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Adjust outputs and output handling
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* Make the outdir/make output an optional step
* Include outputs from the workflow so it can more easily be integrated
  into other workflows
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@scanon
scanon committed Jun 2, 2021
1 parent 378433f commit 2a6dfaf
Showing 1 changed file with 58 additions and 34 deletions.
92 changes: 58 additions & 34 deletions jgi_assembly.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -19,17 +19,34 @@ workflow jgi_metaASM {
call read_mapping_pairs {
input: reads=input_file, ref=create_agp.outcontigs, container=bbtools_container, memory=memory, threads=threads
}
call make_output {
input: outdir= outdir, bbcms_output=bbcms.out1, assy_output=assy.out, agp_output=create_agp.outcontigs,mapping_output=read_mapping_pairs.outcovfile
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
}
}
output {
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 = 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
}
parameter_meta{
input_file: "illumina paired-end interleaved fastq files"
Expand All @@ -55,38 +72,44 @@ workflow jgi_metaASM {
}

task make_output{
String outdir
String bbcms_output
String assy_output
String agp_output
String mapping_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}/final_assembly ${outdir}/bbcms ${outdir}/mapping
bbcms_path=`dirname ${bbcms_output}`
assy_path=`dirname ${assy_output}`
agp_path=`dirname ${agp_output}`
mapping_path=`dirname ${mapping_output}`
mv -f $bbcms_path/* ${outdir}/bbcms
mv -f $assy_path ${outdir}/
mv -f $agp_path/* ${outdir}/final_assembly
mv -f $mapping_path/* ${outdir}/mapping
mkdir -p ${outdir}
cp ${contigs} ${scaffolds} ${agp} ${bam} \
${samgz} ${covstats} ${asmstats} ${outdir}
chmod 764 -R ${outdir}
fi
}
runtime {
docker: container
mem: "1 GiB"
cpu: 1
}
output{
String outcontigs = "${outdir}/final_assembly/assembly_contigs.fna"
String outscaffolds = "${outdir}/final_assembly/assembly_scaffolds.fna"
String outagp = "${outdir}/final_assembly/assembly.agp"
String outbam = "${outdir}/mapping/pairedMapped_sorted.bam"
String outsamgz = "${outdir}/mapping/pairedMapped.sam.gz"
String outcovstats = "${outdir}/mapping/covstats.txt"
String outasmstats = "${outdir}/final_assembly/stats.json"
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}"
}
}
Expand Down Expand Up @@ -127,7 +150,7 @@ task read_mapping_pairs{
cat ${sep=" " reads} > infile.fastq
export mapping_input="infile.fastq"
fi

bbmap.sh -Xmx${default="105G" memory} threads=${jvm_threads} nodisk=true interleaved=true ambiguous=random in=$mapping_input ref=${ref} out=${filename_unsorted} covstats=${filename_cov} bamscript=${filename_bamscript}
samtools sort -m100M -@ ${jvm_threads} ${filename_unsorted} -o ${filename_sorted}
samtools index ${filename_sorted}
Expand Down Expand Up @@ -161,7 +184,7 @@ task create_agp {
cpu: 16
}
command{
echo $(curl --fail --max-time 10 --silent http://169.254.169.254/latest/meta-data/public-hostname)
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
Expand All @@ -177,6 +200,7 @@ task create_agp {
File outcontigs = filename_contigs
File outscaffolds = filename_scaffolds
File outagp = filename_agp
File outstats = "stats.json"
File outlegend = filename_legend
File outresources = filename_resources
}
Expand Down Expand Up @@ -205,7 +229,7 @@ task assy {
sleep 30
export TIME="time result\ncmd:%C\nreal %es\nuser %Us \nsys %Ss \nmemory:%MKB \ncpu %P"
set -eo pipefail

spades.py -m 2000 -o ${outprefix} --only-assembler -k 33,55,77,99,127 --meta -t ${spades_cpu} -1 ${infile1} -2 ${infile2}
}
output {
Expand Down Expand Up @@ -242,7 +266,7 @@ task bbcms {
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
if file --mime -b ${input_files[0]} | grep gzip; then
cat ${sep=" " input_files} > infile.fastq.gz
export bbcms_input="infile.fastq.gz"
fi
Expand Down

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