diff --git a/jgi_assembly.wdl b/jgi_assembly.wdl index 9225ded..f54cfab 100755 --- a/jgi_assembly.wdl +++ b/jgi_assembly.wdl @@ -4,12 +4,8 @@ workflow jgi_metaASM { String? threads String input_file String proj - String resource - String informed_by String rename_contig_prefix="scaffold" Float uniquekmer=1000 - String? git_url="https://github.com/microbiomedata/mg_annotation/releases/tag/0.1" - String? url_root="https://data.microbiomedata.org/data/" String bbtools_container="microbiomedata/bbtools:38.96" String spades_container="microbiomedata/spades:3.15.0" Boolean paired = true @@ -41,11 +37,7 @@ workflow jgi_metaASM { input: proj=proj, start=stage.start, - git_url=git_url, - url_root=url_root, container="microbiomedata/workflowmeta:1.1.1", - informed_by=informed_by, - resource=resource, input_file=input_file, fasta=create_agp.outcontigs, scaffold=create_agp.outscaffolds, @@ -64,7 +56,6 @@ workflow jgi_metaASM { File samgz=finish_asm.outsamgz File covstats=finish_asm.outcovstats File asmstats=finish_asm.outasmstats - File objects=finish_asm.objects File asminfo=make_info_file.asminfo } @@ -149,14 +140,10 @@ task finish_asm { File? covstats File asmstats String container - String git_url - String informed_by String proj String prefix=sub(proj, ":", "_") String orig_prefix="scaffold" String sed="s/${orig_prefix}_/${proj}_/g" - String resource - String url_root String start command<<< @@ -184,28 +171,6 @@ task finish_asm { # Remove an extra field from the stats cat ${asmstats} |jq 'del(.filename)' > stats.json - - /scripts/generate_object_json.py \ - --type "nmdc:MetagenomeAssembly" \ - --set metagenome_assembly_set \ - --part ${proj} \ - -p "name=Metagenome Assembly Activity for ${proj}" \ - was_informed_by=${informed_by} \ - started_at_time=${start} \ - ended_at_time=$end \ - execution_resource=${resource} \ - git_url=${git_url} \ - version="v1.0.3-beta" \ - --url ${url_root}${proj}/assembly/ \ - --extra stats.json \ - --inputs ${input_file[0]} ${input_file[1]} \ - --outputs \ - ${prefix}_contigs.fna "Final assembly contigs fasta" "Assembly Contigs" "Assembly contigs for ${proj}" \ - ${prefix}_scaffolds.fna "Final assembly scaffolds fasta" "Assembly Scaffolds" "Assembly scaffolds for ${proj}" \ - ${prefix}_covstats.txt "Assembled contigs coverage information" "Assembly Coverage Stats" "Coverage Stats for ${proj}" \ - ${prefix}_assembly.agp "An AGP format file that describes the assembly" "Assembly AGP" "AGP for ${proj}" \ - ${prefix}_pairedMapped_sorted.bam "Sorted bam file of reads mapping back to the final assembly" "Assembly Coverage BAM" "Sorted Bam for ${proj}" - >>> output { File outcontigs = "${prefix}_contigs.fna" @@ -215,7 +180,6 @@ task finish_asm { File outsamgz = "${prefix}_pairedMapped.sam.gz" File outcovstats = "${prefix}_covstats.txt" File outasmstats = "stats.json" - File objects = "objects.json" } runtime { @@ -382,7 +346,6 @@ task bbcms { String container String? memory Boolean paired = true - String filename_outfile="input.corr.fastq.gz" String filename_outfile1="input.corr.left.fastq.gz" String filename_outfile2="input.corr.right.fastq.gz"