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replace cp with cp -f #211
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@pdimens
pdimens committed Feb 26, 2025
1 parent f5cfc13 commit 18ba2e4
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Showing 16 changed files with 23 additions and 26 deletions.
4 changes: 2 additions & 2 deletions harpy/snakefiles/align_bwa.smk
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Expand Up @@ -233,7 +233,7 @@ rule sample_reports:
f"{envdir}/r.yaml"
shell:
"""
cp {input.qmd} {output.qmd}
cp -f {input.qmd} {output.qmd}
BXSTATS=$(realpath {input.bxstats})
COVFILE=$(realpath {input.coverage})
MOLCOV=$(realpath {input.molecule_coverage})
Expand Down Expand Up @@ -302,7 +302,7 @@ rule barcode_report:
f"{envdir}/r.yaml"
shell:
"""
cp {input.qmd} {output.qmd}
cp -f {input.qmd} {output.qmd}
INPATH=$(realpath {params})
quarto render {output.qmd} --log {log} --quiet -P indir:$INPATH
"""
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4 changes: 2 additions & 2 deletions harpy/snakefiles/align_ema.smk
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Expand Up @@ -325,7 +325,7 @@ rule sample_reports:
f"{envdir}/r.yaml"
shell:
"""
cp {input.qmd} {output.qmd}
cp -f {input.qmd} {output.qmd}
BXSTATS=$(realpath {input.bxstats})
COVFILE=$(realpath {input.coverage})
MOLCOV=$(realpath {input.molecule_coverage})
Expand Down Expand Up @@ -379,7 +379,7 @@ rule barcode_report:
f"{envdir}/r.yaml"
shell:
"""
cp {input.qmd} {output.qmd}
cp -f {input.qmd} {output.qmd}
INPATH=$(realpath {params})
quarto render {output.qmd} --log {log} --quiet -P indir:$INPATH
"""
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4 changes: 2 additions & 2 deletions harpy/snakefiles/align_strobealign.smk
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Expand Up @@ -224,7 +224,7 @@ rule sample_reports:
f"{envdir}/r.yaml"
shell:
"""
cp {input.qmd} {output.qmd}
cp -f {input.qmd} {output.qmd}
BXSTATS=$(realpath {input.bxstats})
COVFILE=$(realpath {input.coverage})
MOLCOV=$(realpath {input.molecule_coverage})
Expand Down Expand Up @@ -293,7 +293,7 @@ rule barcode_report:
f"{envdir}/r.yaml"
shell:
"""
cp {input.qmd} {output.qmd}
cp -f {input.qmd} {output.qmd}
INPATH=$(realpath {params})
quarto render {output.qmd} --log {log} --quiet -P indir:$INPATH
"""
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4 changes: 2 additions & 2 deletions harpy/snakefiles/impute.smk
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Expand Up @@ -176,7 +176,7 @@ rule contig_report:
f"{envdir}/r.yaml"
shell:
"""
cp {input.qmd} {output.qmd}
cp -f {input.qmd} {output.qmd}
STATS=$(realpath {input.statsfile})
PLOTDIR=$(realpath {input.plotdir})
quarto render {output.qmd} --log {log} --quiet -P statsfile:$STATS -P plotdir:$PLOTDIR {params}
Expand Down Expand Up @@ -268,7 +268,7 @@ rule impute_reports:
f"{envdir}/r.yaml"
shell:
"""
cp {input.qmd} {output.qmd}
cp -f {input.qmd} {output.qmd}
COMPARE=$(realpath {input.comparison})
INFOSCORE=$(realpath {input.infoscore})
quarto render {output.qmd} --log {log} --quiet -P compare:$COMPARE -P info:$INFOSCORE {params}
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5 changes: 1 addition & 4 deletions harpy/snakefiles/phase.smk
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Expand Up @@ -14,9 +14,6 @@ onerror:
wildcard_constraints:
sample = r"[a-zA-Z0-9._-]+"

##TODO MANUAL PRUNING OF SWITCH ERRORS
# https://github.com/vibansal/HapCUT2/blob/master/outputformat.md

pruning = config["prune"]
molecule_distance = config["molecule_distance"]
extra = config.get("extra", "")
Expand Down Expand Up @@ -282,7 +279,7 @@ rule phase_report:
f"{envdir}/r.yaml"
shell:
"""
cp {input.qmd} {output.qmd}
cp -f {input.qmd} {output.qmd}
INFILE=$(realpath {input.data})
quarto render {output.qmd} --log {log} --quiet -P blockfile:$INFILE
"""
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2 changes: 1 addition & 1 deletion harpy/snakefiles/preflight_bam.smk
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Expand Up @@ -76,7 +76,7 @@ rule create_report:
f"{envdir}/r.yaml"
shell:
"""
cp {input.qmd} {output.qmd}
cp -f {input.qmd} {output.qmd}
INFILE=$(realpath {input.data})
quarto render {output.qmd} --log {log} --quiet -P infile:$INFILE
"""
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2 changes: 1 addition & 1 deletion harpy/snakefiles/preflight_fastq.smk
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Expand Up @@ -91,7 +91,7 @@ rule create_report:
f"{envdir}/r.yaml"
shell:
"""
cp {input.qmd} {output.qmd}
cp -f {input.qmd} {output.qmd}
INFILE=$(realpath {input.data})
quarto render {output.qmd} --log {log} --quiet -P infile:$INFILE
"""
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2 changes: 1 addition & 1 deletion harpy/snakefiles/qc.smk
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Expand Up @@ -176,7 +176,7 @@ rule barcode_report:
f"{envdir}/r.yaml"
shell:
"""
cp {input.qmd} {output.qmd}
cp -f {input.qmd} {output.qmd}
INPATH=$(realpath {params})
quarto render {output.qmd} --log {log} --quiet -P indir:$INPATH
"""
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2 changes: 1 addition & 1 deletion harpy/snakefiles/snp_freebayes.smk
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Expand Up @@ -221,7 +221,7 @@ rule variant_report:
f"{envdir}/r.yaml"
shell:
"""
cp {input.qmd} {output.qmd}
cp -f {input.qmd} {output.qmd}
INPATH=$(realpath {input.data})
quarto render {output.qmd} --log {log} --quiet -P infile:$INPATH {params}
"""
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2 changes: 1 addition & 1 deletion harpy/snakefiles/snp_mpileup.smk
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Expand Up @@ -256,7 +256,7 @@ rule variant_report:
f"{envdir}/r.yaml"
shell:
"""
cp {input.qmd} {output.qmd}
cp -f {input.qmd} {output.qmd}
INPATH=$(realpath {input.data})
quarto render {output.qmd} --log {log} --quiet -P infile:$INPATH {params}
"""
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2 changes: 1 addition & 1 deletion harpy/snakefiles/sv_leviathan.smk
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Expand Up @@ -214,7 +214,7 @@ rule sample_reports:
f"{envdir}/r.yaml"
shell:
"""
cp {input.qmd} {output.qmd}
cp -f {input.qmd} {output.qmd}
FAIDX=$(realpath {input.faidx})
STATS=$(realpath {input.statsfile})
quarto render {output.qmd} --log {log} --quiet -P faidx:$FAIDX -P statsfile:$STATS {params}
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4 changes: 2 additions & 2 deletions harpy/snakefiles/sv_leviathan_pop.smk
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Expand Up @@ -269,7 +269,7 @@ rule group_reports:
f"{envdir}/r.yaml"
shell:
"""
cp {input.qmd} {output.qmd}
cp -f {input.qmd} {output.qmd}
FAIDX=$(realpath {input.faidx})
STATS=$(realpath {input.statsfile})
quarto render {output.qmd} --log {log} --quiet -P faidx:$FAIDX -P statsfile:$STATS {params}
Expand All @@ -294,7 +294,7 @@ rule aggregate_report:
f"{envdir}/r.yaml"
shell:
"""
cp {input.qmd} {output.qmd}
cp -f {input.qmd} {output.qmd}
FAIDX=$(realpath {input.faidx})
INPATH=$(realpath {params.statsdir})
quarto render {output.qmd} --log {log} --quiet -P faidx:$FAIDX -P statsdir:$INPATH {params.contigs}
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2 changes: 1 addition & 1 deletion harpy/snakefiles/sv_naibr.smk
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Expand Up @@ -226,7 +226,7 @@ rule sample_reports:
f"{envdir}/r.yaml"
shell:
"""
cp {input.qmd} {output.qmd}
cp -f {input.qmd} {output.qmd}
FAIDX=$(realpath {input.faidx})
BEDPE=$(realpath {input.bedpe})
quarto render {output.qmd} --log {log} --quiet -P faidx:$FAIDX -P bedpe:$BEDPE {params}
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2 changes: 1 addition & 1 deletion harpy/snakefiles/sv_naibr_phase.smk
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Expand Up @@ -284,7 +284,7 @@ rule sample_reports:
f"{envdir}/r.yaml"
shell:
"""
cp {input.qmd} {output.qmd}
cp -f {input.qmd} {output.qmd}
FAIDX=$(realpath {input.faidx})
BEDPE=$(realpath {input.bedpe})
quarto render {output.qmd} --log {log} --quiet -P faidx:$FAIDX -P bedpe:$BEDPE {params}
Expand Down
4 changes: 2 additions & 2 deletions harpy/snakefiles/sv_naibr_pop.smk
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Expand Up @@ -256,7 +256,7 @@ rule group_reports:
f"{envdir}/r.yaml"
shell:
"""
cp {input.qmd} {output.qmd}
cp -f {input.qmd} {output.qmd}
FAIDX=$(realpath {input.faidx})
BEDPE=$(realpath {input.bedpe})
quarto render {output.qmd} --log {log} --quiet -P faidx:$FAIDX -P bedpe:$BEDPE {params}
Expand All @@ -281,7 +281,7 @@ rule aggregate_report:
f"{envdir}/r.yaml"
shell:
"""
cp {input.qmd} {output.qmd}
cp -f {input.qmd} {output.qmd}
FAIDX=$(realpath {input.faidx})
INPATH=$(realpath {params.bedpedir})
quarto render {output.qmd} --log {log} --quiet -P faidx:$FAIDX -P bedpedir:$INPATH {params.contigs}
Expand Down
4 changes: 2 additions & 2 deletions harpy/snakefiles/sv_naibr_pop_phase.smk
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Expand Up @@ -342,7 +342,7 @@ rule sample_reports:
f"{envdir}/r.yaml"
shell:
"""
cp {input.qmd} {output.qmd}
cp -f {input.qmd} {output.qmd}
FAIDX=$(realpath {input.faidx})
BEDPE=$(realpath {input.bedpe})
quarto render {output.qmd} --log {log} --quiet -P faidx:$FAIDX -P bedpe:$BEDPE {params}
Expand All @@ -367,7 +367,7 @@ rule aggregate_report:
f"{envdir}/r.yaml"
shell:
"""
cp {input.qmd} {output.qmd}
cp -f {input.qmd} {output.qmd}
FAIDX=$(realpath {input.faidx})
INPATH=$(realpath {params.bedpedir})
quarto render {output.qmd} --log {log} --quiet -P faidx:$FAIDX -P bedpedir:$INPATH {params.contigs}
Expand Down

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