Skip to content

GitLab

Commit 3d66eec1 authored by Anna Buschart's avatar Anna Buschart
Browse files

Delete Vis.smk

parent cbef915a
Pipeline #46339 failed with stages
Hide whitespace changes
Inline Side-by-side
Showing with 0 additions and 194 deletions
workflow/rules/modules/multi/Vis.smk deleted 100644 → 0
View file @ cbef915a
localrules: VIS
stats_figs =[]
if "preprocessing" in IMP_STEPS or MG or MT:
stats_figs.append(expand("Visualization/{types}.reads.png",types=TYPES))
if "assembly" in IMP_STEPS or CONTIGS:
stats_figs.append(expand("Visualization/Assembly_{fig}.png", fig=["length_hist","cov_hist","gc_hist","cov_gc_scatter"]))
if "analysis" in IMP_STEPS:
stats_figs.append(expand("Visualization/Analysis_{fig}.png", fig=["length_hist","cov_hist","cov_scatter","func_sets"]))
if "taxonomy" in IMP_STEPS:
stats_figs.append(expand("Visualization/Taxonomy_{type}_kraken_tree.png", type=TYPES))
stats_figs.append("Visualization/Taxonomy_kraken_plot.png")
stats_figs.append(expand("Visualization/Taxonomy_{type}_mOTU_tree.png", type=TYPES))
stats_figs.append("Visualization/Taxonomy_mOTU_plot.png")
if "binning" in IMP_STEPS:
stats_figs.append("Visualization/Binning_alluvial.png")
stats_figs.append(expand("Visualization/Binning_{type}_depth.png",type=TYPES))
if "binny" in BIN_STEPS:
stats_figs.append("Visualization/Binning_vizbin.png")
rule vis_stats:
input:
stats_figs
output:
touch("status/stats.visualized")
rule visualize_read_stats:
input:
"Stats/all_stats.Rdata"
output:
report(expand("Visualization/{types}.reads.png",types=TYPES),
caption="../../report/stats/Reads.rst",category="Preprocessing")
resources:
runtime = "1:00:00",
mem = MEMCORE
log: "logs/visualize_read_stats.log"
message: "visualize_read_stats: Plotting reads figure."
threads: 1
conda: ENVDIR + "/IMP_visualize.yaml"
script:
SRCDIR + "/visualize_reads.R"
rule visualize_assembly_stats:
input:
"Stats/all_stats.Rdata"
output:
report("Visualization/Assembly_length_hist.png",caption="../../report/stats/Assembly_length.rst",category="Assembly"),
report("Visualization/Assembly_cov_hist.png",caption="../../report/stats/Assembly_cov.rst",category="Assembly"),
report("Visualization/Assembly_gc_hist.png",caption="../../report/stats/Assembly_gc.rst",category="Assembly"),
report("Visualization/Assembly_cov_gc_scatter.png",caption="../../report/stats/Assembly_cov_gc.rst",category="Assembly")
resources:
runtime = "2:00:00",
mem = MEMCORE
log: "logs/visualize_assembly_stats.log"
message: "visualize_assembly_stats: Plotting figures for contigs."
threads: 1
conda: ENVDIR + "/IMP_visualize.yaml"
script:
SRCDIR + "/visualize_assembly.R"
rule visualize_analysis_stats:
input:
"Stats/all_stats.Rdata"
output:
report("Visualization/Analysis_length_hist.png",caption="../../report/stats/Analysis_length.rst",category="Analysis"),
report("Visualization/Analysis_cov_hist.png",caption="../../report/stats/Analysis_cov.rst",category="Analysis"),
report("Visualization/Analysis_cov_scatter.png",caption="../../report/stats/Analysis_cov_scat.rst",category="Analysis"),
report("Visualization/Analysis_func_sets.png",caption="../../report/stats/Analysis_func.rst",category="Analysis")
resources:
runtime = "2:00:00",
mem = MEMCORE
log: "logs/visualize_analysis_stats.log"
message: "visualize_analysis_stats: Plotting gene figures."
threads: 1
conda: ENVDIR + "/IMP_visualize.yaml"
script:
SRCDIR + "/visualize_analysis.R"
if CONTIGS or "assembly" in IMP_STEPS:
rule visualize_kraken_reads:
input:
"Stats/all_stats.Rdata",
"Analysis/taxonomy/kraken/%s.kraken.parsed.tsv" %ASS
output:
report(expand("Visualization/Taxonomy_{type}_kraken_tree.png",type=TYPES),caption="../../report/stats/Taxonomy_kraken_withAssembly.rst",category="Taxonomy"),
report("Visualization/Taxonomy_kraken_plot.png",caption="../../report/stats/Taxonomy_kraken_scatter_withAssembly.rst",category="Taxonomy")
resources:
runtime = "2:00:00",
mem = MEMCORE
log: "logs/visualize_kraken_reads.log"
message: "visualize_kraken_reads: Plotting taxonomy results."
threads: 1
conda: ENVDIR + "/IMP_visualize.yaml"
script:
SRCDIR + "/visualize_taxonomy_kraken_withAssembly.R"
else:
rule visualize_kraken_reads:
input:
"Stats/all_stats.Rdata"
output:
report(expand("Visualization/Taxonomy_{type}_kraken_tree.png",type=TYPES),caption="../../report/stats/Taxonomy_kraken.rst",category="Taxonomy"),
report("Visualization/Taxonomy_kraken_plot.png",caption="../../report/stats/Taxonomy_kraken_scatter.rst",category="Taxonomy")
resources:
runtime = "2:00:00",
mem = MEMCORE
log: "logs/visualize_kraken_reads.log"
message: "visualize_kraken_reads: Plotting taxonomy results."
threads: 1
conda: ENVDIR + "/IMP_visualize.yaml"
script:
SRCDIR + "/visualize_taxonomy_kraken.R"
if "analysis" in IMP_STEPS:
rule visualize_mOTU_reads:
input:
"Stats/all_stats.Rdata",
"Analysis/taxonomy/mOTU_links/bestPresentHitPhylogeny.tsv"
output:
report(expand("Visualization/Taxonomy_{type}_mOTU_tree.png",type=TYPES),caption="../../report/stats/Taxonomy_mOTU_withAnalysis.rst",category="Taxonomy"),
report("Visualization/Taxonomy_mOTU_plot.png",caption="../../report/stats/Taxonomy_mOTU_withAnalysis.rst",category="Taxonomy"),
resources:
runtime = "2:00:00",
mem = MEMCORE
log: "logs/visualize_mOTU_reads.log"
message: "visualize_mOTU_reads: Plotting taxonomy results."
threads: 1
conda: ENVDIR + "/IMP_visualize.yaml"
script:
SRCDIR + "/visualize_mOTU_withAnalysis.R"
else:
rule visualize_mOTU_reads:
input:
"Stats/all_stats.Rdata"
output:
report(expand("Visualization/Taxonomy_{type}_mOTU_tree.png",type=TYPES),caption="../../report/stats/Taxonomy_mOTU.rst",category="Taxonomy"),
report("Visualization/Taxonomy_mOTU_plot.png",caption="../../report/stats/Taxonomy_mOTU.rst",category="Taxonomy"),
resources:
runtime = "2:00:00",
mem = MEMCORE
log: "logs/visualize_mOTU_reads.log"
message: "visualize_mOTU_reads: Plotting taxonomy results."
threads: 1
conda: ENVDIR + "/IMP_visualize.yaml"
script:
SRCDIR + "/visualize_mOTU.R"
if "binny" in BIN_STEPS:
rule visualize_bins:
input:
stats="Stats/all_stats.Rdata",
bins=expand("Binning/{binner}/scaffold2bin.tsv",binner=BIN_STEPS),
dastool="Binning/selected_DASTool_scaffolds2bin.txt",
vizbin="Binning/binny/%s.vizbin.with-contig-names.points" %ASS
output:
report("Visualization/Binning_alluvial.png",caption="../../report/stats/Binning_alluvial.rst",category="Binning"),
report(expand("Visualization/Binning_{type}_depth.png",type=TYPES),caption="../../report/stats/Binning_depth.rst",category="Binning"),
report("Visualization/Binning_vizbin.png",caption="../../report/stats/Binning_vizbin.rst",category="Binning")
resources:
runtime = "2:00:00",
mem = MEMCORE
log: "logs/visualize_bins.log"
message: "visualize_bins: Plotting binning results."
threads: 1
conda: ENVDIR + "/IMP_visualize.yaml"
script:
SRCDIR + "/visualize_binning.R"
else:
rule visualize_bins:
input:
stats="Stats/all_stats.Rdata",
bins=expand("Binning/{binner}/scaffold2bin.tsv",binner=BIN_STEPS),
dastool="Binning/selected_DASTool_scaffolds2bin.txt"
output:
report("Visualization/Binning_alluvial.png",caption="../../report/stats/Binning_alluvial.rst",category="Binning"),
report(expand("Visualization/Binning_{type}_depth.png",type=TYPES),caption="../../report/stats/Binning_depth.rst",category="Binning")
resources:
runtime = "2:00:00",
mem = MEMCORE
log: "logs/visualize_bins.log"
message: "visualize_bins: Plotting binning results."
threads: 1
conda: ENVDIR + "/IMP_visualize.yaml"
script:
SRCDIR + "/visualize_binning.R"
# master command
rule VIS:
input:
vis_target
output:
touch('status/visualize.done')
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment