From 57bd993461b1d87944a004bdbfa9052e7259d75c Mon Sep 17 00:00:00 2001
From: Valentina Galata <valentina.galata@uni.lu>
Date: Thu, 23 Jul 2020 09:59:41 +0200
Subject: [PATCH] cleanup: replace out/err log by log; changed params for
metaquast
---
workflow/rules/analysis.smk | 66 ++++++++++++++++---------------------
workflow/steps/analysis.smk | 45 +++++++------------------
2 files changed, 40 insertions(+), 71 deletions(-)
diff --git a/workflow/rules/analysis.smk b/workflow/rules/analysis.smk
index e05cd28..239f7a8 100644
--- a/workflow/rules/analysis.smk
+++ b/workflow/rules/analysis.smk
@@ -5,12 +5,11 @@
rule analysis_quast:
input:
- os.path.join(RESULTS_DIR, "assembly/{rtype}/{tool}/ASSEMBLY.fasta")
+ os.path.join(RESULTS_DIR, "assembly/{rtype}/{tool}/ASSEMBLY.FILTERED.fasta")
output:
os.path.join(RESULTS_DIR, "analysis/quast/{rtype}/{tool}/report.tsv")
log:
- out="logs/quast.{rtype}.{tool}.out.log",
- err="logs/quast.{rtype}.{tool}.err.log"
+ "logs/quast.{rtype}.{tool}.log"
wildcard_constraints:
rtype="|".join(READ_TYPES),
tool="|".join(ASSEMBLERS)
@@ -19,9 +18,11 @@ rule analysis_quast:
conda:
os.path.join(ENV_DIR, "quast.yaml")
message:
- "Assess assembly quality w/ QUAST: {input}"
+ "metaQUAST: {input}"
shell:
- "(date && metaquast.py --max-ref-number 0 --threads {threads} {input} -o $(dirname {output}) && date) 2> {log.err} > {log.out}"
+ "(date && "
+ "metaquast.py --max-ref-number 0 --min-contig 0 --contig-thresholds 0,1000,2000,5000 --threads {threads} {input} -o $(dirname {output}) && "
+ "date) &> {log}"
##################################################
# Proteins
@@ -33,8 +34,7 @@ rule analysis_bbmap_rename:
output:
temp(os.path.join(RESULTS_DIR, "analysis/cdhit/{rtype}_{tool}.faa"))
log:
- out="logs/analysis_bbmap_rename_{rtype}.{tool}.out.log",
- err="logs/analysis_bbmap_rename_{rtype}.{tool}.err.log"
+ "logs/analysis_bbmap_rename_{rtype}.{tool}.log"
wildcard_constraints:
rtype="|".join(READ_TYPES),
tool="|".join(ASSEMBLERS)
@@ -48,7 +48,7 @@ rule analysis_bbmap_rename:
message:
"BBMAP: rename FASTA entries in {input}"
shell:
- "(date && rename.sh in={input} out={output} prefix={params.prefix} ignorejunk=t && date) 2> {log.err} > {log.out}"
+ "(date && rename.sh in={input} out={output} prefix={params.prefix} ignorejunk=t && date) &> {log}"
rule analysis_cdhit:
input:
@@ -58,8 +58,7 @@ rule analysis_cdhit:
faa12=os.path.join(RESULTS_DIR, "analysis/cdhit/{rtype1}_{tool1}__{rtype2}_{tool2}.faa"),
faa21=os.path.join(RESULTS_DIR, "analysis/cdhit/{rtype2}_{tool2}__{rtype1}_{tool1}.faa")
log:
- out="logs/analysis_cdhit.{rtype1}.{tool1}.{rtype2}.{tool2}.out.log",
- err="logs/analysis_cdhit.{rtype1}.{tool1}.{rtype2}.{tool2}.err.log"
+ "logs/analysis_cdhit.{rtype1}.{tool1}.{rtype2}.{tool2}.log"
wildcard_constraints:
rtype1="|".join(READ_TYPES),
rtype2="|".join(READ_TYPES),
@@ -74,14 +73,14 @@ rule analysis_cdhit:
"(date && "
"cd-hit-2d -i {input.faa1} -i2 {input.faa2} -o {output.faa12} -c 0.9 -n 5 -d 0 -M 16000 -T 8 && "
"cd-hit-2d -i {input.faa2} -i2 {input.faa1} -o {output.faa21} -c 0.9 -n 5 -d 0 -M 16000 -T 8 && "
- "date) 2> {log.err} > {log.out}"
+ "date) &> {log}"
##################################################
# Circular contigs
rule circ_contigs_fasta:
input:
- os.path.join(RESULTS_DIR, "assembly/{rtype}/{tool}/ASSEMBLY.fasta")
+ os.path.join(RESULTS_DIR, "assembly/{rtype}/{tool}/ASSEMBLY.FILTERED.fasta")
output:
split1=temp(os.path.join(RESULTS_DIR, "analysis/circ_blast/{rtype}/{tool}/ASSEMBLY.split.1.fasta")),
split2=temp(os.path.join(RESULTS_DIR, "analysis/circ_blast/{rtype}/{tool}/ASSEMBLY.split.2.fasta"))
@@ -123,8 +122,7 @@ rule circ_contigs_blastn:
output:
os.path.join(RESULTS_DIR, "analysis/circ_blast/{rtype}/{tool}/ASSEMBLY.tsv")
log:
- out="logs/circ_blast.{rtype}.{tool}.out.log",
- err="logs/circ_blast.{rtype}.{tool}.err.log"
+ "logs/circ_blast.{rtype}.{tool}.log"
wildcard_constraints:
rtype="|".join(READ_TYPES),
tool="|".join(ASSEMBLERS)
@@ -136,7 +134,7 @@ rule circ_contigs_blastn:
shell:
"(date && "
"blastn -task megablast -num_alignments 50 -perc_identity 95 {params.outfmt} -query {input.fasta} -db {params.db} -out {output} && "
- "date) 2> {log.err} > {log.out}"
+ "date) &> {log}"
rule circ_contigs_filter:
input:
@@ -174,18 +172,17 @@ rule circ_contigs_filter:
# Assemblies
rule mash_sketch:
input:
- os.path.join(RESULTS_DIR, "assembly/{rtype}/{tool}/ASSEMBLY.fasta")
+ os.path.join(RESULTS_DIR, "assembly/{rtype}/{tool}/ASSEMBLY.FILTERED.fasta")
output:
os.path.join(RESULTS_DIR, "assembly/{rtype}/{tool}/ASSEMBLY.msh")
log:
- out="logs/mash.sketch.{rtype}.{tool}.out.log",
- err="logs/mash.sketch.{rtype}.{tool}.err.log"
+ "logs/mash.sketch.{rtype}.{tool}.log"
threads:
1
conda:
os.path.join(ENV_DIR, "mash.yaml")
shell:
- "(date && ofile={output} && mash sketch -k 31 -s 10000 -S 42 -o ${{ofile%.*}} {input} && date) 2> {log.err} > {log.out}"
+ "(date && ofile={output} && mash sketch -k 31 -s 10000 -S 42 -o ${{ofile%.*}} {input} && date) &> {log}"
rule mash_sketch_paste:
input:
@@ -207,8 +204,7 @@ rule mash_dist:
output:
os.path.join(RESULTS_DIR, "analysis/mash/contigs.dist")
log:
- out="logs/mash.dist.contigs.out.log",
- err="logs/mash.dist.contigs.err.log"
+ "logs/mash.dist.contigs.log"
threads:
config["mash"]["threads"]
conda:
@@ -216,27 +212,26 @@ rule mash_dist:
shell:
"(date && "
"mash dist -t -p {threads} {input} {input} > {output} && "
- "date) 2> {log.err} > {log.out}"
+ "date) &> {log}"
# Contigs
rule mash_sketch_contigs:
input:
- os.path.join(RESULTS_DIR, "assembly/{rtype}/{tool}/ASSEMBLY.fasta")
+ os.path.join(RESULTS_DIR, "assembly/{rtype}/{tool}/ASSEMBLY.FILTERED.fasta")
output:
os.path.join(RESULTS_DIR, "assembly/{rtype}/{tool}/ASSEMBLY.contigs.msh")
log:
- out="logs/mash.sketch.{rtype}.{tool}.contigs.out.log",
- err="logs/mash.sketch.{rtype}.{tool}.contigs.err.log"
+ "logs/mash.sketch.{rtype}.{tool}.contigs.log"
threads:
1
conda:
os.path.join(ENV_DIR, "mash.yaml")
shell:
- "(date && ofile={output} && mash sketch -i -k 31 -s 1000 -S 42 -o ${{ofile%.*}} {input} && date) 2> {log.err} > {log.out}"
+ "(date && ofile={output} && mash sketch -i -k 31 -s 1000 -S 42 -o ${{ofile%.*}} {input} && date) &> {log}"
rule mash_screen_contigs:
input:
- fasta=expand(os.path.join(RESULTS_DIR, "assembly/{rtype_tool}/ASSEMBLY.fasta"), rtype_tool=["%s/%s" % (rtype, tool) for rtype, tool in READ_ASSEMBLERS]),
+ fasta=expand(os.path.join(RESULTS_DIR, "assembly/{rtype_tool}/ASSEMBLY.FILTERED.fasta"), rtype_tool=["%s/%s" % (rtype, tool) for rtype, tool in READ_ASSEMBLERS]),
msh=expand(os.path.join(RESULTS_DIR, "assembly/{rtype_tool}/ASSEMBLY.contigs.msh"), rtype_tool=["%s/%s" % (rtype, tool) for rtype, tool in READ_ASSEMBLERS])
output:
expand(os.path.join(RESULTS_DIR, "analysis/mash/screen.{rtype_tool}.tsv"), rtype_tool=["%s.%s" % (rtype, tool) for rtype, tool in READ_ASSEMBLERS])
@@ -252,12 +247,11 @@ rule mash_screen_contigs:
# rule analysis_mmseqs2_db:
# input:
-# os.path.join(RESULTS_DIR, "assembly/{rtype}/{tool}/ASSEMBLY.fasta")
+# os.path.join(RESULTS_DIR, "assembly/{rtype}/{tool}/ASSEMBLY.FILTERED.fasta")
# output:
# os.path.join(RESULTS_DIR, "analysis/mmseqs2/{rtype}/{tool}/ASSEMBLY_db")
# log:
-# out="logs/mmseqs2_db.{rtype}.{tool}.out.log",
-# err="logs/mmseqs2_db.{rtype}.{tool}.err.log"
+# "logs/mmseqs2_db.{rtype}.{tool}.log"
# wildcard_constraints:
# rtype="|".join(READ_TYPES),
# tool="|".join(ASSEMBLERS)
@@ -266,7 +260,7 @@ rule mash_screen_contigs:
# message:
# "Create MMseqs2 DB from {input}"
# shell:
-# "(date && mmseqs createdb {input} {output} && date) 2> {log.err} > {log.out}"
+# "(date && mmseqs createdb {input} {output} && date) &> {log}"
# rule analysis_mmseqs2_compare:
# input:
@@ -275,8 +269,7 @@ rule mash_screen_contigs:
# output:
# os.path.join(RESULTS_DIR, "analysis/mmseqs2/comparison/{rtype1}_{tool1}__{rtype2}_{tool2}")
# log:
-# out="logs/mmseqs2.{rtype1}.{tool1}.{rtype2}.{tool2}.out.log",
-# err="logs/mmseqs2.{rtype1}.{tool1}.{rtype2}.{tool2}.err.log"
+# "logs/mmseqs2.{rtype1}.{tool1}.{rtype2}.{tool2}.log"
# wildcard_constraints:
# rtype1="|".join(READ_TYPES),
# rtype2="|".join(READ_TYPES),
@@ -290,7 +283,7 @@ rule mash_screen_contigs:
# "Create MMseqs2 compare: {input}"
# shell:
# # TODO: "mmseqs2_tmp" ??? (see old files)
-# "(date && mmseqs rbh {input.db1} {input.db2} {output} --min-seq-id 0.9 --threads {threads} && date) 2> {log.err} > {log.out}"
+# "(date && mmseqs rbh {input.db1} {input.db2} {output} --min-seq-id 0.9 --threads {threads} && date) &> {log}"
# rule analysis_mmseqs2_m8_convert:
# input:
@@ -300,11 +293,10 @@ rule mash_screen_contigs:
# output:
# os.path.join(RESULTS_DIR, "analysis/mmseqs2/comparison/{rtype1}_{tool1}__{rtype2}_{tool2}.m8")
# log:
-# out="logs/mmseqs2_convert.{rtype1}.{tool1}.{rtype2}.{tool2}.out.log",
-# err="logs/mmseqs2_convert.{rtype1}.{tool1}.{rtype2}.{tool2}.err.log"
+# "logs/mmseqs2_convert.{rtype1}.{tool1}.{rtype2}.{tool2}.log"
# conda:
# os.path.join(ENV_DIR, "cd-hit.yaml")
# message:
# "Create MMseqs2 compare: {input}"
# shell:
-# "(date && mmseqs convertalis {input.db1} {input.db2} {input.rbh} {output} && date) 2> {log.err} > {log.out}"
+# "(date && mmseqs convertalis {input.db1} {input.db2} {input.rbh} {output} && date) &> {log}"
diff --git a/workflow/steps/analysis.smk b/workflow/steps/analysis.smk
index 4f07f73..afe736d 100644
--- a/workflow/steps/analysis.smk
+++ b/workflow/steps/analysis.smk
@@ -3,56 +3,33 @@
include:
"../rules/analysis.smk"
-# NOTE: Using "shell: touch ..." to avoid the rule from being autodetected as `localrule`.
-# This is needed so that an email can be sent upon event changes for this rule.
-
rule ANALYSIS:
input:
- "status/analysis_assembly.done",
- "status/analysis_proteins.done",
- "status/analysis_circ.done",
- "status/analysis_mash.done"
- output:
- touch("status/analysis.done")
-
-rule ANALYSIS_ASSEMBLY:
- input:
+ # quast
expand(
os.path.join(RESULTS_DIR, "analysis/quast/{rtype_tool}/report.tsv"),
rtype_tool=["%s/%s" % (rtype, tool) for rtype, tool in READ_ASSEMBLERS]
- )
- output:
- touch("status/analysis_assembly.done")
-
-rule ANALYSIS_PROTEINS:
- input:
+ ) if "quast" in config["steps_analysis"] else [],
+ # cdhit
expand(
os.path.join(RESULTS_DIR, "analysis/cdhit/{combi}.faa"),
combi=["%s_%s__%s_%s" % (p[0][0], p[0][1], p[1][0], p[1][1]) for p in READ_ASSEMBLER_PAIRS]
- ),
+ ) if "cdhit" in config["steps_analysis"] else [],
expand(
os.path.join(RESULTS_DIR, "analysis/cdhit/{combi}.faa"),
combi=["%s_%s__%s_%s" % (p[1][0], p[1][1], p[0][0], p[0][1]) for p in READ_ASSEMBLER_PAIRS]
- )
- output:
- touch("status/analysis_proteins.done")
-
-rule ANALYSIS_CIRC:
- input:
+ ) if "cdhit" in config["steps_analysis"] else [],
+ # blast, circ. contigs
expand(
os.path.join(RESULTS_DIR, "analysis/circ_blast/{rtype_tool}/ASSEMBLY.{ctype}.tsv"),
rtype_tool=["%s/%s" % (rtype, tool) for rtype, tool in READ_ASSEMBLERS],
ctype=["circ", "compl"]
- )
- output:
- touch("status/analysis_circ.done")
-
-rule ANALYSIS_MASH:
- input:
- os.path.join(RESULTS_DIR, "analysis/mash/contigs.dist"),
+ ) if "blast_circ" in config["steps_analysis"] else [],
+ # mash
+ [os.path.join(RESULTS_DIR, "analysis/mash/contigs.dist")] if "mash_dist" in config["steps_analysis"] else [],
expand(
os.path.join(RESULTS_DIR, "analysis/mash/screen.{rtype_tool}.tsv"),
rtype_tool=["%s.%s" % (rtype, tool) for rtype, tool in READ_ASSEMBLERS]
- )
+ ) if "mash_screen" in config["steps_analysis"] else [],
output:
- touch("status/analysis_mash.done")
+ touch("status/analysis.done")
--
GitLab