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CW-1162 option to run DE without assembly transcriptome

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This commit is contained in:
Sarah Griffiths 2022-11-16 12:16:38 +00:00
parent 7040a043d4
commit cd1f97de4e
6 changed files with 138 additions and 88 deletions
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19
.gitlab-ci.yml
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@ -20,7 +20,7 @@ docker-run:
parallel:
matrix:
- MATRIX_NAME: [
"fusions", "differential_expression", "isoforms"
"fusions", "differential_expression", "only_differential_expression", "isoforms"
]
rules:
# NOTE As we're overriding the rules block for the included docker-run
@ -48,5 +48,18 @@ docker-run:
--de_analysis \
--ref_genome differential_expression/hg38_chr20.fa \
--ref_annotation differential_expression/gencode.v22.annotation.chr20.gtf \
--direct_rna"
NF_IGNORE_PROCESSES: preprocess_reads,merge_transcriptomes
--direct_rna --minimap_index_opts \\-k15"
NF_IGNORE_PROCESSES: preprocess_reads,merge_transcriptomes
- if: $MATRIX_NAME == "only_differential_expression"
variables:
NF_BEFORE_SCRIPT: tar -xzvf test_data/differential_expression.tar.gz
NF_WORKFLOW_OPTS: "--fastq differential_expression/differential_expression_fastq \
--de_analysis \
--ref_genome differential_expression/hg38_chr20.fa \
--ref_annotation differential_expression/gencode.v22.annotation.chr20.gtf \
--direct_rna --minimap_index_opts \\-k15 \
--ref_transcriptome differential_expression/ref_transcriptome.fasta \
--transcriptome_assembly false"
NF_IGNORE_PROCESSES: >
preprocess_reads,merge_transcriptomes,assemble_transcripts,
build_minimap_index,get_transcriptome,merge_gff_bundles,run_gffcompare,build_minimap_index,split_bam

1
CHANGELOG.md
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@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
### Added
- Demo differential expression data in repository.
- Improved DE explanation in docs
- Option to turn off transcript assembly steps with param transcript_assembly
### Fixed
- Fix JAFFAL terminating workflow when no fusions found.
- Error if condition sheet and sample sheet don't match.

19
bin/report.py
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@ -867,7 +867,7 @@ def main():
"--alignment_stats", required=False, default=None, nargs='*',
help="TSV summary file of alignment statistics")
parser.add_argument(
"--gff_annotation", required=True, nargs='+',
"--gff_annotation", required=False, nargs='+',
help="transcriptome annotation gff file")
parser.add_argument(
"--gffcompare_dir", required=False, default=None, nargs='*',
@ -922,17 +922,16 @@ def main():
pychopper_plots(report, args.pychop_report)
# Results
transcriptome_summary(
report, args.gff_annotation, sample_ids, denovo=args.denovo)
if args.gff_annotation is not None:
transcriptome_summary(
report, args.gff_annotation, sample_ids, denovo=args.denovo)
df_tmaps = gff_compare_plots(
report,
[Path(x) for x in args.gffcompare_dir],
sample_ids)
if args.gffcompare_dir is not None:
df_tmaps = gff_compare_plots(
report,
[Path(x) for x in args.gffcompare_dir],
sample_ids)
report.write(args.report)
if df_tmaps is not None:
transcript_table(report, df_tmaps, args.isoform_table_nrows)
if args.cluster_qc_dirs is not None:

179
main.nf
View File

@ -307,13 +307,13 @@ process makeReport {
path versions
path "params.json"
val denovo
path pychopper_report
path jaffal_csv
tuple val(sample_ids),
path(seq_summaries),
path(aln_stats),
path(gffcmp_dir),
path(gff_annotation)
path "pychopper_report/*"
path"jaffal_csv/*"
val sample_ids
path seq_summaries
path "aln_stats/*"
path gffcmp_dir
path "gff_annotation/*"
path "de_report/*"
path "seqkit/*"
output:
@ -322,30 +322,45 @@ process makeReport {
// Convert the sample_id arrayList.
sids = new BlankSeparatedList(sample_ids)
def report_name = "wf-transcriptomes-report.html"
def OPT_ALN = denovo ? '' : "--alignment_stats ${aln_stats}"
def OPT_DENOVO = denovo ? "--denovo" : ''
def OPT_PC_REPORT = pychopper_report.name.startsWith('OPTIONAL_FILE') ? '' : "--pychop_report ${pychopper_report}"
def OPT_JAFFAL_CSV = jaffal_csv.name.startsWith('OPTIONAL_FILE') ? '' : "--jaffal_csv ${jaffal_csv}"
"""
if [ -e "de_report/OPTIONAL_FILE" ]; then
if [ -f "de_report/OPTIONAL_FILE" ]; then
dereport=""
else
dereport="--de_report true --de_stats "seqkit/*""
mv de_report/*.gtf de_report/stringtie_merged.gtf
fi
if [ -f "gff_annotation/OPTIONAL_FILE" ]; then
OPT_GFF=""
else
OPT_GFF="--gffcompare_dir ${gffcmp_dir} --gff_annotation gff_annotation/*"
fi
if [ -f "jaffal_csv/OPTIONAL_FILE" ]; then
OPT_JAFFAL_CSV=""
else
OPT_JAFFAL_CSV="--jaffal_csv jaffal_csv/*"
fi
if [ -f "aln_stats/OPTIONAL_FILE" ]; then
OPT_ALN=""
else
OPT_ALN="--alignment_stats aln_stats/*"
fi
if [ -f "pychopper_report/OPTIONAL_FILE" ]; then
OPT_PC_REPORT=""
else
OPT_PC_REPORT="--pychop_report pychopper_report/*"
fi
report.py --report $report_name \
--versions $versions \
--params params.json \
$OPT_ALN \
$OPT_PC_REPORT \
\$OPT_ALN \
\$OPT_PC_REPORT \
--sample_ids $sids \
--summaries $seq_summaries \
--gffcompare_dir $gffcmp_dir \
--gff_annotation $gff_annotation \
\$OPT_GFF \
--isoform_table_nrows $params.isoform_table_nrows \
$OPT_JAFFAL_CSV \
\$OPT_JAFFAL_CSV \
$OPT_DENOVO \
\$dereport
@ -417,47 +432,61 @@ workflow pipeline {
full_len_reads = summariseConcatReads.out.input_reads
pychopper_report = file("$projectDir/data/OPTIONAL_FILE")
}
if (params.denovo){
println("Doing de novo assembly")
assembly = denovo_assembly(full_len_reads, ref_genome)
} else {
build_minimap_index(ref_genome)
println("Doing reference based transcript analysis")
assembly = reference_assembly(build_minimap_index.out.index, ref_genome, full_len_reads)
}
split_bam(assembly.bam)
assemble_transcripts(split_bam.out.bundles.flatMap(map_sample_ids_cls), ref_annotation)
merge_gff_bundles(assemble_transcripts.out.gff_bundles.groupTuple())
use_ref_ann = !ref_annotation.name.startsWith('OPTIONAL_FILE')
run_gffcompare(merge_gff_bundles.out.gff, ref_annotation)
if (params.denovo){
// Use the per-sample, de novo-assembled CDS
seq_for_transcriptome_build = assembly.cds
}else {
// For reference based assembly, there is only one reference
// So map this reference to all sample_ids
seq_for_transcriptome_build = sample_ids.flatten().combine(Channel.fromPath(params.ref_genome))
}
if (params.transcriptome_assembly){
if (params.denovo){
println("Doing de novo assembly")
assembly = denovo_assembly(full_len_reads, ref_genome)
} else {
build_minimap_index(ref_genome)
println("Doing reference based transcript analysis")
assembly = reference_assembly(build_minimap_index.out.index, ref_genome, full_len_reads)
}
assembly_stats = assembly.stats.map{ it -> it[1]}.collect()
split_bam(assembly.bam)
assemble_transcripts(split_bam.out.bundles.flatMap(map_sample_ids_cls), ref_annotation)
merge_gff_bundles(assemble_transcripts.out.gff_bundles.groupTuple())
use_ref_ann = !ref_annotation.name.startsWith('OPTIONAL_FILE')
run_gffcompare(merge_gff_bundles.out.gff, ref_annotation)
if (params.denovo){
// Use the per-sample, de novo-assembled CDS
seq_for_transcriptome_build = assembly.cds
}else {
// For reference based assembly, there is only one reference
// So map this reference to all sample_ids
seq_for_transcriptome_build = sample_ids.flatten().combine(Channel.fromPath(params.ref_genome))
}
get_transcriptome(
merge_gff_bundles.out.gff
.join(run_gffcompare.out.gffcmp_dir)
.join(seq_for_transcriptome_build))
gff_compare = run_gffcompare.out.gffcmp_dir.map{ it -> it[1]}.collect()
merge_gff = merge_gff_bundles.out.gff.map{ it -> it[1]}.collect()
results = Channel.empty()
}else
{
gff_compare = file("$projectDir/data/OPTIONAL_FILE")
merge_gff = file("$projectDir/data/OPTIONAL_FILE")
assembly_stats = file("$projectDir/data/OPTIONAL_FILE")
use_ref_ann = false
results = Channel.empty()
}
if (jaffal_refBase){
gene_fusions(full_len_reads, jaffal_refBase, jaffal_genome, jaffal_annotation)
jaffal_out = gene_fusions.out.results_csv.collectFile(keepHeader: true, name: 'jaffal.csv')
}else{
jaffal_out = file("$projectDir/data/OPTIONAL_FILE_1")
gene_fusions(full_len_reads, jaffal_refBase, jaffal_genome, jaffal_annotation)
jaffal_out = gene_fusions.out.results_csv.collectFile(keepHeader: true, name: 'jaffal.csv')
}else{
jaffal_out = file("$projectDir/data/OPTIONAL_FILE")
}
get_transcriptome(
merge_gff_bundles.out.gff
.join(run_gffcompare.out.gffcmp_dir)
.join(seq_for_transcriptome_build))
if (params.de_analysis){
@ -484,44 +513,44 @@ workflow pipeline {
de_report = file("$projectDir/data/OPTIONAL_FILE")
count_transcripts_file = file("$projectDir/data/OPTIONAL_FILE")
}
makeReport(
software_versions,
workflow_params,
params.denovo,
pychopper_report,
jaffal_out,
summariseConcatReads.out.summary
.join(assembly.stats)
.join(run_gffcompare.out.gffcmp_dir)
.join(merge_gff_bundles.out.gff)
.toList().transpose().toList(),
summariseConcatReads.out.summary.map{it->it[0]}.collect(),
summariseConcatReads.out.summary.map{it->it[1]}.collect(),
assembly_stats,
gff_compare,
merge_gff,
de_report,
count_transcripts_file)
report = makeReport.out.report
results = results.concat(makeReport.out.report)
if (use_ref_ann){
results = run_gffcompare.output.gffcmp_dir
.concat(
results = run_gffcompare.output.gffcmp_dir.concat(
assembly.stats,
get_transcriptome.out.transcriptome.flatMap(map_sample_ids_cls))
.map {it -> it[1]}
.concat(makeReport.out.report)
.concat(results)
}
if (!use_ref_ann && !params.denovo){
results = assembly.stats
.concat(
if (!use_ref_ann && !params.denovo && params.transcriptome_assembly){
results = assembly.stats.concat(
get_transcriptome.out.transcriptome.flatMap(map_sample_ids_cls))
.map {it -> it[1]}
.concat(makeReport.out.report)
.concat(results)
}
if (params.denovo){
results = assembly.cds
.concat(assembly.stats,
results = assembly.cds.concat(
assembly.stats,
seq_for_transcriptome_build,
get_transcriptome.out.transcriptome.flatMap(map_sample_ids_cls),
merge_gff_bundles.out.gff,
@ -534,7 +563,7 @@ workflow pipeline {
return l
})
.map {it -> it[1]}
.concat(makeReport.out.report)
.concat(results)
}
if (params.jaffal_refBase){
results = results
@ -586,8 +615,9 @@ workflow {
if (params.ref_annotation){
ref_annotation = file(params.ref_annotation, type: "file")
if (!ref_annotation.exists()) {
error = "--annotation: File doesn't exist, check path."
error = "--ref_annotation: File doesn't exist, check path."
}
}else{
ref_annotation = file("$projectDir/data/OPTIONAL_FILE")
@ -602,6 +632,7 @@ workflow {
}
ref_transcriptome = file("$projectDir/data/OPTIONAL_FILE")
if (params.ref_transcriptome){
log.info("Reference Transcriptome provided will be used for differential expression.")
ref_transcriptome = file(params.ref_transcriptome, type:"file")
}
if (params.de_analysis){

1
nextflow.config
View File

@ -15,6 +15,7 @@ params {
fastq = null
ref_genome = null
ref_annotation = null
transcriptome_assembly = true
threads = 4
// Thresholds for viewing isoforms in report table
isoform_table_nrows = 5000

7
nextflow_schema.json
View File

@ -45,6 +45,11 @@
"format": "file-path",
"demo_data": "${projectDir}/test_data/SIRV_isoforms.gtf",
"description": "A reference annotation of gff format"
},
"transcriptome_assembly": {
"type": "boolean",
"default": true,
"description": "Find a reference assembly and use in differential expression analysis, set to false if you want to use exisiting ref_transcriptome."
}
},
"required": [
@ -263,7 +268,7 @@
"type": "string",
"default": "null",
"format": "file-path",
"description": "Transcriptome reference file"
"description": "Transcriptome reference file, if supplied will be used instead of finding transcriptome using reference assembly or denovo methods"
},
"min_gene_expr": {
"type": "integer",