Merge branch 'assembly-sampletable' into subset-vamb

metagenome-atlas · Jul 26, 2023 · 9f7ac64 · 9f7ac64
2 parents 2160cda + e7d3b3e
commit 9f7ac64
Show file tree

Hide file tree

Showing 5 changed files with 15 additions and 16 deletions.
diff --git a/workflow/Snakefile b/workflow/Snakefile
@@ -33,6 +33,9 @@ min_version("6.1")
 container: "docker://continuumio/miniconda3:4.4.10"
 
 
+
+
+
 wildcard_constraints:
     binner="[A-Za-z]+",
 
@@ -170,7 +173,7 @@ rule binning:
 
 rule assembly_one_sample:
     input:
-        "{sample}/{sample}_contigs.fasta",
+        get_assembly,
         "{sample}/sequence_alignment/{sample}.bam",
         "{sample}/assembly/contig_stats/postfilter_coverage_stats.txt",
         "{sample}/assembly/contig_stats/final_contig_stats.txt",

diff --git a/workflow/rules/assemble.smk b/workflow/rules/assemble.smk
@@ -605,7 +605,7 @@ rule finalize_contigs:
 
 rule calculate_contigs_stats:
     input:
-        "{sample}/{sample}_contigs.fasta",
+        get_assembly,
     output:
         "{sample}/assembly/contig_stats/final_contig_stats.txt",
     conda:
@@ -643,7 +643,7 @@ rule align_reads_to_final_contigs:
 
 rule pileup_contigs_sample:
     input:
-        fasta="{sample}/{sample}_contigs.fasta",
+        fasta=get_assembly,
         bam="{sample}/sequence_alignment/{sample}.bam",
     output:
         covhist="{sample}/assembly/contig_stats/postfilter_coverage_histogram.txt",
@@ -697,7 +697,7 @@ rule create_bam_index:
 
 rule predict_genes:
     input:
-        "{sample}/{sample}_contigs.fasta",
+        get_assembly,
     output:
         fna="{sample}/annotation/predicted_genes/{sample}.fna",
         faa="{sample}/annotation/predicted_genes/{sample}.faa",

diff --git a/workflow/rules/binning.smk b/workflow/rules/binning.smk
@@ -1,14 +1,12 @@
 from glob import glob
 
-BINNING_CONTIGS = "{sample}/{sample}_contigs.fasta"
-
 
 include: "bin_quality.smk"
 
 
 rule pileup_for_binning:
     input:
-        fasta=BINNING_CONTIGS,
+        fasta=get_assembly,
         bam="{sample}/sequence_alignment/{sample_reads}.bam",
     output:
         covstats="{sample}/binning/coverage/{sample_reads}_coverage_stats.txt",
@@ -79,7 +77,7 @@ rule combine_coverages:
 rule run_concoct:
     input:
         coverage="{sample}/binning/coverage/combined_coverage.tsv",
-        fasta=BINNING_CONTIGS,
+        fasta=get_assembly,
     output:
         "{{sample}}/binning/concoct/intermediate_files/clustering_gt{}.csv".format(
             config["concoct"]["min_contig_length"]
@@ -159,7 +157,7 @@ def get_metabat_sensitivity():
 rule metabat:
     input:
         depth_file=rules.get_metabat_depth_file.output,
-        contigs=BINNING_CONTIGS,
+        contigs=get_assembly,
     output:
         "{sample}/binning/metabat/cluster_attribution.tmp",
     params:
@@ -190,7 +188,7 @@ rule metabat:
 
 rule maxbin:
     input:
-        fasta=BINNING_CONTIGS,
+        fasta=get_assembly,
         abund="{sample}/binning/coverage/{sample}_coverage.txt",
     output:
         directory("{sample}/binning/maxbin/intermediate_files"),
@@ -307,7 +305,7 @@ rule get_maxbin_cluster_attribution:
 rule get_bins:
     input:
         cluster_attribution="{sample}/binning/{binner}/cluster_attribution.tsv",
-        contigs=BINNING_CONTIGS,
+        contigs=get_assembly,
     output:
         directory("{sample}/binning/{binner}/bins"),
     conda:
@@ -337,7 +335,7 @@ rule run_das_tool:
             "{{sample}}/binning/DASTool/{binner}.scaffolds2bin",
             binner=config["binner"],
         ),
-        contigs=BINNING_CONTIGS,
+        contigs=get_assembly,
         proteins="{sample}/annotation/predicted_genes/{sample}.faa",
     output:
         "{sample}/binning/DASTool/{sample}_DASTool_summary.tsv",

diff --git a/workflow/rules/cobinning.smk b/workflow/rules/cobinning.smk
@@ -8,7 +8,7 @@ localrules:
 
 rule filter_contigs:
     input:
-        "{sample}/{sample}_contigs.fasta",
+        get_assembly,
     output:
         temp("Intermediate/cobinning/filtered_contigs/{sample}.fasta"),
     params:
@@ -46,8 +46,6 @@ def get_filtered_contigs_of_bingroup(wildcards):
         )
 
     return {
-        # Trigers rerun if contigs change
-        "flag": expand("{sample}/{sample}_contigs.fasta", sample=samples_of_group),
         "fasta": ancient(
             expand(rules.filter_contigs.output[0], sample=samples_of_group)
         ),

diff --git a/workflow/rules/semibin.smk b/workflow/rules/semibin.smk
@@ -35,7 +35,7 @@ rule semibin_generate_data_multi:
 
 rule semibin_train:
     input:
-        flag="{sample}/{sample}_contigs.fasta",
+        flag = get_assembly,
         fasta_sample=rules.filter_contigs.output[0],
         bams=get_bams_of_bingroup,
         data_folder=rules.semibin_generate_data_multi.output[0],