From 923e099cab423ec35c5c681e70b782ca1425069b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?C=C3=A9dric=20Midoux?= <cedric.midoux@inrae.fr>
Date: Mon, 1 Feb 2021 16:24:20 +0100
Subject: [PATCH] checkpoint metabat checkm
---
binning.smk | 31 +++++++++++++++----------------
global.smk | 3 +--
2 files changed, 16 insertions(+), 18 deletions(-)
diff --git a/binning.smk b/binning.smk
index 9a26c6a..52c8363 100644
--- a/binning.smk
+++ b/binning.smk
@@ -2,10 +2,8 @@ checkpoint metabat:
input:
unpack(contigs_input)
output:
- clusters = directory("work/metabat/{sample}")
+ clusters = directory("work/metabat/{sample}/bin")
params:
- #output = "{output}/{sample}",
- output = "work/metabat/{sample}/{sample}",
clustrsize = 200000
threads:
8
@@ -14,7 +12,7 @@ checkpoint metabat:
"&& "
"metabat2 "
"--inFile {input} "
- "--outFile {params.output} "
+ "--outFile {output}/{wildcards.sample} "
"--minContig 5000 "
"--minClsSize {params.clustrsize} "
"--numThreads {threads} "
@@ -25,10 +23,10 @@ checkpoint metabat:
rule metabat_kaiju:
input:
- clustr = "work/metabat/{sample}/{sample}.{num}.fa",
+ clustr = "work/metabat/{sample}/bin/{sample}.{num}.fa",
kaiju = "report/contigs_{sample}-taxNames.tsv"
output:
- "work/metabat/{sample}/{sample}.{num}_kaiju.tsv"
+ "work/metabat/{sample}/kaiju/{sample}.{num}_kaiju.tsv"
shell:
"grep "
"'>' "
@@ -42,27 +40,28 @@ rule metabat_kaiju:
"> "
"{output} "
-def aggregate_metabat(wildcards):
- checkpoint_output = checkpoints.metabat.get(**wildcards).output.clusters
- return expand("work/metabat/{sample}/{sample}.{i}_kaiju.tsv", sample=wildcards.sample, i=glob_wildcards(os.path.join(checkpoint_output, "{sample}.{i}")).i)
+def aggregate_metabat_kaiju(wildcards):
+ checkpoint_output = checkpoints.metabat.get(**wildcards).output[0]
+ return expand("work/metabat/{sample}/kaiju/{sample}.{i}_kaiju.tsv",
+ sample=wildcards.sample,
+ i=glob_wildcards(os.path.join(checkpoint_output, "{sample}.{i}.fa")).i)
-rule resume_metabat:
+rule metabat_kaiju_done:
input:
- aggregate_metabat
+ aggregate_metabat_kaiju
output:
- done = temp("work/metabat/{sample}.done")
+ temp("work/metabat/{sample}/kaiju.done")
shell:
- "touch {output.done} "
+ "touch {output}"
rule checkm:
input:
- "work/metabat/{sample}/{sample}.unbinned.fa"
+ directory("work/metabat/{sample}/bin")
output:
"work/checkm/{sample}/lineage.ms"
threads:
4
params:
- input = lambda wildcards, input: os.path.dirname(str(input)),
output = lambda wildcards, output: os.path.dirname(str(output))
shell:
"conda activate checkm-genome-1.0.18 "
@@ -71,7 +70,7 @@ rule checkm:
"lineage_wf "
"-t {threads} "
"-x fa "
- "{params.input} "
+ "{input} "
"{params.output} "
"&& "
"conda deactivate "
diff --git a/global.smk b/global.smk
index 45ac098..f27ef96 100644
--- a/global.smk
+++ b/global.smk
@@ -16,7 +16,6 @@ rule all:
"report/diamond_swissprot_coassembly.tsv",
"report/contigs_coassembly-taxNames.tsv",
"report/genes_coassembly-taxNames.tsv",
- "work/metabat/coassembly.done",
"work/checkm/coassembly/lineage.ms",
#catalogue
"report/quast_results/report.html",
@@ -25,7 +24,7 @@ rule all:
"report/contigs_catalogue-taxNames.tsv",
#add-on
expand("work/addon/{sample}.small_contigs.taxNames.tsv", sample=config["SAMPLES"]),
- #expand("work/addon/catalogue.{sample}.unmapped.taxNames.tsv", sample=config["SAMPLES"]),
+ #expand("work/addon/catalogue-{sample}.unmapped.taxNames.tsv", sample=config["SAMPLES"]),
#virome
expand("report/viromeQC-{sample}.txt", sample=config["SAMPLES"]),
expand("work/virhostmatcher/{sample}/done", sample=config["SAMPLES"]),
--
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