switch to impg latest, add rule to output node length

Dockerfile

@@ -82,15 +82,6 @@ RUN wget https://github.com/samtools/samtools/releases/download/1.21/samtools-1.
 	&& cd .. \
 	&& rm -rf samtools-1.21
 
-##install strobealign
-RUN git clone https://github.com/ksahlin/strobealign \
-	&& cd strobealign \
-	&& cmake -B build -DCMAKE_C_FLAGS="-msse4.2" -DCMAKE_CXX_FLAGS="-msse4.2" \
-	&& cmake --build build -j 8 \
-	&& cd ..
-
-ENV PATH /opt/strobealign/build:$PATH
-
 ##install bwa-mem
 RUN git clone https://github.com/lh3/bwa.git \
 	&& cd bwa \
@@ -158,7 +149,7 @@ RUN git clone https://github.com/AndreaGuarracino/gfainject \
 ##install impg
 RUN git clone https://github.com/pangenome/impg \
 	&& cd impg \
-	&& git checkout 37b18e18123d92fa5fa824a4e15d8aa7cad3b6db \
+	&& git checkout 15248982d5a873b36e5fe4547b265f9f172cfb54 \
 	&& cargo install --force --path . \
 	&& cp target/release/impg ../impg-tmp \
 	&& cd .. \

cosigt_smk/workflow/Snakefile

@@ -28,6 +28,7 @@ for region in config['region']:
         cosigt_input.append(config['output'] + '/cosigt/'+ sample + '/' + region + '/cosigt_genotype.tsv')
         cosigt_input.append(config['output'] + '/bwa-mem2/'+ sample + '/' + region + '.realigned.bam.all.pdf')
     cosigt_input.append(config['output'] + '/odgi/viz/' + region + '.png')
+    cosigt_input.append(config['output'] + '/odgi/view/' + region + '.node.length.tsv')
     if region in config['annotations']:
         cosigt_input.append(config['output'] + '/odgi/untangle/' + region + '.gggenes.pdf')
 

cosigt_smk/workflow/envs/impg.yaml

@@ -2,4 +2,4 @@ channels:
  - conda-forge
  - bioconda
 dependencies:
-  - impg=0.2.2
+  - impg=0.2.3

cosigt_smk/workflow/rules/gafpack.smk

@@ -23,5 +23,6 @@ rule gafpack_coverage:
 		gafpack \
 		--gfa {input.gfa} \
 		--gaf {input.gaf} \
-		--len-scale --weight-queries | gzip > {output}
+		--len-scale \
+		--weight-queries | gzip > {output}
 		'''

cosigt_smk/workflow/rules/impg.smk

@@ -23,6 +23,7 @@ rule impg_project:
 	shell:
 		'''
 		impg \
+		query \
 		-p {input.paf} \
 		-b {input.bed} | \
 		grep -v \

cosigt_smk/workflow/rules/odgi.smk

@@ -78,14 +78,14 @@ rule odgi_paths_matrix:
 		cut -f 1,4- | gzip > {output}
 		'''
 
-rule odgi_view_len:
+rule odgi_view_node_length:
 	'''
 	https://github.com/pangenome/odgi
 	'''
 	input:
 		rules.odgi_view.output
 	output:
-		config['output'] + '/odgi/view/{region}.len.tsv'
+		config['output'] + '/odgi/view/{region}.node.length.tsv'
 	threads:
 		1
 	resources:
@@ -96,38 +96,13 @@ rule odgi_view_len:
 	conda:
 		'../envs/odgi.yaml'
 	benchmark:
-		'benchmarks/{region}.odgi_view_len.benchmark.txt'
+		'benchmarks/{region}.odgi_view_node_length.benchmark.txt'
 	shell:
 		'''
 		grep '^S' {input} | \
 		awk '{{print("node."$2,length($3))}}' OFS="\\t" > {output}
 		'''
 
-rule filter_odgi_matrix:
-	'''
-	https://github.com/davidebolo1993/cosigt
-	'''
-	input:
-		coverage=rules.odgi_chop.output,
-		size=rules.odgi_view_len.output
-	output:
-		config['output'] + '/odgi/paths/matrix_flt/{region}.tsv.gz'
-	threads:
-		1
-	resources:
-		mem_mb=lambda wildcards, attempt: attempt * config['default']['mem_mb'],
-		time=lambda wildcards, attempt: attempt * config['default']['time']
-	container:
-		'docker://davidebolo1993/cosigt_workflow:latest'
-	#conda:
-		#'../envs/odgi.yaml'
-	benchmark:
-		'benchmarks/{region}.filter_odgi_matrix.benchmark.txt'
-	shell:
-		'''
-		flt {input.coverage} {input.size} | gzip > {output}
-		'''
-
 rule odgi_similarity:
 	'''
 	https://github.com/pangenome/odgi