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Merge pull request #25 from microbiomedata/21-stats-file
21 Added in stats file for outputs
2 parents 8d7df73 + 34e83d1 commit 1274bc9

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6 files changed

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‎docs/index.rst

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Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
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Metagenome Assembly Workflow (v1.0.2)
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========================================
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=====================================
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.. image:: workflow_assembly.png
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:scale: 60%

‎docs/workflow_assembly.png

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‎input.json

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Original file line numberDiff line numberDiff line change
@@ -1,7 +1,7 @@
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{
2-
"jgi_metaAssembly.input_files":["https://data.microbiomedata.org/data/test_data/11809.7.220839.TCCTGAG-ACTGCAT.fastq.gz"],
2+
"jgi_metaAssembly.input_files":["/global/cfs/cdirs/m3408/www/test_data/SRR13128014.pacbio.subsample.ccs.fastq.gz"],
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"jgi_metaAssembly.proj":"nmdc:503125_160870",
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"jgi_metaAssembly.memory": "105G",
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"jgi_metaAssembly.threads": "16",
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"jgi_metaAssembly.shortRead": true
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"jgi_metaAssembly.shortRead": false
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}

‎jgi_assembly.wdl

Lines changed: 72 additions & 67 deletions
Original file line numberDiff line numberDiff line change
@@ -3,7 +3,7 @@ import "shortReads_assembly.wdl" as srma
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import "make_interleaved_WDL/make_interleaved_reads.wdl" as int
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import "https://code.jgi.doe.gov/BFoster/jgi_meta_wdl/-/raw/bc7c4371ea0fa83355bada341ec353b9feb3eff2/metagenome_improved/metaflye.wdl" as lrma
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6-
workflow jgi_metaAssembly{
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workflow jgi_metaAssembly {
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input {
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Boolean shortRead
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String proj
@@ -20,62 +20,60 @@ workflow jgi_metaAssembly{
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String minimap2_container = "staphb/minimap2:2.25"
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String minimap2_parameters = "-a -x map-hifi -t 32"
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String samtools_container = "staphb/samtools:1.18"
23-
String bbtools_container = "microbiomedata/bbtools:38.96"
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String bbtools_container = "microbiomedata/bbtools:39.03"
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String spades_container="staphb/spades:4.0.0"
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}
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if (shortRead) {
29-
if (length(input_files) > 1){
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call int.make_interleaved_reads{
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input:
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input_files = input_files,
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container = bbtools_container
34-
29+
if (length(input_files) > 1) {
30+
call int.make_interleaved_reads {
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input:
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input_files = input_files,
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container = "microbiomedata/bbtools:38.96"
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}
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}
37-
call srma.jgi_metaASM{
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call srma.jgi_metaASM {
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input:
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memory = memory,
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threads = threads,
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input_file = if length(input_files) > 1 then make_interleaved_reads.interleaved_fastq else input_files[0],
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proj = proj,
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bbtools_container = bbtools_container,
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spades_container = spades_container
45-
38+
memory = memory,
39+
threads = threads,
40+
input_file = if length(input_files) > 1 then make_interleaved_reads.interleaved_fastq else input_files[0],
41+
proj = proj,
42+
bbtools_container = "microbiomedata/bbtools:38.96",
43+
spades_container = spades_container
4644
}
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4846
}
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if (!shortRead) {
50-
call lrma.metaflye{
48+
call lrma.metaflye {
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input:
52-
proj = proj,
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input_fastq = input_files,
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flye_container = flye_container,
55-
flye_parameters = flye_parameters,
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smrtlink_container = smrtlink_container,
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racon_container = racon_container,
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minimap2_container = minimap2_container,
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minimap2_parameters = minimap2_parameters,
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samtools_container = samtools_container,
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bbtools_container = bbtools_container
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proj = proj,
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input_fastq = input_files,
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flye_container = flye_container,
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flye_parameters = flye_parameters,
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smrtlink_container = smrtlink_container,
55+
racon_container = racon_container,
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minimap2_container = minimap2_container,
57+
minimap2_parameters = minimap2_parameters,
58+
samtools_container = samtools_container,
59+
bbtools_container = bbtools_container
6260
}
63-
call finish_lrasm{
61+
call finish_lrasm {
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input:
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proj = proj,
66-
prefix = prefix,
67-
container = bbtools_container,
68-
contigs = metaflye.final_contigs,
69-
bam = metaflye.final_bam,
70-
scaffolds = metaflye.final_scaffolds,
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agp = metaflye.final_agp,
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legend = metaflye.final_legend,
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basecov = metaflye.final_basecov,
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sam = metaflye.final_sam,
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output_file = metaflye.final_output_file,
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stats = metaflye.final_stats,
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summary_stats = metaflye.final_summary_stats,
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pileup_out = metaflye.final_pileup_out
63+
proj = proj,
64+
prefix = prefix,
65+
container = bbtools_container,
66+
contigs = metaflye.final_contigs,
67+
bam = metaflye.final_bam,
68+
scaffolds = metaflye.final_scaffolds,
69+
agp = metaflye.final_agp,
70+
legend = metaflye.final_legend,
71+
basecov = metaflye.final_basecov,
72+
sam = metaflye.final_sam,
73+
output_file = metaflye.final_output_file,
74+
stats = metaflye.final_stats,
75+
summary_stats = metaflye.final_summary_stats,
76+
pileup_out = metaflye.final_pileup_out
7977
}
8078
}
8179
output {
@@ -100,33 +98,34 @@ workflow jgi_metaAssembly{
10098
File? sr_bam=jgi_metaASM.bam
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File? sr_samgz=jgi_metaASM.samgz
102100
File? sr_covstats=jgi_metaASM.covstats
103-
File? sr_asmstats=jgi_metaASM.asmstats
104101
File? sr_asminfo=jgi_metaASM.asminfo
105102
File? sr_bbcms_fq = jgi_metaASM.bbcms_fastq
106-
103+
104+
#Both
105+
File? stats = if (shortRead) then jgi_metaASM.asmstats else finish_lrasm.asm_stats
107106
}
108107
}
109108

110109

111110
task finish_lrasm {
112111
input {
113-
File contigs
114-
File bam
115-
File scaffolds
116-
File agp
117-
File legend
118-
File basecov
119-
File sam
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File output_file
121-
File stats
122-
File summary_stats
123-
File pileup_out
124-
String container
125-
String proj
126-
String prefix
127-
String orig_prefix="scaffold"
128-
String sed="s/~{orig_prefix}_/~{proj}_/g"
129-
# String start
112+
File contigs
113+
File bam
114+
File scaffolds
115+
File agp
116+
File legend
117+
File basecov
118+
File sam
119+
File output_file
120+
File stats
121+
File summary_stats
122+
File pileup_out
123+
String container
124+
String proj
125+
String prefix
126+
String orig_prefix="scaffold"
127+
String sed="s/~{orig_prefix}_/~{proj}_/g"
128+
# String start
130129
}
131130
command<<<
132131
@@ -144,12 +143,17 @@ task finish_lrasm {
144143
cat ~{basecov} | sed ~{sed} > ~{prefix}_contigs.sorted.bam.pileup.basecov
145144
cat ~{pileup_out} | sed ~{sed} > ~{prefix}_contigs.sorted.bam.pileup.out
146145
147-
## Bam file
148-
samtools view -h ~{bam} | sed ~{sed} | \
149-
samtools view -hb -o ~{prefix}_pairedMapped_sorted.bam
150-
## Sam.gz file
151-
samtools view -h ~{sam} | sed ~{sed} | \
152-
gzip -c - > ~{prefix}_pairedMapped.sam.gz
146+
## Bam file
147+
samtools view -h ~{bam} | sed ~{sed} | \
148+
samtools view -hb -o ~{prefix}_pairedMapped_sorted.bam
149+
## Sam.gz file
150+
samtools view -h ~{sam} | sed ~{sed} | \
151+
gzip -c - > ~{prefix}_pairedMapped.sam.gz
152+
153+
# stats file
154+
bbstats.sh format=8 in=~{scaffolds} out=stats.json
155+
sed -i 's/l_gt50k/l_gt50K/g' stats.json
156+
cat stats.json |jq 'del(.filename)' > stats.json
153157
154158
>>>
155159
output {
@@ -164,6 +168,7 @@ task finish_lrasm {
164168
File final_stats = "~{prefix}_contigs.sam.stats"
165169
File final_summary_stats = "~{prefix}_summary.stats"
166170
File final_pileup_out = "~{prefix}_contigs.sorted.bam.pileup.out"
171+
File asm_stats = "stats.json"
167172
}
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169174
runtime {

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