output_dir"])),
cHG_CTOB=temp(expand("{out}/methylation_calling/CHG_CTOB_{{sample}}_trimmed_filt_merged.1_bismark_bt2_pe.txt",out=config["output_dir"])),
cHG_OB=temp(expand("{out}/methylation_calling/CHG_CTOB_{{sample}}_trimmed_filt_merged.1_bismark_bt2_pe.txt",out=config["output_dir"])),
cG_CTOB=temp(expand("{out}/methylation_calling/CG_CTOB_{{sample}}_trimmed_filt_merged.1_bismark_bt2_pe.txt",out=config["output_dir"])),
cG_OB=temp(expand("{out}/methylation_calling/CG_CTOB_{{sample}}_trimmed_filt_merged.1_bismark_bt2_pe.txt",out=config["output_dir"])),
cHH_CTOT=temp(expand("{out}/methylation_calling/CHH_CTOT_{{sample}}_trimmed_filt_merged.1_bismark_bt2_pe.txt",out=config["output_dir"])),
cHG_OB=temp(expand("{out}/methylation_calling/CHG_OB_{{sample}}_trimmed_filt_merged.1_bismark_bt2_pe.txt",out=config["output_dir"])),
cG_OB=temp(expand("{out}/methylation_calling/CpG_OB_{{sample}}_trimmed_filt_merged.1_bismark_bt2_pe.txt",out=config["output_dir"])),
cHH_OT=temp(expand("{out}/methylation_calling/CHH_OT_{{sample}}_trimmed_filt_merged.1_bismark_bt2_pe.txt",out=config["output_dir"])),
cHG_CTOT=temp(expand("{out}/methylation_calling/CHG_CTOT_{{sample}}_trimmed_filt_merged.1_bismark_bt2_pe.txt",out=config["output_dir"])),
cHG_OT=temp(expand("{out}/methylation_calling/CHG_CTOT_{{sample}}_trimmed_filt_merged.1_bismark_bt2_pe.txt",out=config["output_dir"])),
cG_CTOT=temp(expand("{out}/methylation_calling/CG_CTOT_{{sample}}_trimmed_filt_merged.1_bismark_bt2_pe.txt",out=config["output_dir"])),
cG_OT=temp(expand("{out}/methylation_calling/CG_CTOT_{{sample}}_trimmed_filt_merged.1_bismark_bt2_pe.txt",out=config["output_dir"]))
cHG_OT=temp(expand("{out}/methylation_calling/CHG_OT_{{sample}}_trimmed_filt_merged.1_bismark_bt2_pe.txt",out=config["output_dir"])),
cG_OT=temp(expand("{out}/methylation_calling/CpG_OT_{{sample}}_trimmed_filt_merged.1_bismark_bt2_pe.txt",out=config["output_dir"]))

params:
out=expand("{path}",path=config["output_dir"]),
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