diff --git a/jgi_assembly.wdl b/jgi_assembly.wdl
index 7cc3091..7720971 100755
--- a/jgi_assembly.wdl
+++ b/jgi_assembly.wdl
@@ -1,70 +1,69 @@
 workflow jgi_metaASM {
-    Array[File] input_file
-    String outdir
-    String? threads
+    String? outdir
     String? memory
+    String? threads
+    String input_file
+    String proj
+    String resource
+    String informed_by
     String rename_contig_prefix="scaffold"
-    #String bbtools_container="microbiomedata/bbtools:38.94"
-    String bbtools_container="microbiomedata/bbtools@sha256:b433db110ef6cdcac4d236afabff95bfe153228063f5d9234306e78657ddbe36"
-    #String spades_container="microbiomedata/spades:3.15.0"
-    String spades_container="microbiomedata/spades@sha256:1d94ec809bcb52cd4560de0993d14f24c38e1f88facc7cbb2aba66723c20fd13"
+    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
+
+    call stage {
+        input:
+        container=bbtools_container,
+        input_file=input_file
+    }
+
+
     call bbcms {
-          input: input_files=input_file, container=bbtools_container, memory = memory, paired = paired
+          input: input_files=stage.assembly_input, container=bbtools_container, memory=memory,  paired = paired
     }
     call assy {
-         input: infile1=bbcms.out1, infile2=bbcms.out2, container=spades_container, paired = paired
+         input: infile1=bbcms.out1, infile2=bbcms.out2, container=spades_container, threads=threads,  paired = paired
     }
     call create_agp {
-         input: scaffolds_in=assy.out, container=bbtools_container, memory = memory, rename_contig_prefix = rename_contig_prefix
+         input: scaffolds_in=assy.out, container=bbtools_container, rename_contig_prefix = rename_contig_prefix, memory=memory
     }
     call read_mapping_pairs {
-         input: reads=input_file, ref=create_agp.outcontigs, container=bbtools_container, memory = memory, threads = threads, paired = paired
+         input: reads=input_file, ref=create_agp.outcontigs, container=bbtools_container, memory=memory, threads=threads,  paired = paired
     }
-    if (defined(outdir)) {
-        call make_output {
-             input: outdir=outdir,
-                    contigs=create_agp.outcontigs,
-                    scaffolds=create_agp.outscaffolds,
-                    agp=create_agp.outagp,
-                    bam=read_mapping_pairs.outbamfile,
-                    samgz=read_mapping_pairs.outsamfile,
-                    covstats=read_mapping_pairs.outcovfile,
-                    asmstats=create_agp.outstats,
-                    container=bbtools_container
-        }
+
+    call finish_asm {
+        input:
+        proj=proj,
+        start=stage.start,
+        git_url=git_url,
+        url_root=url_root,
+        container="microbiomedata/workflowmeta:1.1.0",
+        informed_by=informed_by,
+        resource=resource,
+        input_file=input_file,
+        fasta=create_agp.outcontigs,
+        scaffold=create_agp.outscaffolds,
+        agp=create_agp.outagp,
+        bam=read_mapping_pairs.outbamfile,
+        samgz=read_mapping_pairs.outsamfile,
+        covstats=read_mapping_pairs.outcovfile,
+        asmstats=create_agp.outstats
     }
+ 
     output {
-        File contig = create_agp.outcontigs
-        File scaffold = create_agp.outscaffolds
-        File agp=create_agp.outagp
-        File bam=read_mapping_pairs.outbamfile
-        File samgz=read_mapping_pairs.outsamfile
-        File covstats=read_mapping_pairs.outcovfile
-        File asmstats=create_agp.outstats
-        File? final_contig = make_output.outcontigs
-        File? final_scaffold = make_output.outscaffolds
-        File? final_agp = make_output.outagp
-        File? final_covstat = make_output.outcovstats
-        File? final_samgz = make_output.outsamgz
-        File? final_bam = make_output.outbam
-        File? final_asmstat = make_output.outasmstats
+        File contig=finish_asm.outcontigs
+        File scaffold=finish_asm.outscaffolds
+        File agp=finish_asm.outagp
+        File bam=finish_asm.outbam
+        File samgz=finish_asm.outsamgz
+        File covstats=finish_asm.outcovstats
+        File asmstats=finish_asm.outasmstats
+        File objects=finish_asm.objects
     }
-    parameter_meta{
-	input_file: "illumina paired-end interleaved fastq files"
-	outdir: "the final output directory path"
-	rename_contig_prefix: "contig prefix for fasta header, default: scaffold"
-	final_contig: "assembled contigs fasta file"
-	final_scaffold: "assembled scaffold fasta file"
-	final_agp: "assembled AGP file"
-	final_covstat: "contig coverage stats file"
-	final_samgz: "reads aligned to contigs sam file with gz compressed"
-	final_bam: "reads aligned to contigs bam file"
-	final_asmstat: "assembled scaffold/contigs statistical numbers"
-    #    memory: "optional for jvm memory for bbtools, ex: 32G"
-    #    threads: "optional for jvm/spades threads for bbtools ex: 16"
-    }
-
+ 
     meta {
         author: "Chienchi Lo, B10, LANL"
         email: "chienchi@lanl.gov"
@@ -73,139 +72,171 @@ workflow jgi_metaASM {
 
 }
 
-task bbcms {
-     Array[File] input_files
-     String container
-     String? memory
-     Boolean paired = true
+task stage {
+   String container
+   String input_file
+   String? memory = "4G"
+   String target = "staged.fastq.gz"
+   String output1 = "input.left.fastq.gz"
+   String output2 = "input.right.fastq.gz"
 
-     String filename_outfile="input.corr.fastq.gz"
-     String filename_outfile1="input.corr.left.fastq.gz"
-     String filename_outfile2="input.corr.right.fastq.gz"
-     String filename_readlen="readlen.txt"
-     String filename_outlog="stdout.log"
-     String filename_errlog="stderr.log"
-     String filename_kmerfile="unique31mer.txt"
-     String filename_counts="counts.metadata.json"
+   command <<<
+       set -e
+       if [ $( echo ${input_file}|egrep -c "https*:") -gt 0 ] ; then
+           wget ${input_file} -O ${target}
+       else
+           ln ${input_file} ${target} || cp ${input_file} ${target}
+       fi
 
-     runtime {
-		docker: container
-		time: "12:00:00"
-		memory: "115G"
-		cpu:  16
-     }
+        reformat.sh -Xmx${default="10G" memory} in=${target} out1=${output1} out2=${output2}    
+       # Capture the start time
+       date --iso-8601=seconds > start.txt
 
-     command {
-        set -eo pipefail
-        if file --mime -b ${input_files[0]} | grep gzip; then
-             cat ${sep=" " input_files} > infile.fastq.gz
-             export bbcms_input="infile.fastq.gz"
-        fi
+   >>>
 
-        if file --mime -b ${input_files[0]} | grep plain; then
-             cat ${sep=" " input_files} > infile.fastq
-             export bbcms_input="infile.fastq"
-        fi
+   output{
+      Array[File] assembly_input = [output1, output2]
+      String start = read_string("start.txt")
+   }
+   runtime {
+     cpu:  2
+     maxRetries: 1
+     docker: container
+   }
+}
 
-        bbcms.sh -Xmx${default="105G" memory} metadatafile=${filename_counts} mincount=2 highcountfraction=0.6 in=$bbcms_input out=${filename_outfile} > >(tee -a ${filename_outlog}) 2> >(tee -a ${filename_errlog} >&2) && grep Unique ${filename_errlog} | rev |  cut -f 1 | rev  > ${filename_kmerfile}
+task finish_asm {
+    String input_file
+    File fasta
+    File scaffold
+    File? agp
+    File bam
+    File? samgz
+    File? covstats
+    File asmstats
+    String container
+    String git_url
+    String informed_by
+    String proj
+    String prefix=sub(proj, ":", "_")
+    String orig_prefix="scaffold"
+    String sed="s/${orig_prefix}_/${proj}_/g"
+    String resource
+    String url_root
+    String start
+ 
+    command<<<
 
-        if ${paired}; then
-            reformat.sh -Xmx${default="105G" memory} in=${filename_outfile} out1=${filename_outfile1} out2=${filename_outfile2}
-        fi
 
-        readlength.sh -Xmx${default="105G" memory} in=${filename_outfile} out=${filename_readlen}
-        rm $bbcms_input
-     }
+        set -e
+        end=`date --iso-8601=seconds`
+        ln ${fasta} ${prefix}_contigs.fna
+        ln ${scaffold} ${prefix}_scaffolds.fna
+        ln ${covstats} ${prefix}_covstats.txt
+        ln ${agp} ${prefix}_assembly.agp
 
-     output {
-            File out = filename_outfile
-            File out1 = if paired then filename_outfile1 else filename_outfile
-            File out2 = if paired then filename_outfile2 else filename_outfile
-            File outreadlen = filename_readlen
-            File stdout = filename_outlog
-            File stderr = filename_errlog
-            File outcounts = filename_counts
-            File outkmer = filename_kmerfile
-     }
-}
+       ## Bam file     
+       samtools view -h ${bam} | sed ${sed} | \
+          samtools view -hb -o ${prefix}_pairedMapped_sorted.bam
+       ## Sam.gz file
+       samtools view -h ${samgz} | sed ${sed} | \
+          gzip -c - > ${prefix}_pairedMapped.sam.gz
 
-task assy {
-     File infile1
-     File infile2
-     String container
-     String? threads
-     String outprefix="spades3"
-     String filename_outfile="${outprefix}/scaffolds.fasta"
-     String filename_spadeslog ="${outprefix}/spades.log"
-     String system_cpu="$(grep \"model name\" /proc/cpuinfo | wc -l)"
-     String spades_cpu=select_first([threads,system_cpu])
-     Boolean paired = true
+       # Remove an extra field from the stats
+       cat ${asmstats} |jq 'del(.filename)' > stats.json
 
-     runtime {
-		docker: container
-		time: "12:00:00"
-		memory: "115G"
-		cpu:  16
-     }
 
-     command{
-        set -eo pipefail
-        if ${paired}; then
-            spades.py -m 2000 -o ${outprefix} --only-assembler -k 33,55,77,99,127  --meta -t ${spades_cpu} -1 ${infile1} -2 ${infile2}
-        else
-            spades.py -m 2000 -o ${outprefix} --only-assembler -k 33,55,77,99,127 -t ${spades_cpu} -s ${infile1}
-        fi
-     }
-     output {
-            File out = filename_outfile
-            File outlog = filename_spadeslog
-     }
-}
+       /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} \
+             --url ${url_root}${proj}/assembly/ \
+             --extra stats.json \
+             --inputs ${input_file} \
+             --outputs \
+             ${prefix}_contigs.fna "Final assembly contigs fasta" "Assembly Contigs"\
+             ${prefix}_scaffolds.fna "Final assembly scaffolds fasta" "Assembly Scaffolds"\
+             ${prefix}_covstats.txt "Assembled contigs coverage information" "Assembly Coverage Stats"\
+             ${prefix}_assembly.agp "An AGP format file that describes the assembly" "Assembly AGP"\
+             ${prefix}_pairedMapped_sorted.bam "Sorted bam file of reads mapping back to the final assembly" "Assembly Coverage BAM"
 
-task create_agp {
-    File scaffolds_in
-    String? memory
-    String container
-    String rename_contig_prefix
-    String prefix="assembly"
-    String filename_contigs="${prefix}_contigs.fna"
-    String filename_scaffolds="${prefix}_scaffolds.fna"
-    String filename_agp="${prefix}.agp"
-    String filename_legend="${prefix}_scaffolds.legend"
+    >>>
+    output {
+       	File outcontigs = "${prefix}_contigs.fna"
+		File outscaffolds = "${prefix}_scaffolds.fna"
+        File outagp = "${prefix}_assembly.agp"
+		File outbam = "${prefix}_pairedMapped_sorted.bam"
+		File outsamgz = "${prefix}_pairedMapped.sam.gz"
+		File outcovstats = "${prefix}_covstats.txt"
+		File outasmstats = "stats.json"
+        File objects = "objects.json"
+    }
 
     runtime {
-      docker: container
-      time: "12:00:00"
-      memory: "115G"
-      cpu:  16
+        docker: container
+        memory: "1 GiB"
+        cpu:  1
     }
+}
 
-    command{
-        fungalrelease.sh -Xmx${default="105G" memory} in=${scaffolds_in} out=${filename_scaffolds} outc=${filename_contigs} agp=${filename_agp} legend=${filename_legend} mincontig=200 minscaf=200 sortscaffolds=t sortcontigs=t overwrite=t
-        if [ "${rename_contig_prefix}" != "scaffold" ]; then
-            sed -i 's/scaffold/${rename_contig_prefix}_scf/g' ${filename_contigs} ${filename_scaffolds} ${filename_agp} ${filename_legend}
-        fi
-        bbstats.sh format=8 in=${filename_scaffolds} out=stats.json
-        sed -i 's/l_gt50k/l_gt50K/g' stats.json
-    }
-    output{
-	    File outcontigs = filename_contigs
-	    File outscaffolds = filename_scaffolds
-	    File outagp = filename_agp
-	    File outstats = "stats.json"
-    	File outlegend = filename_legend
-    }
+task make_output{
+        String outdir
+        File contigs
+        File scaffolds
+        File agp
+        File bam
+        File samgz
+        File covstats
+        File asmstats
+        String contigs_name=basename(contigs)
+        String scaffolds_name=basename(contigs)
+        String agp_name=basename(contigs)
+        String bam_name=basename(contigs)
+        String samgz_name=basename(contigs)
+        String covstats_name=basename(contigs)
+        String asmstats_name=basename(contigs)
+        String container
+ 
+ 	command{
+ 		if [ ! -z ${outdir} ]; then
+ 			mkdir -p ${outdir}
+ 			cp ${contigs} ${scaffolds} ${agp} ${bam} \
+ 			   ${samgz} ${covstats} ${asmstats} ${outdir}
+ 			chmod 764 -R ${outdir}
+ 		fi
+ 	}
+	runtime {
+                docker: container
+		memory: "1 GiB"
+		cpu:  1
+	}
+	output{
+		File? outcontigs = "${outdir}/${contigs_name}"
+		File? outscaffolds = "${outdir}/${scaffolds_name}"
+		File? outagp = "${outdir}/${agp_name}"
+		File? outbam = "${outdir}/${bam_name}"
+		File? outsamgz = "${outdir}/${samgz_name}"
+		File? outcovstats = "${outdir}/${covstats_name}"
+		File? outasmstats = "${outdir}/${asmstats_name}"
+	}
 }
 
 task read_mapping_pairs{
     Array[File] reads
     File ref
     String container
-    String? threads
     String? memory
+    String? threads
     Boolean paired = true
     String bbmap_interleaved_flag = if paired then 'interleaved=true' else 'interleaved=false'
 
+    String filename_resources="resources.log"
     String filename_unsorted="pairedMapped.bam"
     String filename_outsam="pairedMapped.sam.gz"
     String filename_sorted="pairedMapped_sorted.bam"
@@ -214,15 +245,18 @@ task read_mapping_pairs{
     String filename_cov="covstats.txt"
     String system_cpu="$(grep \"model name\" /proc/cpuinfo | wc -l)"
     String jvm_threads=select_first([threads,system_cpu])
-
     runtime {
-	  docker: container
-      time: "12:00:00"
-      memory: "115G"
-      cpu:  16
-    }
-
+            docker: container
+            memory: "120 GiB"
+	    cpu:  16
+	    maxRetries: 1
+     }
     command{
+        echo $(curl --fail --max-time 10 --silent http://169.254.169.254/latest/meta-data/public-hostname)
+        touch ${filename_resources};
+        curl --fail --max-time 10 --silent https://bitbucket.org/berkeleylab/jgi-meta/get/master.tar.gz | tar --wildcards -zxvf - "*/bin/resources.bash" && ./*/bin/resources.bash > ${filename_resources} &
+        sleep 30
+        export TIME="time result\ncmd:%C\nreal %es\nuser %Us \nsys  %Ss \nmemory:%MKB \ncpu %P"
         set -eo pipefail
         if [[ ${reads[0]}  == *.gz ]] ; then
              cat ${sep=" " reads} > infile.fastq.gz
@@ -244,50 +278,139 @@ task read_mapping_pairs{
       File outbamfileidx = filename_sorted_idx
       File outcovfile = filename_cov
       File outsamfile = filename_outsam
+      File outresources = filename_resources
   }
 }
 
-task make_output{
-        String outdir
-        File contigs
-        File scaffolds
-        File agp
-        File bam
-        File samgz
-        File covstats
-        File asmstats
-        String contigs_name=basename(contigs)
-        String scaffolds_name=basename(contigs)
-        String agp_name=basename(contigs)
-        String bam_name=basename(contigs)
-        String samgz_name=basename(contigs)
-        String covstats_name=basename(contigs)
-        String asmstats_name=basename(contigs)
-        String container
-
- 	command{
-        if [ -n ${outdir} ]; then
-            mkdir -p ${outdir}
-            cp ${contigs} ${scaffolds} ${agp} ${bam} \
-            ${samgz} ${covstats} ${asmstats} ${outdir}
-            chmod 764 -R ${outdir}
+task create_agp {
+    File scaffolds_in
+    String? memory
+    String container
+    String rename_contig_prefix
+    String filename_resources="resources.log"
+    String prefix="assembly"
+    String filename_contigs="${prefix}_contigs.fna"
+    String filename_scaffolds="${prefix}_scaffolds.fna"
+    String filename_agp="${prefix}.agp"
+    String filename_legend="${prefix}_scaffolds.legend"
+    runtime {
+            docker: container
+            memory: "120 GiB"
+	    cpu:  16
+     }
+    command{
+	echo $(curl --fail --max-time 10 --silent http://169.254.169.254/latest/meta-data/public-hostname)
+        touch ${filename_resources};
+        curl --fail --max-time 10 --silent https://bitbucket.org/berkeleylab/jgi-meta/get/master.tar.gz | tar --wildcards -zxvf - "*/bin/resources.bash" && ./*/bin/resources.bash > ${filename_resources} &	
+        sleep 30
+        export TIME="time result\ncmd:%C\nreal %es\nuser %Us \nsys  %Ss \nmemory:%MKB \ncpu %P"
+        fungalrelease.sh -Xmx${default="105G" memory} in=${scaffolds_in} out=${filename_scaffolds} outc=${filename_contigs} agp=${filename_agp} legend=${filename_legend} mincontig=200 minscaf=200 sortscaffolds=t sortcontigs=t overwrite=t
+        if [ "${rename_contig_prefix}" != "scaffold" ]; then
+            sed -i 's/scaffold/${rename_contig_prefix}_scf/g' ${filename_contigs} ${filename_scaffolds} ${filename_agp} ${filename_legend}
         fi
+	bbstats.sh format=8 in=${filename_scaffolds} out=stats.json
+	sed -i 's/l_gt50k/l_gt50K/g' stats.json
+    }
+    output{
+	File outcontigs = filename_contigs
+	File outscaffolds = filename_scaffolds
+	File outagp = filename_agp
+	File outstats = "stats.json"
+    	File outlegend = filename_legend
+    	File outresources = filename_resources
     }
+}
 
-	runtime {
-        docker: container
-		time: "12:00:00"
-		memory: "115G"
-		cpu: 16
-	}
+task assy {
+     File infile1
+     File infile2
+     String container
+     String? threads
+     String filename_resources="resources.log"
+     String outprefix="spades3"
+     String filename_outfile="${outprefix}/scaffolds.fasta"
+     String filename_spadeslog ="${outprefix}/spades.log"
+     String system_cpu="$(grep \"model name\" /proc/cpuinfo | wc -l)"
+     String spades_cpu=select_first([threads,system_cpu])
+     Boolean paired = true
+     runtime {
+            docker: container
+            memory: "120 GiB"
+	    cpu:  16
+     }
+     command{
+        echo $(curl --fail --max-time 10 --silent http://169.254.169.254/latest/meta-data/public-hostname)
+        touch ${filename_resources};
+        curl --fail --max-time 10 --silent https://bitbucket.org/berkeleylab/jgi-meta/get/master.tar.gz | tar --wildcards -zxvf - "*/bin/resources.bash" && ./*/bin/resources.bash > ${filename_resources} &		
+        sleep 30
+        export TIME="time result\ncmd:%C\nreal %es\nuser %Us \nsys  %Ss \nmemory:%MKB \ncpu %P"
+        set -eo pipefail
+        if ${paired}; then
+            spades.py -m 2000 -o ${outprefix} --only-assembler -k 33,55,77,99,127  --meta -t ${spades_cpu} -1 ${infile1} -2 ${infile2}
+        else
+            spades.py -m 2000 -o ${outprefix} --only-assembler -k 33,55,77,99,127 -t ${spades_cpu} -s ${infile1}
+        fi
+     }
+     output {
+            File out = filename_outfile
+            File outlog = filename_spadeslog
+            File outresources = filename_resources
+     }
+}
 
-	output{
-		File? outcontigs = "${outdir}/${contigs_name}"
-		File? outscaffolds = "${outdir}/${scaffolds_name}"
-		File? outagp = "${outdir}/${agp_name}"
-		File? outbam = "${outdir}/${bam_name}"
-		File? outsamgz = "${outdir}/${samgz_name}"
-		File? outcovstats = "${outdir}/${covstats_name}"
-		File? outasmstats = "${outdir}/${asmstats_name}"
-	}
+task bbcms {
+     Array[File] input_files
+     String container
+     String? memory
+     Boolean paired = true
+
+     String filename_resources="resources.log"
+     String filename_outfile="input.corr.fastq.gz"
+     String filename_outfile1="input.corr.left.fastq.gz"
+     String filename_outfile2="input.corr.right.fastq.gz"
+     String filename_readlen="readlen.txt"
+     String filename_outlog="stdout.log"
+     String filename_errlog="stderr.log"
+     String filename_kmerfile="unique31mer.txt"
+     String filename_counts="counts.metadata.json"
+     runtime {
+            docker: container
+            memory: "120 GiB"
+	    cpu:  16
+     }
+
+     command {
+        echo $(curl --fail --max-time 10 --silent http://169.254.169.254/latest/meta-data/public-hostname)
+        touch ${filename_resources};
+        curl --fail --max-time 10 --silent https://bitbucket.org/berkeleylab/jgi-meta/get/master.tar.gz | tar --wildcards -zxvf - "*/bin/resources.bash" && ./*/bin/resources.bash > ${filename_resources} &		
+        sleep 30
+        export TIME="time result\ncmd:%C\nreal %es\nuser %Us \nsys  %Ss \nmemory:%MKB \ncpu %P"
+        set -eo pipefail
+        if file --mime -b ${input_files[0]} | grep gzip; then
+             cat ${sep=" " input_files} > infile.fastq.gz
+             export bbcms_input="infile.fastq.gz"
+        fi
+	if file --mime -b ${input_files[0]} | grep plain; then
+             cat ${sep=" " input_files} > infile.fastq
+             export bbcms_input="infile.fastq"
+        fi
+        bbcms.sh -Xmx${default="105G" memory} metadatafile=${filename_counts} mincount=2 highcountfraction=0.6 in=$bbcms_input out=${filename_outfile} > >(tee -a ${filename_outlog}) 2> >(tee -a ${filename_errlog} >&2) && grep Unique ${filename_errlog} | rev |  cut -f 1 | rev  > ${filename_kmerfile}
+        if ${paired}; then
+            reformat.sh -Xmx${default="105G" memory} in=${filename_outfile} out1=${filename_outfile1} out2=${filename_outfile2}
+        fi
+        readlength.sh -Xmx${default="105G" memory} in=${filename_outfile} out=${filename_readlen}
+        rm $bbcms_input
+     }
+     output {
+            File out = filename_outfile
+            File out1 = if paired then filename_outfile1 else filename_outfile
+            File out2 = if paired then filename_outfile2 else filename_outfile
+            File outreadlen = filename_readlen
+            File stdout = filename_outlog
+            File stderr = filename_errlog
+            File outcounts = filename_counts
+            File outkmer = filename_kmerfile
+            File outresources = filename_resources
+     }
 }
+